Multiple sequence alignment - TraesCS3D01G347000

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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 TraesCS3D01G347000 chr3D 100.000 3515 0 0 1 3515 458627657 458624143 0.000000e+00 6492
1 TraesCS3D01G347000 chr3D 98.750 80 1 0 46 125 458627538 458627459 3.660000e-30 143
2 TraesCS3D01G347000 chr3D 98.750 80 1 0 120 199 458627612 458627533 3.660000e-30 143
3 TraesCS3D01G347000 chr3B 94.890 2916 103 27 628 3515 605668575 605665678 0.000000e+00 4518
4 TraesCS3D01G347000 chr3B 94.167 120 5 1 201 318 605675980 605675861 7.750000e-42 182
5 TraesCS3D01G347000 chr3A 90.542 2971 153 64 201 3132 600929702 600926821 0.000000e+00 3812
6 TraesCS3D01G347000 chr3A 90.793 391 8 3 3128 3515 600926566 600926201 6.780000e-137 497
7 TraesCS3D01G347000 chr1B 92.941 170 10 2 1036 1205 518186086 518185919 2.710000e-61 246
8 TraesCS3D01G347000 chr1D 93.293 164 10 1 1036 1199 385812560 385812398 1.260000e-59 241
9 TraesCS3D01G347000 chr1D 88.344 163 17 2 1036 1198 24353171 24353011 9.960000e-46 195
10 TraesCS3D01G347000 chr1A 93.293 164 10 1 1036 1199 485362965 485362803 1.260000e-59 241
11 TraesCS3D01G347000 chr1A 88.344 163 17 2 1036 1198 579140989 579140829 9.960000e-46 195
12 TraesCS3D01G347000 chr5A 86.170 188 17 7 1018 1198 75979831 75979646 9.960000e-46 195
13 TraesCS3D01G347000 chr5B 88.272 162 17 2 1037 1197 629217212 629217052 3.580000e-45 193


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 TraesCS3D01G347000 chr3D 458624143 458627657 3514 True 2259.333333 6492 99.166667 1 3515 3 chr3D.!!$R1 3514
1 TraesCS3D01G347000 chr3B 605665678 605668575 2897 True 4518.000000 4518 94.890000 628 3515 1 chr3B.!!$R1 2887
2 TraesCS3D01G347000 chr3A 600926201 600929702 3501 True 2154.500000 3812 90.667500 201 3515 2 chr3A.!!$R1 3314

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
112 113 0.032678 GCTGCTATCGCTGAAGCCTA 59.967 55.0 0.00 0.0 37.97 3.93 F
186 187 0.032678 GCTGCTATCGCTGAAGCCTA 59.967 55.0 0.00 0.0 37.97 3.93 F
573 596 0.034896 TGTTTCGAGAACAGAGCCCC 59.965 55.0 8.47 0.0 0.00 5.80 F
652 680 0.107831 AGCTCACCACGGCACTTTTA 59.892 50.0 0.00 0.0 0.00 1.52 F
659 689 0.312729 CACGGCACTTTTAACCCCAC 59.687 55.0 0.00 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 1834 1.280421 AGGGACACAGCTCAAAGGATC 59.720 52.381 0.00 0.0 0.00 3.36 R
1914 1986 4.081406 ACAGCCTTCATGAATGCAACTAA 58.919 39.130 29.62 0.0 34.93 2.24 R
1988 2060 8.809066 TGTACCAACTTAAGTATTAGAGAGCAA 58.191 33.333 8.92 0.0 0.00 3.91 R
2389 2463 8.879759 TGTTTAGCTTCAAAATCGAAGTATAGG 58.120 33.333 0.00 0.0 43.61 2.57 R
2666 2740 4.153673 AGGGCAGAAGATTCATGAAGAG 57.846 45.455 14.54 1.4 0.00 2.85 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
21 22 4.510167 ATCTCAACCTAATGTGGGAAGG 57.490 45.455 0.00 0.00 36.42 3.46
22 23 3.256704 TCTCAACCTAATGTGGGAAGGT 58.743 45.455 0.00 0.00 45.62 3.50
23 24 3.009033 TCTCAACCTAATGTGGGAAGGTG 59.991 47.826 0.00 0.00 42.86 4.00
24 25 2.714250 TCAACCTAATGTGGGAAGGTGT 59.286 45.455 0.00 0.00 42.86 4.16
25 26 3.081804 CAACCTAATGTGGGAAGGTGTC 58.918 50.000 0.00 0.00 42.86 3.67
26 27 2.632537 ACCTAATGTGGGAAGGTGTCT 58.367 47.619 0.00 0.00 42.08 3.41
27 28 2.305927 ACCTAATGTGGGAAGGTGTCTG 59.694 50.000 0.00 0.00 42.08 3.51
28 29 2.305927 CCTAATGTGGGAAGGTGTCTGT 59.694 50.000 0.00 0.00 0.00 3.41
29 30 2.276732 AATGTGGGAAGGTGTCTGTG 57.723 50.000 0.00 0.00 0.00 3.66
30 31 1.140312 ATGTGGGAAGGTGTCTGTGT 58.860 50.000 0.00 0.00 0.00 3.72
31 32 1.796017 TGTGGGAAGGTGTCTGTGTA 58.204 50.000 0.00 0.00 0.00 2.90
32 33 2.334977 TGTGGGAAGGTGTCTGTGTAT 58.665 47.619 0.00 0.00 0.00 2.29
33 34 2.708861 TGTGGGAAGGTGTCTGTGTATT 59.291 45.455 0.00 0.00 0.00 1.89
34 35 3.137544 TGTGGGAAGGTGTCTGTGTATTT 59.862 43.478 0.00 0.00 0.00 1.40
35 36 3.751698 GTGGGAAGGTGTCTGTGTATTTC 59.248 47.826 0.00 0.00 0.00 2.17
36 37 3.000727 GGGAAGGTGTCTGTGTATTTCG 58.999 50.000 0.00 0.00 0.00 3.46
37 38 2.415512 GGAAGGTGTCTGTGTATTTCGC 59.584 50.000 0.00 0.00 0.00 4.70
38 39 2.094762 AGGTGTCTGTGTATTTCGCC 57.905 50.000 0.00 0.00 0.00 5.54
39 40 0.719465 GGTGTCTGTGTATTTCGCCG 59.281 55.000 0.00 0.00 0.00 6.46
40 41 1.425412 GTGTCTGTGTATTTCGCCGT 58.575 50.000 0.00 0.00 0.00 5.68
41 42 1.126113 GTGTCTGTGTATTTCGCCGTG 59.874 52.381 0.00 0.00 0.00 4.94
42 43 1.269883 TGTCTGTGTATTTCGCCGTGT 60.270 47.619 0.00 0.00 0.00 4.49
43 44 1.796459 GTCTGTGTATTTCGCCGTGTT 59.204 47.619 0.00 0.00 0.00 3.32
44 45 1.795872 TCTGTGTATTTCGCCGTGTTG 59.204 47.619 0.00 0.00 0.00 3.33
45 46 1.795872 CTGTGTATTTCGCCGTGTTGA 59.204 47.619 0.00 0.00 0.00 3.18
46 47 1.795872 TGTGTATTTCGCCGTGTTGAG 59.204 47.619 0.00 0.00 0.00 3.02
47 48 0.793861 TGTATTTCGCCGTGTTGAGC 59.206 50.000 0.00 0.00 0.00 4.26
48 49 0.793861 GTATTTCGCCGTGTTGAGCA 59.206 50.000 0.00 0.00 0.00 4.26
49 50 1.075542 TATTTCGCCGTGTTGAGCAG 58.924 50.000 0.00 0.00 0.00 4.24
50 51 2.187599 ATTTCGCCGTGTTGAGCAGC 62.188 55.000 0.00 0.00 0.00 5.25
53 54 2.047274 GCCGTGTTGAGCAGCCTA 60.047 61.111 0.00 0.00 0.00 3.93
54 55 1.671054 GCCGTGTTGAGCAGCCTAA 60.671 57.895 0.00 0.00 0.00 2.69
55 56 1.234615 GCCGTGTTGAGCAGCCTAAA 61.235 55.000 0.00 0.00 0.00 1.85
56 57 0.798776 CCGTGTTGAGCAGCCTAAAG 59.201 55.000 0.00 0.00 0.00 1.85
57 58 1.608025 CCGTGTTGAGCAGCCTAAAGA 60.608 52.381 0.00 0.00 0.00 2.52
58 59 2.143122 CGTGTTGAGCAGCCTAAAGAA 58.857 47.619 0.00 0.00 0.00 2.52
59 60 2.158449 CGTGTTGAGCAGCCTAAAGAAG 59.842 50.000 0.00 0.00 0.00 2.85
60 61 3.403038 GTGTTGAGCAGCCTAAAGAAGA 58.597 45.455 0.00 0.00 0.00 2.87
61 62 4.006319 GTGTTGAGCAGCCTAAAGAAGAT 58.994 43.478 0.00 0.00 0.00 2.40
62 63 5.178797 GTGTTGAGCAGCCTAAAGAAGATA 58.821 41.667 0.00 0.00 0.00 1.98
63 64 5.293079 GTGTTGAGCAGCCTAAAGAAGATAG 59.707 44.000 0.00 0.00 0.00 2.08
64 65 5.187772 TGTTGAGCAGCCTAAAGAAGATAGA 59.812 40.000 0.00 0.00 0.00 1.98
65 66 5.939764 TGAGCAGCCTAAAGAAGATAGAA 57.060 39.130 0.00 0.00 0.00 2.10
66 67 6.491714 TGAGCAGCCTAAAGAAGATAGAAT 57.508 37.500 0.00 0.00 0.00 2.40
67 68 6.286758 TGAGCAGCCTAAAGAAGATAGAATG 58.713 40.000 0.00 0.00 0.00 2.67
68 69 5.619220 AGCAGCCTAAAGAAGATAGAATGG 58.381 41.667 0.00 0.00 0.00 3.16
69 70 5.367937 AGCAGCCTAAAGAAGATAGAATGGA 59.632 40.000 0.00 0.00 0.00 3.41
70 71 5.700373 GCAGCCTAAAGAAGATAGAATGGAG 59.300 44.000 0.00 0.00 0.00 3.86
71 72 6.229733 CAGCCTAAAGAAGATAGAATGGAGG 58.770 44.000 0.00 0.00 0.00 4.30
72 73 5.908247 AGCCTAAAGAAGATAGAATGGAGGT 59.092 40.000 0.00 0.00 0.00 3.85
73 74 5.994668 GCCTAAAGAAGATAGAATGGAGGTG 59.005 44.000 0.00 0.00 0.00 4.00
74 75 5.994668 CCTAAAGAAGATAGAATGGAGGTGC 59.005 44.000 0.00 0.00 0.00 5.01
75 76 3.742433 AGAAGATAGAATGGAGGTGCG 57.258 47.619 0.00 0.00 0.00 5.34
76 77 3.034635 AGAAGATAGAATGGAGGTGCGT 58.965 45.455 0.00 0.00 0.00 5.24
77 78 2.898729 AGATAGAATGGAGGTGCGTG 57.101 50.000 0.00 0.00 0.00 5.34
78 79 1.202580 AGATAGAATGGAGGTGCGTGC 60.203 52.381 0.00 0.00 0.00 5.34
79 80 0.833287 ATAGAATGGAGGTGCGTGCT 59.167 50.000 0.00 0.00 0.00 4.40
80 81 0.175760 TAGAATGGAGGTGCGTGCTC 59.824 55.000 0.00 0.00 0.00 4.26
81 82 2.045926 AATGGAGGTGCGTGCTCC 60.046 61.111 4.82 4.82 37.75 4.70
82 83 2.527951 GAATGGAGGTGCGTGCTCCT 62.528 60.000 14.83 14.83 41.97 3.69
83 84 2.129555 AATGGAGGTGCGTGCTCCTT 62.130 55.000 15.88 0.00 39.70 3.36
84 85 2.032681 GGAGGTGCGTGCTCCTTT 59.967 61.111 15.88 0.00 39.70 3.11
85 86 2.328099 GGAGGTGCGTGCTCCTTTG 61.328 63.158 15.88 0.00 39.70 2.77
86 87 1.598130 GAGGTGCGTGCTCCTTTGT 60.598 57.895 15.88 0.00 39.70 2.83
87 88 1.152963 AGGTGCGTGCTCCTTTGTT 60.153 52.632 9.56 0.00 36.64 2.83
88 89 1.166531 AGGTGCGTGCTCCTTTGTTC 61.167 55.000 9.56 0.00 36.64 3.18
89 90 1.166531 GGTGCGTGCTCCTTTGTTCT 61.167 55.000 5.72 0.00 0.00 3.01
90 91 0.040958 GTGCGTGCTCCTTTGTTCTG 60.041 55.000 0.00 0.00 0.00 3.02
91 92 0.179059 TGCGTGCTCCTTTGTTCTGA 60.179 50.000 0.00 0.00 0.00 3.27
92 93 0.944386 GCGTGCTCCTTTGTTCTGAA 59.056 50.000 0.00 0.00 0.00 3.02
93 94 1.069636 GCGTGCTCCTTTGTTCTGAAG 60.070 52.381 0.00 0.00 0.00 3.02
94 95 1.069636 CGTGCTCCTTTGTTCTGAAGC 60.070 52.381 0.00 0.00 0.00 3.86
95 96 2.225467 GTGCTCCTTTGTTCTGAAGCT 58.775 47.619 0.00 0.00 0.00 3.74
96 97 2.031333 GTGCTCCTTTGTTCTGAAGCTG 60.031 50.000 0.00 0.00 0.00 4.24
97 98 1.068679 GCTCCTTTGTTCTGAAGCTGC 60.069 52.381 0.00 0.00 0.00 5.25
98 99 2.502295 CTCCTTTGTTCTGAAGCTGCT 58.498 47.619 0.00 0.00 0.00 4.24
99 100 3.668447 CTCCTTTGTTCTGAAGCTGCTA 58.332 45.455 0.90 0.00 0.00 3.49
100 101 4.260170 CTCCTTTGTTCTGAAGCTGCTAT 58.740 43.478 0.90 0.00 0.00 2.97
101 102 4.256920 TCCTTTGTTCTGAAGCTGCTATC 58.743 43.478 0.90 3.78 0.00 2.08
102 103 3.063180 CCTTTGTTCTGAAGCTGCTATCG 59.937 47.826 0.90 0.00 0.00 2.92
103 104 1.645034 TGTTCTGAAGCTGCTATCGC 58.355 50.000 0.90 0.00 0.00 4.58
104 105 1.205655 TGTTCTGAAGCTGCTATCGCT 59.794 47.619 0.90 0.00 39.94 4.93
105 106 1.592081 GTTCTGAAGCTGCTATCGCTG 59.408 52.381 0.90 0.00 37.87 5.18
106 107 1.106285 TCTGAAGCTGCTATCGCTGA 58.894 50.000 0.90 0.26 37.87 4.26
107 108 1.478105 TCTGAAGCTGCTATCGCTGAA 59.522 47.619 0.90 0.00 37.87 3.02
108 109 1.859703 CTGAAGCTGCTATCGCTGAAG 59.140 52.381 0.90 0.00 37.87 3.02
109 110 0.581053 GAAGCTGCTATCGCTGAAGC 59.419 55.000 0.90 0.00 37.87 3.86
110 111 0.813210 AAGCTGCTATCGCTGAAGCC 60.813 55.000 0.90 0.00 37.87 4.35
111 112 1.227497 GCTGCTATCGCTGAAGCCT 60.227 57.895 0.00 0.00 37.97 4.58
112 113 0.032678 GCTGCTATCGCTGAAGCCTA 59.967 55.000 0.00 0.00 37.97 3.93
113 114 1.337635 GCTGCTATCGCTGAAGCCTAT 60.338 52.381 0.00 0.00 37.97 2.57
114 115 2.094494 GCTGCTATCGCTGAAGCCTATA 60.094 50.000 0.00 0.00 37.97 1.31
115 116 3.768406 CTGCTATCGCTGAAGCCTATAG 58.232 50.000 12.04 12.04 37.97 1.31
116 117 2.535331 GCTATCGCTGAAGCCTATAGC 58.465 52.381 20.05 20.05 44.65 2.97
138 139 5.440234 CGTAGCTGCCTAAAGAAGATAGA 57.560 43.478 0.00 0.00 0.00 1.98
139 140 5.833082 CGTAGCTGCCTAAAGAAGATAGAA 58.167 41.667 0.00 0.00 0.00 2.10
140 141 6.451393 CGTAGCTGCCTAAAGAAGATAGAAT 58.549 40.000 0.00 0.00 0.00 2.40
141 142 6.364706 CGTAGCTGCCTAAAGAAGATAGAATG 59.635 42.308 0.00 0.00 0.00 2.67
142 143 5.619220 AGCTGCCTAAAGAAGATAGAATGG 58.381 41.667 0.00 0.00 0.00 3.16
143 144 5.367937 AGCTGCCTAAAGAAGATAGAATGGA 59.632 40.000 0.00 0.00 0.00 3.41
144 145 5.700373 GCTGCCTAAAGAAGATAGAATGGAG 59.300 44.000 0.00 0.00 0.00 3.86
145 146 6.179906 TGCCTAAAGAAGATAGAATGGAGG 57.820 41.667 0.00 0.00 0.00 4.30
146 147 5.667626 TGCCTAAAGAAGATAGAATGGAGGT 59.332 40.000 0.00 0.00 0.00 3.85
147 148 5.994668 GCCTAAAGAAGATAGAATGGAGGTG 59.005 44.000 0.00 0.00 0.00 4.00
148 149 5.994668 CCTAAAGAAGATAGAATGGAGGTGC 59.005 44.000 0.00 0.00 0.00 5.01
149 150 3.742433 AGAAGATAGAATGGAGGTGCG 57.258 47.619 0.00 0.00 0.00 5.34
150 151 3.034635 AGAAGATAGAATGGAGGTGCGT 58.965 45.455 0.00 0.00 0.00 5.24
151 152 2.898729 AGATAGAATGGAGGTGCGTG 57.101 50.000 0.00 0.00 0.00 5.34
152 153 1.202580 AGATAGAATGGAGGTGCGTGC 60.203 52.381 0.00 0.00 0.00 5.34
153 154 0.833287 ATAGAATGGAGGTGCGTGCT 59.167 50.000 0.00 0.00 0.00 4.40
154 155 0.175760 TAGAATGGAGGTGCGTGCTC 59.824 55.000 0.00 0.00 0.00 4.26
155 156 2.045926 AATGGAGGTGCGTGCTCC 60.046 61.111 4.82 4.82 37.75 4.70
156 157 2.527951 GAATGGAGGTGCGTGCTCCT 62.528 60.000 14.83 14.83 41.97 3.69
157 158 2.129555 AATGGAGGTGCGTGCTCCTT 62.130 55.000 15.88 0.00 39.70 3.36
158 159 2.032681 GGAGGTGCGTGCTCCTTT 59.967 61.111 15.88 0.00 39.70 3.11
159 160 2.328099 GGAGGTGCGTGCTCCTTTG 61.328 63.158 15.88 0.00 39.70 2.77
160 161 1.598130 GAGGTGCGTGCTCCTTTGT 60.598 57.895 15.88 0.00 39.70 2.83
161 162 1.152963 AGGTGCGTGCTCCTTTGTT 60.153 52.632 9.56 0.00 36.64 2.83
162 163 1.166531 AGGTGCGTGCTCCTTTGTTC 61.167 55.000 9.56 0.00 36.64 3.18
163 164 1.166531 GGTGCGTGCTCCTTTGTTCT 61.167 55.000 5.72 0.00 0.00 3.01
164 165 0.040958 GTGCGTGCTCCTTTGTTCTG 60.041 55.000 0.00 0.00 0.00 3.02
165 166 0.179059 TGCGTGCTCCTTTGTTCTGA 60.179 50.000 0.00 0.00 0.00 3.27
166 167 0.944386 GCGTGCTCCTTTGTTCTGAA 59.056 50.000 0.00 0.00 0.00 3.02
167 168 1.069636 GCGTGCTCCTTTGTTCTGAAG 60.070 52.381 0.00 0.00 0.00 3.02
168 169 1.069636 CGTGCTCCTTTGTTCTGAAGC 60.070 52.381 0.00 0.00 0.00 3.86
169 170 2.225467 GTGCTCCTTTGTTCTGAAGCT 58.775 47.619 0.00 0.00 0.00 3.74
170 171 2.031333 GTGCTCCTTTGTTCTGAAGCTG 60.031 50.000 0.00 0.00 0.00 4.24
171 172 1.068679 GCTCCTTTGTTCTGAAGCTGC 60.069 52.381 0.00 0.00 0.00 5.25
172 173 2.502295 CTCCTTTGTTCTGAAGCTGCT 58.498 47.619 0.00 0.00 0.00 4.24
173 174 3.668447 CTCCTTTGTTCTGAAGCTGCTA 58.332 45.455 0.90 0.00 0.00 3.49
174 175 4.260170 CTCCTTTGTTCTGAAGCTGCTAT 58.740 43.478 0.90 0.00 0.00 2.97
175 176 4.256920 TCCTTTGTTCTGAAGCTGCTATC 58.743 43.478 0.90 3.78 0.00 2.08
176 177 3.063180 CCTTTGTTCTGAAGCTGCTATCG 59.937 47.826 0.90 0.00 0.00 2.92
177 178 1.645034 TGTTCTGAAGCTGCTATCGC 58.355 50.000 0.90 0.00 0.00 4.58
178 179 1.205655 TGTTCTGAAGCTGCTATCGCT 59.794 47.619 0.90 0.00 39.94 4.93
179 180 1.592081 GTTCTGAAGCTGCTATCGCTG 59.408 52.381 0.90 0.00 37.87 5.18
180 181 1.106285 TCTGAAGCTGCTATCGCTGA 58.894 50.000 0.90 0.26 37.87 4.26
181 182 1.478105 TCTGAAGCTGCTATCGCTGAA 59.522 47.619 0.90 0.00 37.87 3.02
182 183 1.859703 CTGAAGCTGCTATCGCTGAAG 59.140 52.381 0.90 0.00 37.87 3.02
183 184 0.581053 GAAGCTGCTATCGCTGAAGC 59.419 55.000 0.90 0.00 37.87 3.86
184 185 0.813210 AAGCTGCTATCGCTGAAGCC 60.813 55.000 0.90 0.00 37.87 4.35
185 186 1.227497 GCTGCTATCGCTGAAGCCT 60.227 57.895 0.00 0.00 37.97 4.58
186 187 0.032678 GCTGCTATCGCTGAAGCCTA 59.967 55.000 0.00 0.00 37.97 3.93
187 188 1.337635 GCTGCTATCGCTGAAGCCTAT 60.338 52.381 0.00 0.00 37.97 2.57
188 189 2.094494 GCTGCTATCGCTGAAGCCTATA 60.094 50.000 0.00 0.00 37.97 1.31
189 190 3.768406 CTGCTATCGCTGAAGCCTATAG 58.232 50.000 12.04 12.04 37.97 1.31
190 191 2.535331 GCTATCGCTGAAGCCTATAGC 58.465 52.381 20.05 20.05 44.65 2.97
215 216 1.314534 TGCAGGATTTGGTGATGGCG 61.315 55.000 0.00 0.00 0.00 5.69
220 221 2.023673 GGATTTGGTGATGGCGATTGA 58.976 47.619 0.00 0.00 0.00 2.57
262 267 6.860539 AGACTGTAGATTTGATGATCGATTCG 59.139 38.462 0.00 0.00 0.00 3.34
263 268 5.923114 ACTGTAGATTTGATGATCGATTCGG 59.077 40.000 6.18 0.00 0.00 4.30
295 300 2.331194 CAAGCATTGCCAAAGTAGTGC 58.669 47.619 4.70 0.00 40.39 4.40
318 323 8.667463 GTGCATGAAATAATTGGTTTTGCTATT 58.333 29.630 0.00 0.00 0.00 1.73
319 324 8.881743 TGCATGAAATAATTGGTTTTGCTATTC 58.118 29.630 0.00 0.00 0.00 1.75
320 325 8.881743 GCATGAAATAATTGGTTTTGCTATTCA 58.118 29.630 0.00 0.00 0.00 2.57
378 401 9.791820 TTTGATGATTGACATAGTTTGCAATAG 57.208 29.630 0.00 0.00 39.56 1.73
379 402 7.933396 TGATGATTGACATAGTTTGCAATAGG 58.067 34.615 0.00 0.00 39.56 2.57
380 403 7.774625 TGATGATTGACATAGTTTGCAATAGGA 59.225 33.333 0.00 0.00 39.56 2.94
381 404 7.936496 TGATTGACATAGTTTGCAATAGGAA 57.064 32.000 0.00 0.00 34.41 3.36
382 405 8.347004 TGATTGACATAGTTTGCAATAGGAAA 57.653 30.769 0.00 0.00 34.41 3.13
383 406 8.970020 TGATTGACATAGTTTGCAATAGGAAAT 58.030 29.630 0.00 0.00 37.41 2.17
384 407 9.807649 GATTGACATAGTTTGCAATAGGAAATT 57.192 29.630 0.00 0.00 37.41 1.82
385 408 8.984891 TTGACATAGTTTGCAATAGGAAATTG 57.015 30.769 0.00 0.00 37.41 2.32
386 409 8.121305 TGACATAGTTTGCAATAGGAAATTGT 57.879 30.769 0.00 0.00 37.41 2.71
387 410 8.028354 TGACATAGTTTGCAATAGGAAATTGTG 58.972 33.333 0.00 0.00 38.84 3.33
388 411 7.895759 ACATAGTTTGCAATAGGAAATTGTGT 58.104 30.769 0.00 0.00 40.22 3.72
389 412 8.367156 ACATAGTTTGCAATAGGAAATTGTGTT 58.633 29.630 0.00 0.00 41.39 3.32
390 413 9.853555 CATAGTTTGCAATAGGAAATTGTGTTA 57.146 29.630 0.00 0.00 37.41 2.41
415 438 7.396540 AAAAACGAAGATAGATCCTGCAATT 57.603 32.000 0.00 0.00 0.00 2.32
416 439 7.396540 AAAACGAAGATAGATCCTGCAATTT 57.603 32.000 0.00 0.00 0.00 1.82
417 440 7.396540 AAACGAAGATAGATCCTGCAATTTT 57.603 32.000 0.00 0.00 0.00 1.82
418 441 7.396540 AACGAAGATAGATCCTGCAATTTTT 57.603 32.000 0.00 0.00 0.00 1.94
493 516 2.807676 AGGCTTTTCGATGGGTGATTT 58.192 42.857 0.00 0.00 0.00 2.17
494 517 3.165071 AGGCTTTTCGATGGGTGATTTT 58.835 40.909 0.00 0.00 0.00 1.82
495 518 3.578282 AGGCTTTTCGATGGGTGATTTTT 59.422 39.130 0.00 0.00 0.00 1.94
496 519 4.770010 AGGCTTTTCGATGGGTGATTTTTA 59.230 37.500 0.00 0.00 0.00 1.52
497 520 5.102313 GGCTTTTCGATGGGTGATTTTTAG 58.898 41.667 0.00 0.00 0.00 1.85
498 521 5.102313 GCTTTTCGATGGGTGATTTTTAGG 58.898 41.667 0.00 0.00 0.00 2.69
499 522 5.650543 CTTTTCGATGGGTGATTTTTAGGG 58.349 41.667 0.00 0.00 0.00 3.53
500 523 3.290948 TCGATGGGTGATTTTTAGGGG 57.709 47.619 0.00 0.00 0.00 4.79
501 524 2.578940 TCGATGGGTGATTTTTAGGGGT 59.421 45.455 0.00 0.00 0.00 4.95
502 525 3.781407 TCGATGGGTGATTTTTAGGGGTA 59.219 43.478 0.00 0.00 0.00 3.69
503 526 4.414182 TCGATGGGTGATTTTTAGGGGTAT 59.586 41.667 0.00 0.00 0.00 2.73
504 527 5.103855 TCGATGGGTGATTTTTAGGGGTATT 60.104 40.000 0.00 0.00 0.00 1.89
534 557 9.443323 TTTAGATTAGATGAAAATTCGTGGTGA 57.557 29.630 0.00 0.00 0.00 4.02
547 570 2.282745 GGTGAAGCCCAAGCAGCT 60.283 61.111 0.00 0.00 44.19 4.24
552 575 4.938838 AGCCCAAGCAGCTTCTTT 57.061 50.000 4.07 0.00 43.56 2.52
553 576 3.138214 AGCCCAAGCAGCTTCTTTT 57.862 47.368 4.07 0.00 43.56 2.27
573 596 0.034896 TGTTTCGAGAACAGAGCCCC 59.965 55.000 8.47 0.00 0.00 5.80
574 597 0.673956 GTTTCGAGAACAGAGCCCCC 60.674 60.000 5.85 0.00 0.00 5.40
577 600 1.125093 TCGAGAACAGAGCCCCCAAA 61.125 55.000 0.00 0.00 0.00 3.28
579 602 1.817740 CGAGAACAGAGCCCCCAAAAA 60.818 52.381 0.00 0.00 0.00 1.94
614 642 1.740025 CCTCAACGAAAGAAGCCCATC 59.260 52.381 0.00 0.00 0.00 3.51
622 650 3.313526 CGAAAGAAGCCCATCTAACATGG 59.686 47.826 0.00 0.00 38.88 3.66
625 653 1.678101 GAAGCCCATCTAACATGGTGC 59.322 52.381 0.00 3.56 37.48 5.01
636 664 3.710209 AACATGGTGCTAGAAGAAGCT 57.290 42.857 0.00 0.00 43.19 3.74
642 670 2.342179 GTGCTAGAAGAAGCTCACCAC 58.658 52.381 0.00 0.00 43.19 4.16
643 671 1.067565 TGCTAGAAGAAGCTCACCACG 60.068 52.381 0.00 0.00 43.19 4.94
652 680 0.107831 AGCTCACCACGGCACTTTTA 59.892 50.000 0.00 0.00 0.00 1.52
658 688 0.824182 CCACGGCACTTTTAACCCCA 60.824 55.000 0.00 0.00 0.00 4.96
659 689 0.312729 CACGGCACTTTTAACCCCAC 59.687 55.000 0.00 0.00 0.00 4.61
796 826 1.715862 TTCTCCAGCGTCCGATCTCG 61.716 60.000 0.00 0.00 39.44 4.04
918 951 2.933906 GTGCGTTTGATTTCGATCCCTA 59.066 45.455 0.00 0.00 0.00 3.53
926 961 0.340558 TTTCGATCCCTACCCTCCCA 59.659 55.000 0.00 0.00 0.00 4.37
929 964 0.905337 CGATCCCTACCCTCCCATCC 60.905 65.000 0.00 0.00 0.00 3.51
934 969 1.679969 CCTACCCTCCCATCCCCTCT 61.680 65.000 0.00 0.00 0.00 3.69
1505 1565 2.064762 GCTCACTGTCAGTACTTGCTG 58.935 52.381 4.85 0.00 37.81 4.41
1536 1596 8.681806 TGACAATAATTCTCTTGTTTTGTGTCA 58.318 29.630 0.00 0.00 35.80 3.58
1537 1597 9.683069 GACAATAATTCTCTTGTTTTGTGTCAT 57.317 29.630 0.00 0.00 35.80 3.06
1632 1693 7.848223 ATGTGATCTTGTAATCAATTCGACA 57.152 32.000 0.00 0.00 37.41 4.35
1639 1711 8.940768 TCTTGTAATCAATTCGACATACATGA 57.059 30.769 0.00 0.00 34.48 3.07
1649 1721 9.469239 CAATTCGACATACATGATATTGATTCG 57.531 33.333 0.00 0.00 0.00 3.34
1666 1738 4.743151 TGATTCGCTGATACGTTTCATACC 59.257 41.667 9.19 1.20 0.00 2.73
1694 1766 5.752955 GCAAAACAAAATGCAGTTTCCTCTA 59.247 36.000 9.56 0.00 42.12 2.43
1723 1795 8.852135 TCCTAGTTTAAACATAACCACAAAAGG 58.148 33.333 20.06 8.56 0.00 3.11
1762 1834 1.014352 GGCCACATAACCTGCGTTAG 58.986 55.000 0.00 0.00 37.86 2.34
1778 1850 3.589988 CGTTAGATCCTTTGAGCTGTGT 58.410 45.455 0.00 0.00 37.87 3.72
1811 1883 9.770097 AATCAGGTATATAGTTGTCACTTGATG 57.230 33.333 0.00 0.00 36.45 3.07
1903 1975 5.751680 CATGCTTTCCAGTTTCATATACCG 58.248 41.667 0.00 0.00 0.00 4.02
1934 2006 4.338879 ACTTAGTTGCATTCATGAAGGCT 58.661 39.130 36.20 23.49 46.93 4.58
2389 2463 2.825532 ACCATCACTTGCCATTACAACC 59.174 45.455 0.00 0.00 0.00 3.77
2666 2740 7.660208 TCTTCTTTTCAGTGGTTTGTATAGTCC 59.340 37.037 0.00 0.00 0.00 3.85
2668 2742 7.159372 TCTTTTCAGTGGTTTGTATAGTCCTC 58.841 38.462 0.00 0.00 0.00 3.71
2692 2766 6.600822 TCTTCATGAATCTTCTGCCCTTTTAG 59.399 38.462 8.96 0.00 0.00 1.85
2702 2776 3.507233 TCTGCCCTTTTAGCAAGTGAATG 59.493 43.478 0.00 0.00 40.35 2.67
2768 2844 3.795623 ATGCATGTTTCATGCTTCCTC 57.204 42.857 27.05 6.19 44.79 3.71
2775 2851 5.695851 TGTTTCATGCTTCCTCTTTCTTC 57.304 39.130 0.00 0.00 0.00 2.87
2799 2875 6.972328 TCAGTAAATTTCACAAAACTGTCAGC 59.028 34.615 13.52 0.00 0.00 4.26
2823 2899 7.331440 AGCATTTTGAACAAATTCATCGCATAA 59.669 29.630 0.82 0.00 44.36 1.90
2879 2956 7.441836 ACAGTTGAATACACTGTTGTATCTCA 58.558 34.615 0.00 2.91 46.45 3.27
2913 2990 8.778059 TGAATTAAGGGTTGACTCTTATGGTAT 58.222 33.333 4.42 0.00 0.00 2.73
3099 3178 8.051901 ACCTACATTGGAGTTTTTACAATAGC 57.948 34.615 0.00 0.00 33.40 2.97
3106 3185 4.412207 GAGTTTTTACAATAGCGGGCTTG 58.588 43.478 0.00 0.00 0.00 4.01
3261 3601 4.173290 TCATGATGATCATTGGCTGGAA 57.827 40.909 10.14 0.00 34.28 3.53
3262 3602 4.538738 TCATGATGATCATTGGCTGGAAA 58.461 39.130 10.14 0.00 34.28 3.13
3263 3603 4.340097 TCATGATGATCATTGGCTGGAAAC 59.660 41.667 10.14 0.00 34.28 2.78
3264 3604 3.972133 TGATGATCATTGGCTGGAAACT 58.028 40.909 10.14 0.00 0.00 2.66
3265 3605 5.114764 TGATGATCATTGGCTGGAAACTA 57.885 39.130 10.14 0.00 0.00 2.24
3266 3606 5.508567 TGATGATCATTGGCTGGAAACTAA 58.491 37.500 10.14 0.00 0.00 2.24
3267 3607 5.951148 TGATGATCATTGGCTGGAAACTAAA 59.049 36.000 10.14 0.00 0.00 1.85
3268 3608 5.902613 TGATCATTGGCTGGAAACTAAAG 57.097 39.130 0.00 0.00 0.00 1.85
3269 3609 4.158394 TGATCATTGGCTGGAAACTAAAGC 59.842 41.667 0.00 0.00 36.17 3.51
3270 3610 3.495331 TCATTGGCTGGAAACTAAAGCA 58.505 40.909 0.00 0.00 38.73 3.91
3271 3611 3.255642 TCATTGGCTGGAAACTAAAGCAC 59.744 43.478 0.00 0.00 38.73 4.40
3272 3612 1.616159 TGGCTGGAAACTAAAGCACC 58.384 50.000 0.00 0.00 38.73 5.01
3273 3613 1.144913 TGGCTGGAAACTAAAGCACCT 59.855 47.619 0.00 0.00 38.73 4.00
3274 3614 1.541588 GGCTGGAAACTAAAGCACCTG 59.458 52.381 0.00 0.00 38.73 4.00
3275 3615 1.541588 GCTGGAAACTAAAGCACCTGG 59.458 52.381 0.00 0.00 36.91 4.45
3276 3616 2.814097 GCTGGAAACTAAAGCACCTGGA 60.814 50.000 0.00 0.00 36.91 3.86
3277 3617 3.486383 CTGGAAACTAAAGCACCTGGAA 58.514 45.455 0.00 0.00 0.00 3.53
3278 3618 3.486383 TGGAAACTAAAGCACCTGGAAG 58.514 45.455 0.00 0.00 0.00 3.46
3491 3857 4.638304 ACTTATAGTTGTGCGGTGTTTCT 58.362 39.130 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.852578 ACCTTCCCACATTAGGTTGAGAT 59.147 43.478 0.00 0.00 39.19 2.75
1 2 3.009033 CACCTTCCCACATTAGGTTGAGA 59.991 47.826 0.00 0.00 40.24 3.27
2 3 3.244911 ACACCTTCCCACATTAGGTTGAG 60.245 47.826 0.00 0.00 40.24 3.02
3 4 2.714250 ACACCTTCCCACATTAGGTTGA 59.286 45.455 0.00 0.00 40.24 3.18
4 5 3.081804 GACACCTTCCCACATTAGGTTG 58.918 50.000 0.00 0.00 40.24 3.77
5 6 2.986728 AGACACCTTCCCACATTAGGTT 59.013 45.455 0.00 0.00 40.24 3.50
6 7 2.305927 CAGACACCTTCCCACATTAGGT 59.694 50.000 0.00 0.00 42.92 3.08
7 8 2.305927 ACAGACACCTTCCCACATTAGG 59.694 50.000 0.00 0.00 35.14 2.69
8 9 3.244561 ACACAGACACCTTCCCACATTAG 60.245 47.826 0.00 0.00 0.00 1.73
9 10 2.708861 ACACAGACACCTTCCCACATTA 59.291 45.455 0.00 0.00 0.00 1.90
10 11 1.494721 ACACAGACACCTTCCCACATT 59.505 47.619 0.00 0.00 0.00 2.71
11 12 1.140312 ACACAGACACCTTCCCACAT 58.860 50.000 0.00 0.00 0.00 3.21
12 13 1.796017 TACACAGACACCTTCCCACA 58.204 50.000 0.00 0.00 0.00 4.17
13 14 3.418684 AATACACAGACACCTTCCCAC 57.581 47.619 0.00 0.00 0.00 4.61
14 15 3.556213 CGAAATACACAGACACCTTCCCA 60.556 47.826 0.00 0.00 0.00 4.37
15 16 3.000727 CGAAATACACAGACACCTTCCC 58.999 50.000 0.00 0.00 0.00 3.97
16 17 2.415512 GCGAAATACACAGACACCTTCC 59.584 50.000 0.00 0.00 0.00 3.46
17 18 2.415512 GGCGAAATACACAGACACCTTC 59.584 50.000 0.00 0.00 0.00 3.46
18 19 2.423577 GGCGAAATACACAGACACCTT 58.576 47.619 0.00 0.00 0.00 3.50
19 20 1.671850 CGGCGAAATACACAGACACCT 60.672 52.381 0.00 0.00 0.00 4.00
20 21 0.719465 CGGCGAAATACACAGACACC 59.281 55.000 0.00 0.00 0.00 4.16
21 22 1.126113 CACGGCGAAATACACAGACAC 59.874 52.381 16.62 0.00 0.00 3.67
22 23 1.269883 ACACGGCGAAATACACAGACA 60.270 47.619 16.62 0.00 0.00 3.41
23 24 1.425412 ACACGGCGAAATACACAGAC 58.575 50.000 16.62 0.00 0.00 3.51
24 25 1.795872 CAACACGGCGAAATACACAGA 59.204 47.619 16.62 0.00 0.00 3.41
25 26 1.795872 TCAACACGGCGAAATACACAG 59.204 47.619 16.62 0.00 0.00 3.66
26 27 1.795872 CTCAACACGGCGAAATACACA 59.204 47.619 16.62 0.00 0.00 3.72
27 28 1.463528 GCTCAACACGGCGAAATACAC 60.464 52.381 16.62 0.00 0.00 2.90
28 29 0.793861 GCTCAACACGGCGAAATACA 59.206 50.000 16.62 0.00 0.00 2.29
29 30 0.793861 TGCTCAACACGGCGAAATAC 59.206 50.000 16.62 0.00 0.00 1.89
30 31 1.075542 CTGCTCAACACGGCGAAATA 58.924 50.000 16.62 0.00 0.00 1.40
31 32 1.868997 CTGCTCAACACGGCGAAAT 59.131 52.632 16.62 0.00 0.00 2.17
32 33 2.892334 GCTGCTCAACACGGCGAAA 61.892 57.895 16.62 0.00 0.00 3.46
33 34 3.345808 GCTGCTCAACACGGCGAA 61.346 61.111 16.62 0.00 0.00 4.70
35 36 3.932580 TAGGCTGCTCAACACGGCG 62.933 63.158 4.80 4.80 40.46 6.46
36 37 1.234615 TTTAGGCTGCTCAACACGGC 61.235 55.000 0.00 0.00 38.75 5.68
37 38 0.798776 CTTTAGGCTGCTCAACACGG 59.201 55.000 0.00 0.00 0.00 4.94
38 39 1.795768 TCTTTAGGCTGCTCAACACG 58.204 50.000 0.00 0.00 0.00 4.49
39 40 3.403038 TCTTCTTTAGGCTGCTCAACAC 58.597 45.455 0.00 0.00 0.00 3.32
40 41 3.769739 TCTTCTTTAGGCTGCTCAACA 57.230 42.857 0.00 0.00 0.00 3.33
41 42 5.665459 TCTATCTTCTTTAGGCTGCTCAAC 58.335 41.667 0.00 0.00 0.00 3.18
42 43 5.939764 TCTATCTTCTTTAGGCTGCTCAA 57.060 39.130 0.00 0.00 0.00 3.02
43 44 5.939764 TTCTATCTTCTTTAGGCTGCTCA 57.060 39.130 0.00 0.00 0.00 4.26
44 45 5.700373 CCATTCTATCTTCTTTAGGCTGCTC 59.300 44.000 0.00 0.00 0.00 4.26
45 46 5.367937 TCCATTCTATCTTCTTTAGGCTGCT 59.632 40.000 0.00 0.00 0.00 4.24
46 47 5.615289 TCCATTCTATCTTCTTTAGGCTGC 58.385 41.667 0.00 0.00 0.00 5.25
47 48 6.183361 ACCTCCATTCTATCTTCTTTAGGCTG 60.183 42.308 0.00 0.00 0.00 4.85
48 49 5.908247 ACCTCCATTCTATCTTCTTTAGGCT 59.092 40.000 0.00 0.00 0.00 4.58
49 50 5.994668 CACCTCCATTCTATCTTCTTTAGGC 59.005 44.000 0.00 0.00 0.00 3.93
50 51 5.994668 GCACCTCCATTCTATCTTCTTTAGG 59.005 44.000 0.00 0.00 0.00 2.69
51 52 5.694006 CGCACCTCCATTCTATCTTCTTTAG 59.306 44.000 0.00 0.00 0.00 1.85
52 53 5.128827 ACGCACCTCCATTCTATCTTCTTTA 59.871 40.000 0.00 0.00 0.00 1.85
53 54 4.080863 ACGCACCTCCATTCTATCTTCTTT 60.081 41.667 0.00 0.00 0.00 2.52
54 55 3.452627 ACGCACCTCCATTCTATCTTCTT 59.547 43.478 0.00 0.00 0.00 2.52
55 56 3.034635 ACGCACCTCCATTCTATCTTCT 58.965 45.455 0.00 0.00 0.00 2.85
56 57 3.126831 CACGCACCTCCATTCTATCTTC 58.873 50.000 0.00 0.00 0.00 2.87
57 58 2.743183 GCACGCACCTCCATTCTATCTT 60.743 50.000 0.00 0.00 0.00 2.40
58 59 1.202580 GCACGCACCTCCATTCTATCT 60.203 52.381 0.00 0.00 0.00 1.98
59 60 1.202580 AGCACGCACCTCCATTCTATC 60.203 52.381 0.00 0.00 0.00 2.08
60 61 0.833287 AGCACGCACCTCCATTCTAT 59.167 50.000 0.00 0.00 0.00 1.98
61 62 0.175760 GAGCACGCACCTCCATTCTA 59.824 55.000 0.00 0.00 0.00 2.10
62 63 1.078848 GAGCACGCACCTCCATTCT 60.079 57.895 0.00 0.00 0.00 2.40
63 64 2.109126 GGAGCACGCACCTCCATTC 61.109 63.158 10.67 0.00 46.51 2.67
64 65 2.045926 GGAGCACGCACCTCCATT 60.046 61.111 10.67 0.00 46.51 3.16
68 69 1.166531 AACAAAGGAGCACGCACCTC 61.167 55.000 8.52 0.00 36.01 3.85
69 70 1.152963 AACAAAGGAGCACGCACCT 60.153 52.632 1.78 1.78 38.66 4.00
70 71 1.166531 AGAACAAAGGAGCACGCACC 61.167 55.000 0.00 0.00 0.00 5.01
71 72 0.040958 CAGAACAAAGGAGCACGCAC 60.041 55.000 0.00 0.00 0.00 5.34
72 73 0.179059 TCAGAACAAAGGAGCACGCA 60.179 50.000 0.00 0.00 0.00 5.24
73 74 0.944386 TTCAGAACAAAGGAGCACGC 59.056 50.000 0.00 0.00 0.00 5.34
74 75 1.069636 GCTTCAGAACAAAGGAGCACG 60.070 52.381 0.00 0.00 0.00 5.34
75 76 2.031333 CAGCTTCAGAACAAAGGAGCAC 60.031 50.000 0.00 0.00 0.00 4.40
76 77 2.224606 CAGCTTCAGAACAAAGGAGCA 58.775 47.619 0.00 0.00 0.00 4.26
77 78 1.068679 GCAGCTTCAGAACAAAGGAGC 60.069 52.381 0.00 0.00 0.00 4.70
78 79 2.502295 AGCAGCTTCAGAACAAAGGAG 58.498 47.619 0.00 0.00 0.00 3.69
79 80 2.645838 AGCAGCTTCAGAACAAAGGA 57.354 45.000 0.00 0.00 0.00 3.36
80 81 3.063180 CGATAGCAGCTTCAGAACAAAGG 59.937 47.826 0.00 0.00 0.00 3.11
81 82 4.256140 CGATAGCAGCTTCAGAACAAAG 57.744 45.455 0.00 0.00 0.00 2.77
102 103 1.271102 AGCTACGCTATAGGCTTCAGC 59.729 52.381 9.35 9.35 36.99 4.26
103 104 2.924454 GCAGCTACGCTATAGGCTTCAG 60.924 54.545 1.04 0.00 36.40 3.02
104 105 1.000163 GCAGCTACGCTATAGGCTTCA 60.000 52.381 1.04 0.00 36.40 3.02
105 106 1.670380 GGCAGCTACGCTATAGGCTTC 60.670 57.143 1.04 0.00 36.40 3.86
106 107 0.318762 GGCAGCTACGCTATAGGCTT 59.681 55.000 1.04 0.00 36.40 4.35
107 108 0.540830 AGGCAGCTACGCTATAGGCT 60.541 55.000 1.04 0.00 36.40 4.58
108 109 1.174783 TAGGCAGCTACGCTATAGGC 58.825 55.000 1.04 0.00 36.40 3.93
109 110 3.506455 TCTTTAGGCAGCTACGCTATAGG 59.494 47.826 1.04 0.00 36.40 2.57
110 111 4.768130 TCTTTAGGCAGCTACGCTATAG 57.232 45.455 0.00 0.00 36.40 1.31
111 112 4.825634 TCTTCTTTAGGCAGCTACGCTATA 59.174 41.667 0.00 0.00 36.40 1.31
112 113 3.637229 TCTTCTTTAGGCAGCTACGCTAT 59.363 43.478 0.00 0.00 36.40 2.97
113 114 3.021695 TCTTCTTTAGGCAGCTACGCTA 58.978 45.455 0.00 0.00 36.40 4.26
114 115 1.825474 TCTTCTTTAGGCAGCTACGCT 59.175 47.619 0.00 0.00 40.77 5.07
115 116 2.295253 TCTTCTTTAGGCAGCTACGC 57.705 50.000 0.00 0.00 0.00 4.42
116 117 5.440234 TCTATCTTCTTTAGGCAGCTACG 57.560 43.478 0.00 0.00 0.00 3.51
117 118 6.648725 CCATTCTATCTTCTTTAGGCAGCTAC 59.351 42.308 0.00 0.00 0.00 3.58
118 119 6.554982 TCCATTCTATCTTCTTTAGGCAGCTA 59.445 38.462 0.00 0.00 0.00 3.32
119 120 5.367937 TCCATTCTATCTTCTTTAGGCAGCT 59.632 40.000 0.00 0.00 0.00 4.24
120 121 5.615289 TCCATTCTATCTTCTTTAGGCAGC 58.385 41.667 0.00 0.00 0.00 5.25
121 122 6.183361 ACCTCCATTCTATCTTCTTTAGGCAG 60.183 42.308 0.00 0.00 0.00 4.85
122 123 5.667626 ACCTCCATTCTATCTTCTTTAGGCA 59.332 40.000 0.00 0.00 0.00 4.75
123 124 5.994668 CACCTCCATTCTATCTTCTTTAGGC 59.005 44.000 0.00 0.00 0.00 3.93
124 125 5.994668 GCACCTCCATTCTATCTTCTTTAGG 59.005 44.000 0.00 0.00 0.00 2.69
125 126 5.694006 CGCACCTCCATTCTATCTTCTTTAG 59.306 44.000 0.00 0.00 0.00 1.85
126 127 5.128827 ACGCACCTCCATTCTATCTTCTTTA 59.871 40.000 0.00 0.00 0.00 1.85
127 128 4.080863 ACGCACCTCCATTCTATCTTCTTT 60.081 41.667 0.00 0.00 0.00 2.52
128 129 3.452627 ACGCACCTCCATTCTATCTTCTT 59.547 43.478 0.00 0.00 0.00 2.52
129 130 3.034635 ACGCACCTCCATTCTATCTTCT 58.965 45.455 0.00 0.00 0.00 2.85
130 131 3.126831 CACGCACCTCCATTCTATCTTC 58.873 50.000 0.00 0.00 0.00 2.87
131 132 2.743183 GCACGCACCTCCATTCTATCTT 60.743 50.000 0.00 0.00 0.00 2.40
132 133 1.202580 GCACGCACCTCCATTCTATCT 60.203 52.381 0.00 0.00 0.00 1.98
133 134 1.202580 AGCACGCACCTCCATTCTATC 60.203 52.381 0.00 0.00 0.00 2.08
134 135 0.833287 AGCACGCACCTCCATTCTAT 59.167 50.000 0.00 0.00 0.00 1.98
135 136 0.175760 GAGCACGCACCTCCATTCTA 59.824 55.000 0.00 0.00 0.00 2.10
136 137 1.078848 GAGCACGCACCTCCATTCT 60.079 57.895 0.00 0.00 0.00 2.40
137 138 2.109126 GGAGCACGCACCTCCATTC 61.109 63.158 10.67 0.00 46.51 2.67
138 139 2.045926 GGAGCACGCACCTCCATT 60.046 61.111 10.67 0.00 46.51 3.16
142 143 1.166531 AACAAAGGAGCACGCACCTC 61.167 55.000 8.52 0.00 36.01 3.85
143 144 1.152963 AACAAAGGAGCACGCACCT 60.153 52.632 1.78 1.78 38.66 4.00
144 145 1.166531 AGAACAAAGGAGCACGCACC 61.167 55.000 0.00 0.00 0.00 5.01
145 146 0.040958 CAGAACAAAGGAGCACGCAC 60.041 55.000 0.00 0.00 0.00 5.34
146 147 0.179059 TCAGAACAAAGGAGCACGCA 60.179 50.000 0.00 0.00 0.00 5.24
147 148 0.944386 TTCAGAACAAAGGAGCACGC 59.056 50.000 0.00 0.00 0.00 5.34
148 149 1.069636 GCTTCAGAACAAAGGAGCACG 60.070 52.381 0.00 0.00 0.00 5.34
149 150 2.031333 CAGCTTCAGAACAAAGGAGCAC 60.031 50.000 0.00 0.00 0.00 4.40
150 151 2.224606 CAGCTTCAGAACAAAGGAGCA 58.775 47.619 0.00 0.00 0.00 4.26
151 152 1.068679 GCAGCTTCAGAACAAAGGAGC 60.069 52.381 0.00 0.00 0.00 4.70
152 153 2.502295 AGCAGCTTCAGAACAAAGGAG 58.498 47.619 0.00 0.00 0.00 3.69
153 154 2.645838 AGCAGCTTCAGAACAAAGGA 57.354 45.000 0.00 0.00 0.00 3.36
154 155 3.063180 CGATAGCAGCTTCAGAACAAAGG 59.937 47.826 0.00 0.00 0.00 3.11
155 156 4.256140 CGATAGCAGCTTCAGAACAAAG 57.744 45.455 0.00 0.00 0.00 2.77
176 177 1.271102 AGCTACGCTATAGGCTTCAGC 59.729 52.381 9.35 9.35 36.99 4.26
177 178 2.924454 GCAGCTACGCTATAGGCTTCAG 60.924 54.545 1.04 0.00 36.40 3.02
178 179 1.000163 GCAGCTACGCTATAGGCTTCA 60.000 52.381 1.04 0.00 36.40 3.02
179 180 1.000163 TGCAGCTACGCTATAGGCTTC 60.000 52.381 1.04 0.00 36.40 3.86
180 181 1.000283 CTGCAGCTACGCTATAGGCTT 60.000 52.381 0.00 0.00 36.40 4.35
181 182 0.600557 CTGCAGCTACGCTATAGGCT 59.399 55.000 0.00 0.00 36.40 4.58
182 183 0.389166 CCTGCAGCTACGCTATAGGC 60.389 60.000 8.66 0.00 36.40 3.93
183 184 1.248486 TCCTGCAGCTACGCTATAGG 58.752 55.000 8.66 9.87 40.20 2.57
184 185 3.584406 AATCCTGCAGCTACGCTATAG 57.416 47.619 8.66 0.00 36.40 1.31
185 186 3.554960 CCAAATCCTGCAGCTACGCTATA 60.555 47.826 8.66 0.00 36.40 1.31
186 187 2.487934 CAAATCCTGCAGCTACGCTAT 58.512 47.619 8.66 0.00 36.40 2.97
187 188 1.473257 CCAAATCCTGCAGCTACGCTA 60.473 52.381 8.66 0.00 36.40 4.26
188 189 0.745845 CCAAATCCTGCAGCTACGCT 60.746 55.000 8.66 0.00 40.77 5.07
189 190 1.026718 ACCAAATCCTGCAGCTACGC 61.027 55.000 8.66 0.00 0.00 4.42
190 191 0.729116 CACCAAATCCTGCAGCTACG 59.271 55.000 8.66 0.00 0.00 3.51
191 192 2.113860 TCACCAAATCCTGCAGCTAC 57.886 50.000 8.66 0.00 0.00 3.58
192 193 2.646930 CATCACCAAATCCTGCAGCTA 58.353 47.619 8.66 0.00 0.00 3.32
193 194 1.471119 CATCACCAAATCCTGCAGCT 58.529 50.000 8.66 0.00 0.00 4.24
194 195 0.458669 CCATCACCAAATCCTGCAGC 59.541 55.000 8.66 0.00 0.00 5.25
195 196 0.458669 GCCATCACCAAATCCTGCAG 59.541 55.000 6.78 6.78 0.00 4.41
196 197 1.314534 CGCCATCACCAAATCCTGCA 61.315 55.000 0.00 0.00 0.00 4.41
197 198 1.031571 TCGCCATCACCAAATCCTGC 61.032 55.000 0.00 0.00 0.00 4.85
198 199 1.683943 ATCGCCATCACCAAATCCTG 58.316 50.000 0.00 0.00 0.00 3.86
199 200 2.026641 CAATCGCCATCACCAAATCCT 58.973 47.619 0.00 0.00 0.00 3.24
215 216 3.379372 TGCCTAAATTGCTGCTCTCAATC 59.621 43.478 0.00 0.00 33.41 2.67
220 221 2.026449 AGTCTGCCTAAATTGCTGCTCT 60.026 45.455 0.00 0.00 0.00 4.09
290 295 7.385267 AGCAAAACCAATTATTTCATGCACTA 58.615 30.769 0.00 0.00 33.89 2.74
362 385 8.028938 ACACAATTTCCTATTGCAAACTATGTC 58.971 33.333 1.71 0.00 32.55 3.06
367 390 9.606631 TTTTAACACAATTTCCTATTGCAAACT 57.393 25.926 1.71 0.00 32.55 2.66
391 414 7.396540 AATTGCAGGATCTATCTTCGTTTTT 57.603 32.000 0.00 0.00 0.00 1.94
469 492 4.764050 TCACCCATCGAAAAGCCTAATA 57.236 40.909 0.00 0.00 0.00 0.98
475 498 5.102313 CCTAAAAATCACCCATCGAAAAGC 58.898 41.667 0.00 0.00 0.00 3.51
476 499 5.394115 CCCCTAAAAATCACCCATCGAAAAG 60.394 44.000 0.00 0.00 0.00 2.27
481 504 3.012934 ACCCCTAAAAATCACCCATCG 57.987 47.619 0.00 0.00 0.00 3.84
509 532 9.443323 TTCACCACGAATTTTCATCTAATCTAA 57.557 29.630 0.00 0.00 0.00 2.10
519 542 1.611491 GGGCTTCACCACGAATTTTCA 59.389 47.619 0.00 0.00 42.05 2.69
521 544 1.698506 TGGGCTTCACCACGAATTTT 58.301 45.000 0.00 0.00 42.05 1.82
527 550 2.594303 TGCTTGGGCTTCACCACG 60.594 61.111 0.00 0.00 41.03 4.94
528 551 2.924105 GCTGCTTGGGCTTCACCAC 61.924 63.158 0.00 0.00 41.03 4.16
531 554 3.769201 AAGCTGCTTGGGCTTCAC 58.231 55.556 15.16 0.00 45.45 3.18
547 570 5.448632 GGCTCTGTTCTCGAAACAAAAAGAA 60.449 40.000 12.17 0.00 0.00 2.52
549 572 4.282873 GGCTCTGTTCTCGAAACAAAAAG 58.717 43.478 12.17 10.87 0.00 2.27
551 574 2.616842 GGGCTCTGTTCTCGAAACAAAA 59.383 45.455 12.17 5.45 0.00 2.44
552 575 2.218603 GGGCTCTGTTCTCGAAACAAA 58.781 47.619 12.17 2.01 0.00 2.83
553 576 1.542547 GGGGCTCTGTTCTCGAAACAA 60.543 52.381 12.17 5.53 0.00 2.83
573 596 1.202348 GATGTTCGGAGGGCTTTTTGG 59.798 52.381 0.00 0.00 0.00 3.28
574 597 1.202348 GGATGTTCGGAGGGCTTTTTG 59.798 52.381 0.00 0.00 0.00 2.44
577 600 1.208165 AGGGATGTTCGGAGGGCTTT 61.208 55.000 0.00 0.00 0.00 3.51
579 602 2.041265 AGGGATGTTCGGAGGGCT 59.959 61.111 0.00 0.00 0.00 5.19
614 642 4.764172 AGCTTCTTCTAGCACCATGTTAG 58.236 43.478 0.00 0.00 43.68 2.34
622 650 2.342179 GTGGTGAGCTTCTTCTAGCAC 58.658 52.381 0.00 0.00 43.68 4.40
625 653 1.737363 GCCGTGGTGAGCTTCTTCTAG 60.737 57.143 0.00 0.00 0.00 2.43
636 664 1.310904 GGTTAAAAGTGCCGTGGTGA 58.689 50.000 0.00 0.00 0.00 4.02
642 670 1.577421 CGTGGGGTTAAAAGTGCCG 59.423 57.895 0.00 0.00 0.00 5.69
643 671 1.529152 CCCGTGGGGTTAAAAGTGCC 61.529 60.000 0.00 0.00 38.25 5.01
796 826 3.023735 AGGAGGGGTGGGGAATGC 61.024 66.667 0.00 0.00 0.00 3.56
904 937 2.326428 GGAGGGTAGGGATCGAAATCA 58.674 52.381 0.00 0.00 33.21 2.57
918 951 2.706071 GAGAGGGGATGGGAGGGT 59.294 66.667 0.00 0.00 0.00 4.34
926 961 3.675563 GCGCGATCGAGAGGGGAT 61.676 66.667 23.47 0.00 38.10 3.85
948 983 1.678728 GCAAATCAGGACACGGATCCA 60.679 52.381 13.41 0.00 41.73 3.41
950 985 1.936547 GAGCAAATCAGGACACGGATC 59.063 52.381 0.00 0.00 30.92 3.36
951 986 1.740380 CGAGCAAATCAGGACACGGAT 60.740 52.381 0.00 0.00 32.70 4.18
952 987 0.389817 CGAGCAAATCAGGACACGGA 60.390 55.000 0.00 0.00 0.00 4.69
955 990 1.014044 TCGCGAGCAAATCAGGACAC 61.014 55.000 3.71 0.00 0.00 3.67
956 991 0.108186 ATCGCGAGCAAATCAGGACA 60.108 50.000 16.66 0.00 0.00 4.02
957 992 0.302890 CATCGCGAGCAAATCAGGAC 59.697 55.000 16.66 0.00 0.00 3.85
958 993 0.811219 CCATCGCGAGCAAATCAGGA 60.811 55.000 16.66 0.00 0.00 3.86
959 994 0.811219 TCCATCGCGAGCAAATCAGG 60.811 55.000 16.66 6.16 0.00 3.86
1240 1290 2.202623 CGAGGCCGAGGTTCGAAG 60.203 66.667 5.45 0.00 43.74 3.79
1505 1565 9.801714 CAAAACAAGAGAATTATTGTCATTTGC 57.198 29.630 4.93 0.00 38.66 3.68
1533 1593 2.100584 AGAAGCGAGGTGAGATGATGAC 59.899 50.000 0.00 0.00 0.00 3.06
1536 1596 3.030291 AGAAGAAGCGAGGTGAGATGAT 58.970 45.455 0.00 0.00 0.00 2.45
1537 1597 2.425312 GAGAAGAAGCGAGGTGAGATGA 59.575 50.000 0.00 0.00 0.00 2.92
1632 1693 7.976175 ACGTATCAGCGAATCAATATCATGTAT 59.024 33.333 0.00 0.00 35.59 2.29
1639 1711 7.658179 ATGAAACGTATCAGCGAATCAATAT 57.342 32.000 0.00 0.00 35.27 1.28
1649 1721 4.035091 TGCATTGGTATGAAACGTATCAGC 59.965 41.667 0.00 0.00 33.37 4.26
1666 1738 5.456173 GGAAACTGCATTTTGTTTTGCATTG 59.544 36.000 6.78 0.00 46.87 2.82
1694 1766 8.983702 TTGTGGTTATGTTTAAACTAGGACTT 57.016 30.769 18.72 0.00 0.00 3.01
1723 1795 4.875561 CCTAAGTAGGCAGGATCTAACC 57.124 50.000 0.00 0.00 36.53 2.85
1747 1819 4.755266 AAGGATCTAACGCAGGTTATGT 57.245 40.909 0.00 0.00 37.94 2.29
1762 1834 1.280421 AGGGACACAGCTCAAAGGATC 59.720 52.381 0.00 0.00 0.00 3.36
1778 1850 9.442062 TGACAACTATATACCTGATTAAAGGGA 57.558 33.333 0.00 0.00 42.11 4.20
1903 1975 7.862372 TCATGAATGCAACTAAGTTTCTTTCAC 59.138 33.333 0.00 0.00 0.00 3.18
1914 1986 4.081406 ACAGCCTTCATGAATGCAACTAA 58.919 39.130 29.62 0.00 34.93 2.24
1988 2060 8.809066 TGTACCAACTTAAGTATTAGAGAGCAA 58.191 33.333 8.92 0.00 0.00 3.91
2389 2463 8.879759 TGTTTAGCTTCAAAATCGAAGTATAGG 58.120 33.333 0.00 0.00 43.61 2.57
2666 2740 4.153673 AGGGCAGAAGATTCATGAAGAG 57.846 45.455 14.54 1.40 0.00 2.85
2668 2742 5.656213 AAAAGGGCAGAAGATTCATGAAG 57.344 39.130 14.54 0.00 0.00 3.02
2692 2766 7.962918 ACAGATACGTATTTTTCATTCACTTGC 59.037 33.333 9.92 0.00 0.00 4.01
2702 2776 7.684670 TGATTCAGCACAGATACGTATTTTTC 58.315 34.615 9.92 0.00 0.00 2.29
2775 2851 6.751425 TGCTGACAGTTTTGTGAAATTTACTG 59.249 34.615 12.76 12.76 37.76 2.74
2799 2875 8.649841 AGTTATGCGATGAATTTGTTCAAAATG 58.350 29.630 2.11 0.00 34.24 2.32
2879 2956 8.166726 AGAGTCAACCCTTAATTCAAGAGATTT 58.833 33.333 0.00 0.00 36.22 2.17
2913 2990 5.016831 TCTAGAGATTCTAGTGGTTGCACA 58.983 41.667 11.67 0.00 45.11 4.57
3099 3178 2.228822 AGTTGCAGATTTAACAAGCCCG 59.771 45.455 0.00 0.00 0.00 6.13
3106 3185 8.940952 AGAGTATTTCAGAGTTGCAGATTTAAC 58.059 33.333 0.00 0.00 0.00 2.01
3261 3601 1.780919 ACCCTTCCAGGTGCTTTAGTT 59.219 47.619 0.00 0.00 39.24 2.24
3262 3602 1.446016 ACCCTTCCAGGTGCTTTAGT 58.554 50.000 0.00 0.00 39.24 2.24
3270 3610 1.073923 CTGTTAAGCACCCTTCCAGGT 59.926 52.381 0.00 0.00 42.40 4.00
3271 3611 1.073923 ACTGTTAAGCACCCTTCCAGG 59.926 52.381 0.00 0.00 35.81 4.45
3272 3612 2.554032 CAACTGTTAAGCACCCTTCCAG 59.446 50.000 0.00 0.00 36.75 3.86
3273 3613 2.582052 CAACTGTTAAGCACCCTTCCA 58.418 47.619 0.00 0.00 32.47 3.53
3274 3614 1.886542 CCAACTGTTAAGCACCCTTCC 59.113 52.381 0.00 0.00 32.47 3.46
3275 3615 2.583143 ACCAACTGTTAAGCACCCTTC 58.417 47.619 0.00 0.00 32.47 3.46
3276 3616 2.693074 CAACCAACTGTTAAGCACCCTT 59.307 45.455 0.00 0.00 34.69 3.95
3277 3617 2.306847 CAACCAACTGTTAAGCACCCT 58.693 47.619 0.00 0.00 34.69 4.34
3278 3618 2.028876 ACAACCAACTGTTAAGCACCC 58.971 47.619 0.00 0.00 34.69 4.61
3279 3619 2.685897 TCACAACCAACTGTTAAGCACC 59.314 45.455 0.00 0.00 34.69 5.01
3280 3620 4.290155 CATCACAACCAACTGTTAAGCAC 58.710 43.478 0.00 0.00 34.69 4.40
3281 3621 3.317711 CCATCACAACCAACTGTTAAGCA 59.682 43.478 0.00 0.00 34.69 3.91
3282 3622 3.857010 GCCATCACAACCAACTGTTAAGC 60.857 47.826 0.00 0.00 34.69 3.09
3283 3623 3.569701 AGCCATCACAACCAACTGTTAAG 59.430 43.478 0.00 0.00 34.69 1.85
3284 3624 3.317711 CAGCCATCACAACCAACTGTTAA 59.682 43.478 0.00 0.00 34.69 2.01
3285 3625 2.884012 CAGCCATCACAACCAACTGTTA 59.116 45.455 0.00 0.00 34.69 2.41
3478 3844 2.712539 CGCAAGAAACACCGCACA 59.287 55.556 0.00 0.00 43.02 4.57


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

AutoCloner maintained by Alex Coulton.