Multiple sequence alignment - TraesCS2D01G108400

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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 TraesCS2D01G108400 chr2D 100.000 2445 0 0 1 2445 60135236 60132792 0.000000e+00 4516.0
1 TraesCS2D01G108400 chr2D 97.655 2132 44 4 317 2445 49235686 49233558 0.000000e+00 3655.0
2 TraesCS2D01G108400 chr2D 94.196 224 7 5 1 221 563471810 563471590 1.080000e-88 337.0
3 TraesCS2D01G108400 chr2D 95.082 122 6 0 197 318 609889467 609889346 2.480000e-45 193.0
4 TraesCS2D01G108400 chr6D 97.700 2130 43 4 319 2445 15752860 15754986 0.000000e+00 3657.0
5 TraesCS2D01G108400 chr6D 93.921 329 7 6 1 318 323092487 323092161 3.660000e-133 484.0
6 TraesCS2D01G108400 chr7D 97.513 2131 48 3 318 2445 222762111 222759983 0.000000e+00 3637.0
7 TraesCS2D01G108400 chr7D 97.328 2133 53 2 316 2445 549829745 549831876 0.000000e+00 3620.0
8 TraesCS2D01G108400 chr7D 97.198 2141 50 8 311 2445 64670349 64672485 0.000000e+00 3613.0
9 TraesCS2D01G108400 chr5D 97.419 2131 48 4 319 2445 421576774 421578901 0.000000e+00 3624.0
10 TraesCS2D01G108400 chr1D 97.418 2130 50 3 319 2445 433932745 433934872 0.000000e+00 3624.0
11 TraesCS2D01G108400 chr3D 97.371 2130 52 2 319 2445 588147313 588145185 0.000000e+00 3620.0
12 TraesCS2D01G108400 chr3D 97.371 2130 51 3 319 2445 511305768 511307895 0.000000e+00 3618.0
13 TraesCS2D01G108400 chr3D 96.250 320 9 3 1 318 17415606 17415924 2.790000e-144 521.0
14 TraesCS2D01G108400 chrUn 93.249 237 14 2 83 318 329674887 329675122 5.000000e-92 348.0
15 TraesCS2D01G108400 chrUn 90.291 103 4 3 12 109 320317087 320317188 1.970000e-26 130.0
16 TraesCS2D01G108400 chr1A 97.037 135 3 1 93 226 9514828 9514694 2.450000e-55 226.0
17 TraesCS2D01G108400 chr1A 95.556 135 5 1 93 226 9499622 9499488 5.300000e-52 215.0
18 TraesCS2D01G108400 chr7B 92.593 108 3 4 12 116 674549696 674549591 1.510000e-32 150.0
19 TraesCS2D01G108400 chr2A 94.000 100 3 2 12 109 181542481 181542383 5.450000e-32 148.0
20 TraesCS2D01G108400 chr3B 93.137 102 2 4 12 109 804983130 804983230 7.050000e-31 145.0
21 TraesCS2D01G108400 chr3B 90.291 103 4 4 12 109 826509915 826510016 1.970000e-26 130.0
22 TraesCS2D01G108400 chr4D 94.624 93 2 3 12 102 468197472 468197381 9.110000e-30 141.0
23 TraesCS2D01G108400 chr6B 95.122 41 1 1 267 306 711461037 711460997 2.030000e-06 63.9


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 TraesCS2D01G108400 chr2D 60132792 60135236 2444 True 4516 4516 100.000 1 2445 1 chr2D.!!$R2 2444
1 TraesCS2D01G108400 chr2D 49233558 49235686 2128 True 3655 3655 97.655 317 2445 1 chr2D.!!$R1 2128
2 TraesCS2D01G108400 chr6D 15752860 15754986 2126 False 3657 3657 97.700 319 2445 1 chr6D.!!$F1 2126
3 TraesCS2D01G108400 chr7D 222759983 222762111 2128 True 3637 3637 97.513 318 2445 1 chr7D.!!$R1 2127
4 TraesCS2D01G108400 chr7D 549829745 549831876 2131 False 3620 3620 97.328 316 2445 1 chr7D.!!$F2 2129
5 TraesCS2D01G108400 chr7D 64670349 64672485 2136 False 3613 3613 97.198 311 2445 1 chr7D.!!$F1 2134
6 TraesCS2D01G108400 chr5D 421576774 421578901 2127 False 3624 3624 97.419 319 2445 1 chr5D.!!$F1 2126
7 TraesCS2D01G108400 chr1D 433932745 433934872 2127 False 3624 3624 97.418 319 2445 1 chr1D.!!$F1 2126
8 TraesCS2D01G108400 chr3D 588145185 588147313 2128 True 3620 3620 97.371 319 2445 1 chr3D.!!$R1 2126
9 TraesCS2D01G108400 chr3D 511305768 511307895 2127 False 3618 3618 97.371 319 2445 1 chr3D.!!$F2 2126

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
106 107 0.25051 TGTGTGTGTGTGTGTGGTGT 60.251 50.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 1934 0.545646 GATCTTCAGCAGCTTCCCCT 59.454 55.0 0.0 0.0 0.0 4.79 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
30 31 4.822685 TTTTGATCATGAATTGTGGGGG 57.177 40.909 0.00 0.00 0.00 5.40
47 48 1.069668 GGGGGCATCATTCATCAAAGC 59.930 52.381 0.00 0.00 0.00 3.51
48 49 1.069668 GGGGCATCATTCATCAAAGCC 59.930 52.381 0.00 0.00 39.86 4.35
49 50 1.758280 GGGCATCATTCATCAAAGCCA 59.242 47.619 0.00 0.00 42.26 4.75
50 51 2.367567 GGGCATCATTCATCAAAGCCAT 59.632 45.455 0.00 0.00 42.26 4.40
51 52 3.390135 GGCATCATTCATCAAAGCCATG 58.610 45.455 0.00 0.00 40.29 3.66
52 53 3.069016 GGCATCATTCATCAAAGCCATGA 59.931 43.478 0.00 0.00 40.29 3.07
53 54 4.049186 GCATCATTCATCAAAGCCATGAC 58.951 43.478 0.00 0.00 29.70 3.06
54 55 4.440940 GCATCATTCATCAAAGCCATGACA 60.441 41.667 0.00 0.00 29.70 3.58
55 56 5.739070 GCATCATTCATCAAAGCCATGACAT 60.739 40.000 0.00 0.00 29.70 3.06
56 57 6.516028 GCATCATTCATCAAAGCCATGACATA 60.516 38.462 0.00 0.00 29.70 2.29
57 58 7.430441 CATCATTCATCAAAGCCATGACATAA 58.570 34.615 0.00 0.00 29.70 1.90
58 59 7.407393 TCATTCATCAAAGCCATGACATAAA 57.593 32.000 0.00 0.00 29.70 1.40
59 60 7.838884 TCATTCATCAAAGCCATGACATAAAA 58.161 30.769 0.00 0.00 29.70 1.52
60 61 8.312564 TCATTCATCAAAGCCATGACATAAAAA 58.687 29.630 0.00 0.00 29.70 1.94
88 89 4.675190 GTCATCTTGACATCCTGTGTTG 57.325 45.455 2.85 0.00 46.22 3.33
89 90 4.067896 GTCATCTTGACATCCTGTGTTGT 58.932 43.478 2.85 0.00 46.22 3.32
90 91 4.067192 TCATCTTGACATCCTGTGTTGTG 58.933 43.478 0.00 0.00 42.36 3.33
91 92 3.558931 TCTTGACATCCTGTGTTGTGT 57.441 42.857 0.00 0.00 42.36 3.72
92 93 3.205338 TCTTGACATCCTGTGTTGTGTG 58.795 45.455 0.00 0.00 42.36 3.82
93 94 2.708216 TGACATCCTGTGTTGTGTGT 57.292 45.000 0.00 0.00 42.36 3.72
94 95 2.287769 TGACATCCTGTGTTGTGTGTG 58.712 47.619 0.00 0.00 42.36 3.82
95 96 2.288666 GACATCCTGTGTTGTGTGTGT 58.711 47.619 0.00 0.00 42.36 3.72
96 97 2.016318 ACATCCTGTGTTGTGTGTGTG 58.984 47.619 0.00 0.00 38.01 3.82
97 98 2.016318 CATCCTGTGTTGTGTGTGTGT 58.984 47.619 0.00 0.00 0.00 3.72
98 99 1.447945 TCCTGTGTTGTGTGTGTGTG 58.552 50.000 0.00 0.00 0.00 3.82
99 100 1.164411 CCTGTGTTGTGTGTGTGTGT 58.836 50.000 0.00 0.00 0.00 3.72
100 101 1.135717 CCTGTGTTGTGTGTGTGTGTG 60.136 52.381 0.00 0.00 0.00 3.82
101 102 1.535028 CTGTGTTGTGTGTGTGTGTGT 59.465 47.619 0.00 0.00 0.00 3.72
102 103 1.265365 TGTGTTGTGTGTGTGTGTGTG 59.735 47.619 0.00 0.00 0.00 3.82
103 104 0.877743 TGTTGTGTGTGTGTGTGTGG 59.122 50.000 0.00 0.00 0.00 4.17
104 105 0.878416 GTTGTGTGTGTGTGTGTGGT 59.122 50.000 0.00 0.00 0.00 4.16
105 106 0.877743 TTGTGTGTGTGTGTGTGGTG 59.122 50.000 0.00 0.00 0.00 4.17
106 107 0.250510 TGTGTGTGTGTGTGTGGTGT 60.251 50.000 0.00 0.00 0.00 4.16
107 108 1.002087 TGTGTGTGTGTGTGTGGTGTA 59.998 47.619 0.00 0.00 0.00 2.90
108 109 1.663643 GTGTGTGTGTGTGTGGTGTAG 59.336 52.381 0.00 0.00 0.00 2.74
109 110 1.276705 TGTGTGTGTGTGTGGTGTAGT 59.723 47.619 0.00 0.00 0.00 2.73
110 111 1.663643 GTGTGTGTGTGTGGTGTAGTG 59.336 52.381 0.00 0.00 0.00 2.74
111 112 1.276705 TGTGTGTGTGTGGTGTAGTGT 59.723 47.619 0.00 0.00 0.00 3.55
112 113 1.663643 GTGTGTGTGTGGTGTAGTGTG 59.336 52.381 0.00 0.00 0.00 3.82
113 114 1.550976 TGTGTGTGTGGTGTAGTGTGA 59.449 47.619 0.00 0.00 0.00 3.58
114 115 2.201732 GTGTGTGTGGTGTAGTGTGAG 58.798 52.381 0.00 0.00 0.00 3.51
115 116 1.828595 TGTGTGTGGTGTAGTGTGAGT 59.171 47.619 0.00 0.00 0.00 3.41
116 117 2.159156 TGTGTGTGGTGTAGTGTGAGTC 60.159 50.000 0.00 0.00 0.00 3.36
117 118 2.100916 GTGTGTGGTGTAGTGTGAGTCT 59.899 50.000 0.00 0.00 0.00 3.24
118 119 2.764010 TGTGTGGTGTAGTGTGAGTCTT 59.236 45.455 0.00 0.00 0.00 3.01
119 120 3.196901 TGTGTGGTGTAGTGTGAGTCTTT 59.803 43.478 0.00 0.00 0.00 2.52
120 121 3.802685 GTGTGGTGTAGTGTGAGTCTTTC 59.197 47.826 0.00 0.00 0.00 2.62
121 122 3.181469 TGTGGTGTAGTGTGAGTCTTTCC 60.181 47.826 0.00 0.00 0.00 3.13
122 123 3.069729 GTGGTGTAGTGTGAGTCTTTCCT 59.930 47.826 0.00 0.00 0.00 3.36
123 124 3.321111 TGGTGTAGTGTGAGTCTTTCCTC 59.679 47.826 0.00 0.00 0.00 3.71
124 125 3.306156 GGTGTAGTGTGAGTCTTTCCTCC 60.306 52.174 0.00 0.00 0.00 4.30
125 126 3.574826 GTGTAGTGTGAGTCTTTCCTCCT 59.425 47.826 0.00 0.00 0.00 3.69
126 127 4.039366 GTGTAGTGTGAGTCTTTCCTCCTT 59.961 45.833 0.00 0.00 0.00 3.36
127 128 5.243283 GTGTAGTGTGAGTCTTTCCTCCTTA 59.757 44.000 0.00 0.00 0.00 2.69
128 129 6.017192 TGTAGTGTGAGTCTTTCCTCCTTAT 58.983 40.000 0.00 0.00 0.00 1.73
129 130 5.669164 AGTGTGAGTCTTTCCTCCTTATC 57.331 43.478 0.00 0.00 0.00 1.75
130 131 5.337788 AGTGTGAGTCTTTCCTCCTTATCT 58.662 41.667 0.00 0.00 0.00 1.98
131 132 5.186797 AGTGTGAGTCTTTCCTCCTTATCTG 59.813 44.000 0.00 0.00 0.00 2.90
132 133 4.467795 TGTGAGTCTTTCCTCCTTATCTGG 59.532 45.833 0.00 0.00 0.00 3.86
133 134 4.468153 GTGAGTCTTTCCTCCTTATCTGGT 59.532 45.833 0.00 0.00 0.00 4.00
134 135 5.046231 GTGAGTCTTTCCTCCTTATCTGGTT 60.046 44.000 0.00 0.00 0.00 3.67
135 136 5.187967 TGAGTCTTTCCTCCTTATCTGGTTC 59.812 44.000 0.00 0.00 0.00 3.62
136 137 4.471747 AGTCTTTCCTCCTTATCTGGTTCC 59.528 45.833 0.00 0.00 0.00 3.62
137 138 3.780850 TCTTTCCTCCTTATCTGGTTCCC 59.219 47.826 0.00 0.00 0.00 3.97
138 139 3.508952 TTCCTCCTTATCTGGTTCCCT 57.491 47.619 0.00 0.00 0.00 4.20
139 140 3.047695 TCCTCCTTATCTGGTTCCCTC 57.952 52.381 0.00 0.00 0.00 4.30
140 141 2.050918 CCTCCTTATCTGGTTCCCTCC 58.949 57.143 0.00 0.00 0.00 4.30
141 142 2.360854 CCTCCTTATCTGGTTCCCTCCT 60.361 54.545 0.00 0.00 0.00 3.69
142 143 3.388913 CTCCTTATCTGGTTCCCTCCTT 58.611 50.000 0.00 0.00 0.00 3.36
143 144 3.783082 CTCCTTATCTGGTTCCCTCCTTT 59.217 47.826 0.00 0.00 0.00 3.11
144 145 3.780850 TCCTTATCTGGTTCCCTCCTTTC 59.219 47.826 0.00 0.00 0.00 2.62
145 146 3.117851 CCTTATCTGGTTCCCTCCTTTCC 60.118 52.174 0.00 0.00 0.00 3.13
146 147 2.367947 ATCTGGTTCCCTCCTTTCCT 57.632 50.000 0.00 0.00 0.00 3.36
147 148 1.362224 TCTGGTTCCCTCCTTTCCTG 58.638 55.000 0.00 0.00 0.00 3.86
148 149 1.068121 CTGGTTCCCTCCTTTCCTGT 58.932 55.000 0.00 0.00 0.00 4.00
149 150 1.003696 CTGGTTCCCTCCTTTCCTGTC 59.996 57.143 0.00 0.00 0.00 3.51
150 151 1.363246 GGTTCCCTCCTTTCCTGTCT 58.637 55.000 0.00 0.00 0.00 3.41
151 152 1.279558 GGTTCCCTCCTTTCCTGTCTC 59.720 57.143 0.00 0.00 0.00 3.36
152 153 2.261729 GTTCCCTCCTTTCCTGTCTCT 58.738 52.381 0.00 0.00 0.00 3.10
153 154 2.235155 GTTCCCTCCTTTCCTGTCTCTC 59.765 54.545 0.00 0.00 0.00 3.20
154 155 1.719378 TCCCTCCTTTCCTGTCTCTCT 59.281 52.381 0.00 0.00 0.00 3.10
155 156 1.830477 CCCTCCTTTCCTGTCTCTCTG 59.170 57.143 0.00 0.00 0.00 3.35
156 157 2.558575 CCCTCCTTTCCTGTCTCTCTGA 60.559 54.545 0.00 0.00 0.00 3.27
157 158 3.373830 CCTCCTTTCCTGTCTCTCTGAT 58.626 50.000 0.00 0.00 0.00 2.90
158 159 3.774216 CCTCCTTTCCTGTCTCTCTGATT 59.226 47.826 0.00 0.00 0.00 2.57
159 160 4.382901 CCTCCTTTCCTGTCTCTCTGATTG 60.383 50.000 0.00 0.00 0.00 2.67
160 161 4.420206 TCCTTTCCTGTCTCTCTGATTGA 58.580 43.478 0.00 0.00 0.00 2.57
161 162 4.840680 TCCTTTCCTGTCTCTCTGATTGAA 59.159 41.667 0.00 0.00 0.00 2.69
162 163 5.486775 TCCTTTCCTGTCTCTCTGATTGAAT 59.513 40.000 0.00 0.00 0.00 2.57
163 164 6.013032 TCCTTTCCTGTCTCTCTGATTGAATT 60.013 38.462 0.00 0.00 0.00 2.17
164 165 6.315891 CCTTTCCTGTCTCTCTGATTGAATTC 59.684 42.308 0.00 0.00 0.00 2.17
165 166 6.617782 TTCCTGTCTCTCTGATTGAATTCT 57.382 37.500 7.05 0.00 0.00 2.40
166 167 5.975282 TCCTGTCTCTCTGATTGAATTCTG 58.025 41.667 7.05 0.00 0.00 3.02
167 168 5.718607 TCCTGTCTCTCTGATTGAATTCTGA 59.281 40.000 7.05 0.00 0.00 3.27
168 169 6.044046 CCTGTCTCTCTGATTGAATTCTGAG 58.956 44.000 7.05 6.79 40.88 3.35
169 170 5.975282 TGTCTCTCTGATTGAATTCTGAGG 58.025 41.667 7.05 2.58 40.29 3.86
170 171 4.810491 GTCTCTCTGATTGAATTCTGAGGC 59.190 45.833 7.05 1.65 40.29 4.70
171 172 4.128643 CTCTCTGATTGAATTCTGAGGCC 58.871 47.826 7.05 0.00 40.29 5.19
172 173 3.118112 TCTCTGATTGAATTCTGAGGCCC 60.118 47.826 7.05 0.00 40.29 5.80
173 174 2.848694 TCTGATTGAATTCTGAGGCCCT 59.151 45.455 7.05 0.00 0.00 5.19
174 175 3.118112 TCTGATTGAATTCTGAGGCCCTC 60.118 47.826 2.98 2.98 0.00 4.30
175 176 2.577563 TGATTGAATTCTGAGGCCCTCA 59.422 45.455 13.96 13.96 38.25 3.86
176 177 3.203710 TGATTGAATTCTGAGGCCCTCAT 59.796 43.478 15.20 0.00 39.92 2.90
177 178 3.287867 TTGAATTCTGAGGCCCTCATC 57.712 47.619 15.20 9.53 39.92 2.92
178 179 1.492176 TGAATTCTGAGGCCCTCATCC 59.508 52.381 15.20 2.75 39.92 3.51
179 180 1.773653 GAATTCTGAGGCCCTCATCCT 59.226 52.381 15.20 0.00 39.92 3.24
183 184 2.040464 GAGGCCCTCATCCTCCCA 60.040 66.667 5.69 0.00 43.32 4.37
184 185 1.694169 GAGGCCCTCATCCTCCCAA 60.694 63.158 5.69 0.00 43.32 4.12
185 186 1.695597 AGGCCCTCATCCTCCCAAG 60.696 63.158 0.00 0.00 0.00 3.61
186 187 2.003548 GGCCCTCATCCTCCCAAGT 61.004 63.158 0.00 0.00 0.00 3.16
187 188 1.225704 GCCCTCATCCTCCCAAGTG 59.774 63.158 0.00 0.00 0.00 3.16
188 189 1.225704 CCCTCATCCTCCCAAGTGC 59.774 63.158 0.00 0.00 0.00 4.40
189 190 1.225704 CCTCATCCTCCCAAGTGCC 59.774 63.158 0.00 0.00 0.00 5.01
190 191 1.565390 CCTCATCCTCCCAAGTGCCA 61.565 60.000 0.00 0.00 0.00 4.92
191 192 0.329261 CTCATCCTCCCAAGTGCCAA 59.671 55.000 0.00 0.00 0.00 4.52
192 193 0.776810 TCATCCTCCCAAGTGCCAAA 59.223 50.000 0.00 0.00 0.00 3.28
193 194 1.146774 TCATCCTCCCAAGTGCCAAAA 59.853 47.619 0.00 0.00 0.00 2.44
194 195 1.547372 CATCCTCCCAAGTGCCAAAAG 59.453 52.381 0.00 0.00 0.00 2.27
195 196 0.555769 TCCTCCCAAGTGCCAAAAGT 59.444 50.000 0.00 0.00 0.00 2.66
196 197 1.777878 TCCTCCCAAGTGCCAAAAGTA 59.222 47.619 0.00 0.00 0.00 2.24
197 198 2.378547 TCCTCCCAAGTGCCAAAAGTAT 59.621 45.455 0.00 0.00 0.00 2.12
198 199 2.493278 CCTCCCAAGTGCCAAAAGTATG 59.507 50.000 0.00 0.00 0.00 2.39
199 200 3.420893 CTCCCAAGTGCCAAAAGTATGA 58.579 45.455 0.00 0.00 0.00 2.15
200 201 3.153919 TCCCAAGTGCCAAAAGTATGAC 58.846 45.455 0.00 0.00 0.00 3.06
201 202 3.157087 CCCAAGTGCCAAAAGTATGACT 58.843 45.455 0.00 0.00 0.00 3.41
202 203 4.042311 TCCCAAGTGCCAAAAGTATGACTA 59.958 41.667 0.00 0.00 0.00 2.59
203 204 4.156008 CCCAAGTGCCAAAAGTATGACTAC 59.844 45.833 0.00 0.00 0.00 2.73
204 205 4.142902 CCAAGTGCCAAAAGTATGACTACG 60.143 45.833 0.00 0.00 32.82 3.51
205 206 3.000727 AGTGCCAAAAGTATGACTACGC 58.999 45.455 0.00 0.00 32.82 4.42
206 207 2.095372 GTGCCAAAAGTATGACTACGCC 59.905 50.000 0.00 0.00 32.82 5.68
207 208 2.289756 TGCCAAAAGTATGACTACGCCA 60.290 45.455 0.00 0.00 32.82 5.69
208 209 2.943033 GCCAAAAGTATGACTACGCCAT 59.057 45.455 0.00 0.00 32.82 4.40
209 210 4.124238 GCCAAAAGTATGACTACGCCATA 58.876 43.478 0.00 0.00 32.82 2.74
210 211 4.211374 GCCAAAAGTATGACTACGCCATAG 59.789 45.833 0.00 0.00 36.89 2.23
211 212 4.211374 CCAAAAGTATGACTACGCCATAGC 59.789 45.833 0.00 0.00 33.73 2.97
212 213 4.939052 AAAGTATGACTACGCCATAGCT 57.061 40.909 0.00 0.00 36.60 3.32
213 214 4.939052 AAGTATGACTACGCCATAGCTT 57.061 40.909 0.00 0.00 36.60 3.74
214 215 4.506886 AGTATGACTACGCCATAGCTTC 57.493 45.455 0.00 0.00 36.60 3.86
215 216 4.145807 AGTATGACTACGCCATAGCTTCT 58.854 43.478 0.00 0.00 36.60 2.85
216 217 2.871182 TGACTACGCCATAGCTTCTG 57.129 50.000 0.00 0.00 36.60 3.02
217 218 2.100197 TGACTACGCCATAGCTTCTGT 58.900 47.619 0.00 0.00 36.60 3.41
218 219 2.496070 TGACTACGCCATAGCTTCTGTT 59.504 45.455 0.00 0.00 36.60 3.16
219 220 2.860735 GACTACGCCATAGCTTCTGTTG 59.139 50.000 0.00 0.00 36.60 3.33
220 221 2.233922 ACTACGCCATAGCTTCTGTTGT 59.766 45.455 0.00 0.00 36.60 3.32
221 222 2.185004 ACGCCATAGCTTCTGTTGTT 57.815 45.000 0.00 0.00 36.60 2.83
222 223 3.328382 ACGCCATAGCTTCTGTTGTTA 57.672 42.857 0.00 0.00 36.60 2.41
223 224 3.873910 ACGCCATAGCTTCTGTTGTTAT 58.126 40.909 0.00 0.00 36.60 1.89
224 225 4.261801 ACGCCATAGCTTCTGTTGTTATT 58.738 39.130 0.00 0.00 36.60 1.40
225 226 4.094887 ACGCCATAGCTTCTGTTGTTATTG 59.905 41.667 0.00 0.00 36.60 1.90
226 227 4.094887 CGCCATAGCTTCTGTTGTTATTGT 59.905 41.667 0.00 0.00 36.60 2.71
227 228 5.293324 CGCCATAGCTTCTGTTGTTATTGTA 59.707 40.000 0.00 0.00 36.60 2.41
228 229 6.487103 GCCATAGCTTCTGTTGTTATTGTAC 58.513 40.000 0.00 0.00 35.50 2.90
229 230 6.093495 GCCATAGCTTCTGTTGTTATTGTACA 59.907 38.462 0.00 0.00 35.50 2.90
230 231 7.201732 GCCATAGCTTCTGTTGTTATTGTACAT 60.202 37.037 0.00 0.00 35.50 2.29
231 232 9.325198 CCATAGCTTCTGTTGTTATTGTACATA 57.675 33.333 0.00 0.00 0.00 2.29
235 236 8.227791 AGCTTCTGTTGTTATTGTACATAAACG 58.772 33.333 13.24 0.00 0.00 3.60
236 237 8.225107 GCTTCTGTTGTTATTGTACATAAACGA 58.775 33.333 13.24 10.08 0.00 3.85
237 238 9.525007 CTTCTGTTGTTATTGTACATAAACGAC 57.475 33.333 22.62 22.62 0.00 4.34
238 239 8.590719 TCTGTTGTTATTGTACATAAACGACA 57.409 30.769 26.57 26.57 0.00 4.35
239 240 9.043079 TCTGTTGTTATTGTACATAAACGACAA 57.957 29.630 27.34 20.41 37.47 3.18
240 241 9.653067 CTGTTGTTATTGTACATAAACGACAAA 57.347 29.630 27.34 15.95 36.70 2.83
241 242 9.999009 TGTTGTTATTGTACATAAACGACAAAA 57.001 25.926 26.41 13.46 36.70 2.44
259 260 8.395633 ACGACAAAATTATGAGTAAACCATAGC 58.604 33.333 0.00 0.00 0.00 2.97
260 261 7.582679 CGACAAAATTATGAGTAAACCATAGCG 59.417 37.037 0.00 0.00 0.00 4.26
261 262 8.276252 ACAAAATTATGAGTAAACCATAGCGT 57.724 30.769 0.00 0.00 0.00 5.07
262 263 8.395633 ACAAAATTATGAGTAAACCATAGCGTC 58.604 33.333 0.00 0.00 0.00 5.19
263 264 8.394877 CAAAATTATGAGTAAACCATAGCGTCA 58.605 33.333 0.00 0.00 0.00 4.35
264 265 8.677148 AAATTATGAGTAAACCATAGCGTCAT 57.323 30.769 0.00 0.00 0.00 3.06
265 266 7.891183 ATTATGAGTAAACCATAGCGTCATC 57.109 36.000 0.00 0.00 0.00 2.92
266 267 4.729227 TGAGTAAACCATAGCGTCATCA 57.271 40.909 0.00 0.00 0.00 3.07
267 268 5.079689 TGAGTAAACCATAGCGTCATCAA 57.920 39.130 0.00 0.00 0.00 2.57
268 269 5.670485 TGAGTAAACCATAGCGTCATCAAT 58.330 37.500 0.00 0.00 0.00 2.57
269 270 6.112734 TGAGTAAACCATAGCGTCATCAATT 58.887 36.000 0.00 0.00 0.00 2.32
270 271 6.257849 TGAGTAAACCATAGCGTCATCAATTC 59.742 38.462 0.00 0.00 0.00 2.17
271 272 6.349300 AGTAAACCATAGCGTCATCAATTCT 58.651 36.000 0.00 0.00 0.00 2.40
272 273 5.490139 AAACCATAGCGTCATCAATTCTG 57.510 39.130 0.00 0.00 0.00 3.02
273 274 3.470709 ACCATAGCGTCATCAATTCTGG 58.529 45.455 0.00 0.00 0.00 3.86
274 275 3.134623 ACCATAGCGTCATCAATTCTGGA 59.865 43.478 0.00 0.00 0.00 3.86
275 276 3.744942 CCATAGCGTCATCAATTCTGGAG 59.255 47.826 0.00 0.00 0.00 3.86
276 277 4.375272 CATAGCGTCATCAATTCTGGAGT 58.625 43.478 0.00 0.00 0.00 3.85
277 278 5.509670 CCATAGCGTCATCAATTCTGGAGTA 60.510 44.000 0.00 0.00 0.00 2.59
278 279 3.786635 AGCGTCATCAATTCTGGAGTAC 58.213 45.455 0.00 0.00 0.00 2.73
279 280 3.449018 AGCGTCATCAATTCTGGAGTACT 59.551 43.478 0.00 0.00 0.00 2.73
280 281 3.799420 GCGTCATCAATTCTGGAGTACTC 59.201 47.826 14.87 14.87 0.00 2.59
281 282 4.440802 GCGTCATCAATTCTGGAGTACTCT 60.441 45.833 21.88 0.00 0.00 3.24
282 283 5.655488 CGTCATCAATTCTGGAGTACTCTT 58.345 41.667 21.88 5.70 0.00 2.85
283 284 5.518128 CGTCATCAATTCTGGAGTACTCTTG 59.482 44.000 21.88 16.94 0.00 3.02
284 285 6.402222 GTCATCAATTCTGGAGTACTCTTGT 58.598 40.000 21.88 6.88 0.00 3.16
285 286 6.876257 GTCATCAATTCTGGAGTACTCTTGTT 59.124 38.462 21.88 10.36 0.00 2.83
286 287 6.875726 TCATCAATTCTGGAGTACTCTTGTTG 59.124 38.462 21.88 19.55 0.00 3.33
287 288 6.419484 TCAATTCTGGAGTACTCTTGTTGA 57.581 37.500 21.88 19.09 0.00 3.18
288 289 6.223852 TCAATTCTGGAGTACTCTTGTTGAC 58.776 40.000 21.88 4.60 0.00 3.18
289 290 4.602340 TTCTGGAGTACTCTTGTTGACC 57.398 45.455 21.88 4.49 0.00 4.02
290 291 3.572642 TCTGGAGTACTCTTGTTGACCA 58.427 45.455 21.88 8.95 0.00 4.02
291 292 3.574396 TCTGGAGTACTCTTGTTGACCAG 59.426 47.826 21.88 17.49 43.13 4.00
292 293 3.572642 TGGAGTACTCTTGTTGACCAGA 58.427 45.455 21.88 0.00 0.00 3.86
293 294 4.160329 TGGAGTACTCTTGTTGACCAGAT 58.840 43.478 21.88 0.00 0.00 2.90
294 295 4.593206 TGGAGTACTCTTGTTGACCAGATT 59.407 41.667 21.88 0.00 0.00 2.40
295 296 5.071788 TGGAGTACTCTTGTTGACCAGATTT 59.928 40.000 21.88 0.00 0.00 2.17
296 297 6.269077 TGGAGTACTCTTGTTGACCAGATTTA 59.731 38.462 21.88 0.00 0.00 1.40
297 298 6.590677 GGAGTACTCTTGTTGACCAGATTTAC 59.409 42.308 21.88 0.00 0.00 2.01
298 299 6.465084 AGTACTCTTGTTGACCAGATTTACC 58.535 40.000 0.00 0.00 0.00 2.85
299 300 5.304686 ACTCTTGTTGACCAGATTTACCA 57.695 39.130 0.00 0.00 0.00 3.25
300 301 5.690865 ACTCTTGTTGACCAGATTTACCAA 58.309 37.500 0.00 0.00 0.00 3.67
301 302 5.765182 ACTCTTGTTGACCAGATTTACCAAG 59.235 40.000 0.00 0.00 0.00 3.61
302 303 5.690865 TCTTGTTGACCAGATTTACCAAGT 58.309 37.500 0.00 0.00 32.13 3.16
303 304 6.126409 TCTTGTTGACCAGATTTACCAAGTT 58.874 36.000 0.00 0.00 32.13 2.66
304 305 6.605594 TCTTGTTGACCAGATTTACCAAGTTT 59.394 34.615 0.00 0.00 32.13 2.66
305 306 7.776030 TCTTGTTGACCAGATTTACCAAGTTTA 59.224 33.333 0.00 0.00 32.13 2.01
306 307 7.504924 TGTTGACCAGATTTACCAAGTTTAG 57.495 36.000 0.00 0.00 0.00 1.85
307 308 7.284074 TGTTGACCAGATTTACCAAGTTTAGA 58.716 34.615 0.00 0.00 0.00 2.10
308 309 7.227910 TGTTGACCAGATTTACCAAGTTTAGAC 59.772 37.037 0.00 0.00 0.00 2.59
309 310 7.074653 TGACCAGATTTACCAAGTTTAGACT 57.925 36.000 0.00 0.00 37.87 3.24
310 311 7.514721 TGACCAGATTTACCAAGTTTAGACTT 58.485 34.615 0.00 0.00 46.85 3.01
496 498 2.349755 CCGGTTGGTGGGACGAAT 59.650 61.111 0.00 0.00 0.00 3.34
548 550 1.228429 CATTGGTCCCGGTTGGTGT 60.228 57.895 0.00 0.00 34.77 4.16
634 636 2.246588 TGCCTATATATACCCCTCGCCT 59.753 50.000 0.00 0.00 0.00 5.52
904 906 4.533318 ACCGTGGTGAGCCTCTTA 57.467 55.556 0.00 0.00 35.27 2.10
1014 1017 3.350219 AGTGCGATGGTTTTGGTATCT 57.650 42.857 0.00 0.00 0.00 1.98
1200 1203 8.846211 TGTTGAGAGGTTAAATTTAGTTGAAGG 58.154 33.333 0.00 0.00 0.00 3.46
1311 1315 4.397103 TCACAAGATCAAGATGGATGCAAC 59.603 41.667 0.00 0.00 0.00 4.17
1375 1379 3.557898 CCGAGGCTTGGTATCATTATGCT 60.558 47.826 13.06 0.00 0.00 3.79
1885 1889 2.417515 GGAAGACGGCGAAGAAGAAGAT 60.418 50.000 16.62 0.00 0.00 2.40
1930 1934 1.737236 GAATACGGTGATGCTGCAACA 59.263 47.619 6.36 7.63 0.00 3.33
1989 1993 1.314534 CCCAATGATGCTGCAACGGA 61.315 55.000 6.36 0.00 0.00 4.69
2307 2314 1.144969 CGCAGCAAAGAAGGTCGTAA 58.855 50.000 0.00 0.00 0.00 3.18
2330 2337 2.053244 CCTCTAGGATTGGAGGTGCAT 58.947 52.381 0.00 0.00 42.86 3.96
2404 2411 1.078072 TGAACGCATGCCCGGTATT 60.078 52.632 13.15 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.822685 CCCCCACAATTCATGATCAAAA 57.177 40.909 0.00 0.00 0.00 2.44
27 28 1.069668 GCTTTGATGAATGATGCCCCC 59.930 52.381 0.00 0.00 0.00 5.40
28 29 1.069668 GGCTTTGATGAATGATGCCCC 59.930 52.381 0.00 0.00 33.45 5.80
29 30 1.758280 TGGCTTTGATGAATGATGCCC 59.242 47.619 0.00 0.00 38.23 5.36
30 31 3.069016 TCATGGCTTTGATGAATGATGCC 59.931 43.478 0.00 0.00 39.33 4.40
31 32 4.049186 GTCATGGCTTTGATGAATGATGC 58.951 43.478 0.00 0.00 31.65 3.91
32 33 5.257082 TGTCATGGCTTTGATGAATGATG 57.743 39.130 0.00 0.00 31.65 3.07
33 34 7.591421 TTATGTCATGGCTTTGATGAATGAT 57.409 32.000 0.00 0.00 31.65 2.45
34 35 7.407393 TTTATGTCATGGCTTTGATGAATGA 57.593 32.000 0.00 0.00 31.65 2.57
35 36 8.481974 TTTTTATGTCATGGCTTTGATGAATG 57.518 30.769 0.00 0.00 31.65 2.67
57 58 3.909732 TGTCAAGATGACCCACCTTTTT 58.090 40.909 7.94 0.00 46.40 1.94
58 59 3.593442 TGTCAAGATGACCCACCTTTT 57.407 42.857 7.94 0.00 46.40 2.27
59 60 3.562176 GGATGTCAAGATGACCCACCTTT 60.562 47.826 7.94 0.00 46.40 3.11
60 61 2.025887 GGATGTCAAGATGACCCACCTT 60.026 50.000 7.94 0.00 46.40 3.50
61 62 1.561542 GGATGTCAAGATGACCCACCT 59.438 52.381 7.94 0.00 46.40 4.00
62 63 1.561542 AGGATGTCAAGATGACCCACC 59.438 52.381 7.94 8.30 46.40 4.61
63 64 2.636830 CAGGATGTCAAGATGACCCAC 58.363 52.381 7.94 0.00 46.40 4.61
77 78 2.016318 ACACACACACAACACAGGATG 58.984 47.619 0.00 0.00 46.00 3.51
78 79 2.016318 CACACACACACAACACAGGAT 58.984 47.619 0.00 0.00 0.00 3.24
79 80 1.271108 ACACACACACACAACACAGGA 60.271 47.619 0.00 0.00 0.00 3.86
80 81 1.135717 CACACACACACACAACACAGG 60.136 52.381 0.00 0.00 0.00 4.00
81 82 1.535028 ACACACACACACACAACACAG 59.465 47.619 0.00 0.00 0.00 3.66
82 83 1.265365 CACACACACACACACAACACA 59.735 47.619 0.00 0.00 0.00 3.72
83 84 1.400888 CCACACACACACACACAACAC 60.401 52.381 0.00 0.00 0.00 3.32
84 85 0.877743 CCACACACACACACACAACA 59.122 50.000 0.00 0.00 0.00 3.33
85 86 0.878416 ACCACACACACACACACAAC 59.122 50.000 0.00 0.00 0.00 3.32
86 87 0.877743 CACCACACACACACACACAA 59.122 50.000 0.00 0.00 0.00 3.33
87 88 0.250510 ACACCACACACACACACACA 60.251 50.000 0.00 0.00 0.00 3.72
88 89 1.663643 CTACACCACACACACACACAC 59.336 52.381 0.00 0.00 0.00 3.82
89 90 1.276705 ACTACACCACACACACACACA 59.723 47.619 0.00 0.00 0.00 3.72
90 91 1.663643 CACTACACCACACACACACAC 59.336 52.381 0.00 0.00 0.00 3.82
91 92 1.276705 ACACTACACCACACACACACA 59.723 47.619 0.00 0.00 0.00 3.72
92 93 1.663643 CACACTACACCACACACACAC 59.336 52.381 0.00 0.00 0.00 3.82
93 94 1.550976 TCACACTACACCACACACACA 59.449 47.619 0.00 0.00 0.00 3.72
94 95 2.201732 CTCACACTACACCACACACAC 58.798 52.381 0.00 0.00 0.00 3.82
95 96 1.828595 ACTCACACTACACCACACACA 59.171 47.619 0.00 0.00 0.00 3.72
96 97 2.100916 AGACTCACACTACACCACACAC 59.899 50.000 0.00 0.00 0.00 3.82
97 98 2.384828 AGACTCACACTACACCACACA 58.615 47.619 0.00 0.00 0.00 3.72
98 99 3.454371 AAGACTCACACTACACCACAC 57.546 47.619 0.00 0.00 0.00 3.82
99 100 3.181469 GGAAAGACTCACACTACACCACA 60.181 47.826 0.00 0.00 0.00 4.17
100 101 3.069729 AGGAAAGACTCACACTACACCAC 59.930 47.826 0.00 0.00 0.00 4.16
101 102 3.305720 AGGAAAGACTCACACTACACCA 58.694 45.455 0.00 0.00 0.00 4.17
102 103 3.306156 GGAGGAAAGACTCACACTACACC 60.306 52.174 0.00 0.00 39.27 4.16
103 104 3.574826 AGGAGGAAAGACTCACACTACAC 59.425 47.826 0.00 0.00 39.27 2.90
104 105 3.845860 AGGAGGAAAGACTCACACTACA 58.154 45.455 0.00 0.00 39.27 2.74
105 106 4.875561 AAGGAGGAAAGACTCACACTAC 57.124 45.455 0.00 0.00 39.27 2.73
106 107 6.378564 CAGATAAGGAGGAAAGACTCACACTA 59.621 42.308 0.00 0.00 39.27 2.74
107 108 5.186797 CAGATAAGGAGGAAAGACTCACACT 59.813 44.000 0.00 0.00 39.27 3.55
108 109 5.415221 CAGATAAGGAGGAAAGACTCACAC 58.585 45.833 0.00 0.00 39.27 3.82
109 110 4.467795 CCAGATAAGGAGGAAAGACTCACA 59.532 45.833 0.00 0.00 39.27 3.58
110 111 4.468153 ACCAGATAAGGAGGAAAGACTCAC 59.532 45.833 0.00 0.00 39.27 3.51
111 112 4.689062 ACCAGATAAGGAGGAAAGACTCA 58.311 43.478 0.00 0.00 39.27 3.41
112 113 5.395879 GGAACCAGATAAGGAGGAAAGACTC 60.396 48.000 0.00 0.00 36.76 3.36
113 114 4.471747 GGAACCAGATAAGGAGGAAAGACT 59.528 45.833 0.00 0.00 0.00 3.24
114 115 4.771903 GGAACCAGATAAGGAGGAAAGAC 58.228 47.826 0.00 0.00 0.00 3.01
132 133 2.235155 GAGAGACAGGAAAGGAGGGAAC 59.765 54.545 0.00 0.00 0.00 3.62
133 134 2.112691 AGAGAGACAGGAAAGGAGGGAA 59.887 50.000 0.00 0.00 0.00 3.97
134 135 1.719378 AGAGAGACAGGAAAGGAGGGA 59.281 52.381 0.00 0.00 0.00 4.20
135 136 1.830477 CAGAGAGACAGGAAAGGAGGG 59.170 57.143 0.00 0.00 0.00 4.30
136 137 2.813907 TCAGAGAGACAGGAAAGGAGG 58.186 52.381 0.00 0.00 0.00 4.30
137 138 4.465660 TCAATCAGAGAGACAGGAAAGGAG 59.534 45.833 0.00 0.00 0.00 3.69
138 139 4.420206 TCAATCAGAGAGACAGGAAAGGA 58.580 43.478 0.00 0.00 0.00 3.36
139 140 4.815533 TCAATCAGAGAGACAGGAAAGG 57.184 45.455 0.00 0.00 0.00 3.11
140 141 7.064847 CAGAATTCAATCAGAGAGACAGGAAAG 59.935 40.741 8.44 0.00 0.00 2.62
141 142 6.877855 CAGAATTCAATCAGAGAGACAGGAAA 59.122 38.462 8.44 0.00 0.00 3.13
142 143 6.212187 TCAGAATTCAATCAGAGAGACAGGAA 59.788 38.462 8.44 0.00 0.00 3.36
143 144 5.718607 TCAGAATTCAATCAGAGAGACAGGA 59.281 40.000 8.44 0.00 0.00 3.86
144 145 5.975282 TCAGAATTCAATCAGAGAGACAGG 58.025 41.667 8.44 0.00 0.00 4.00
145 146 6.044046 CCTCAGAATTCAATCAGAGAGACAG 58.956 44.000 8.44 0.00 35.60 3.51
146 147 5.626347 GCCTCAGAATTCAATCAGAGAGACA 60.626 44.000 8.44 0.00 35.60 3.41
147 148 4.810491 GCCTCAGAATTCAATCAGAGAGAC 59.190 45.833 8.44 0.00 35.60 3.36
148 149 4.141756 GGCCTCAGAATTCAATCAGAGAGA 60.142 45.833 8.44 0.00 35.60 3.10
149 150 4.128643 GGCCTCAGAATTCAATCAGAGAG 58.871 47.826 8.44 3.36 35.60 3.20
150 151 3.118112 GGGCCTCAGAATTCAATCAGAGA 60.118 47.826 8.44 0.00 35.60 3.10
151 152 3.117963 AGGGCCTCAGAATTCAATCAGAG 60.118 47.826 0.00 6.57 33.94 3.35
152 153 2.848694 AGGGCCTCAGAATTCAATCAGA 59.151 45.455 0.00 0.00 0.00 3.27
153 154 3.212685 GAGGGCCTCAGAATTCAATCAG 58.787 50.000 28.55 0.00 0.00 2.90
154 155 2.577563 TGAGGGCCTCAGAATTCAATCA 59.422 45.455 32.01 5.83 35.39 2.57
155 156 3.287867 TGAGGGCCTCAGAATTCAATC 57.712 47.619 32.01 2.86 35.39 2.67
156 157 3.436180 GGATGAGGGCCTCAGAATTCAAT 60.436 47.826 36.91 20.69 44.08 2.57
157 158 2.092212 GGATGAGGGCCTCAGAATTCAA 60.092 50.000 36.91 14.95 44.08 2.69
158 159 1.492176 GGATGAGGGCCTCAGAATTCA 59.508 52.381 36.91 16.54 44.08 2.57
159 160 1.773653 AGGATGAGGGCCTCAGAATTC 59.226 52.381 36.91 28.75 44.08 2.17
160 161 1.904440 AGGATGAGGGCCTCAGAATT 58.096 50.000 36.91 23.27 44.08 2.17
161 162 3.670898 AGGATGAGGGCCTCAGAAT 57.329 52.632 36.91 23.64 44.08 2.40
167 168 1.695597 CTTGGGAGGATGAGGGCCT 60.696 63.158 5.25 5.25 38.81 5.19
168 169 2.003548 ACTTGGGAGGATGAGGGCC 61.004 63.158 0.00 0.00 0.00 5.80
169 170 1.225704 CACTTGGGAGGATGAGGGC 59.774 63.158 0.00 0.00 0.00 5.19
170 171 1.225704 GCACTTGGGAGGATGAGGG 59.774 63.158 0.00 0.00 0.00 4.30
171 172 1.225704 GGCACTTGGGAGGATGAGG 59.774 63.158 0.00 0.00 0.00 3.86
172 173 0.329261 TTGGCACTTGGGAGGATGAG 59.671 55.000 0.00 0.00 0.00 2.90
173 174 0.776810 TTTGGCACTTGGGAGGATGA 59.223 50.000 0.00 0.00 0.00 2.92
174 175 1.547372 CTTTTGGCACTTGGGAGGATG 59.453 52.381 0.00 0.00 0.00 3.51
175 176 1.147817 ACTTTTGGCACTTGGGAGGAT 59.852 47.619 0.00 0.00 0.00 3.24
176 177 0.555769 ACTTTTGGCACTTGGGAGGA 59.444 50.000 0.00 0.00 0.00 3.71
177 178 2.286365 TACTTTTGGCACTTGGGAGG 57.714 50.000 0.00 0.00 0.00 4.30
178 179 3.191371 GTCATACTTTTGGCACTTGGGAG 59.809 47.826 0.00 0.00 0.00 4.30
179 180 3.153919 GTCATACTTTTGGCACTTGGGA 58.846 45.455 0.00 0.00 0.00 4.37
180 181 3.157087 AGTCATACTTTTGGCACTTGGG 58.843 45.455 0.00 0.00 0.00 4.12
181 182 4.142902 CGTAGTCATACTTTTGGCACTTGG 60.143 45.833 0.00 0.00 0.00 3.61
182 183 4.669197 GCGTAGTCATACTTTTGGCACTTG 60.669 45.833 0.00 0.00 0.00 3.16
183 184 3.435671 GCGTAGTCATACTTTTGGCACTT 59.564 43.478 0.00 0.00 0.00 3.16
184 185 3.000727 GCGTAGTCATACTTTTGGCACT 58.999 45.455 0.00 0.00 0.00 4.40
185 186 2.095372 GGCGTAGTCATACTTTTGGCAC 59.905 50.000 0.00 0.00 0.00 5.01
186 187 2.289756 TGGCGTAGTCATACTTTTGGCA 60.290 45.455 0.00 0.00 36.97 4.92
187 188 2.352388 TGGCGTAGTCATACTTTTGGC 58.648 47.619 0.00 0.00 36.97 4.52
198 199 2.860735 CAACAGAAGCTATGGCGTAGTC 59.139 50.000 14.88 6.00 44.37 2.59
199 200 2.233922 ACAACAGAAGCTATGGCGTAGT 59.766 45.455 14.88 0.00 44.37 2.73
200 201 2.893637 ACAACAGAAGCTATGGCGTAG 58.106 47.619 9.44 9.44 44.37 3.51
201 202 3.328382 AACAACAGAAGCTATGGCGTA 57.672 42.857 0.00 0.00 44.37 4.42
202 203 2.185004 AACAACAGAAGCTATGGCGT 57.815 45.000 0.00 0.00 44.37 5.68
203 204 4.094887 ACAATAACAACAGAAGCTATGGCG 59.905 41.667 0.00 0.00 44.37 5.69
204 205 5.567138 ACAATAACAACAGAAGCTATGGC 57.433 39.130 0.00 0.00 39.06 4.40
205 206 7.609760 TGTACAATAACAACAGAAGCTATGG 57.390 36.000 0.00 0.00 0.00 2.74
209 210 8.227791 CGTTTATGTACAATAACAACAGAAGCT 58.772 33.333 18.08 0.00 32.02 3.74
210 211 8.225107 TCGTTTATGTACAATAACAACAGAAGC 58.775 33.333 18.08 0.00 32.02 3.86
211 212 9.525007 GTCGTTTATGTACAATAACAACAGAAG 57.475 33.333 18.08 5.61 32.02 2.85
212 213 9.043079 TGTCGTTTATGTACAATAACAACAGAA 57.957 29.630 18.08 0.00 32.02 3.02
213 214 8.590719 TGTCGTTTATGTACAATAACAACAGA 57.409 30.769 18.08 8.48 32.02 3.41
214 215 9.653067 TTTGTCGTTTATGTACAATAACAACAG 57.347 29.630 18.08 6.87 33.44 3.16
215 216 9.999009 TTTTGTCGTTTATGTACAATAACAACA 57.001 25.926 18.08 14.74 33.44 3.33
233 234 8.395633 GCTATGGTTTACTCATAATTTTGTCGT 58.604 33.333 0.00 0.00 0.00 4.34
234 235 7.582679 CGCTATGGTTTACTCATAATTTTGTCG 59.417 37.037 0.00 0.00 0.00 4.35
235 236 8.395633 ACGCTATGGTTTACTCATAATTTTGTC 58.604 33.333 0.00 0.00 0.00 3.18
236 237 8.276252 ACGCTATGGTTTACTCATAATTTTGT 57.724 30.769 0.00 0.00 0.00 2.83
237 238 8.394877 TGACGCTATGGTTTACTCATAATTTTG 58.605 33.333 0.00 0.00 0.00 2.44
238 239 8.500753 TGACGCTATGGTTTACTCATAATTTT 57.499 30.769 0.00 0.00 0.00 1.82
239 240 8.677148 ATGACGCTATGGTTTACTCATAATTT 57.323 30.769 0.00 0.00 0.00 1.82
240 241 7.931407 TGATGACGCTATGGTTTACTCATAATT 59.069 33.333 0.00 0.00 0.00 1.40
241 242 7.441836 TGATGACGCTATGGTTTACTCATAAT 58.558 34.615 0.00 0.00 0.00 1.28
242 243 6.811954 TGATGACGCTATGGTTTACTCATAA 58.188 36.000 0.00 0.00 0.00 1.90
243 244 6.399639 TGATGACGCTATGGTTTACTCATA 57.600 37.500 0.00 0.00 0.00 2.15
244 245 5.276461 TGATGACGCTATGGTTTACTCAT 57.724 39.130 0.00 0.00 0.00 2.90
245 246 4.729227 TGATGACGCTATGGTTTACTCA 57.271 40.909 0.00 0.00 0.00 3.41
246 247 6.480320 AGAATTGATGACGCTATGGTTTACTC 59.520 38.462 0.00 0.00 0.00 2.59
247 248 6.258727 CAGAATTGATGACGCTATGGTTTACT 59.741 38.462 0.00 0.00 0.00 2.24
248 249 6.422223 CAGAATTGATGACGCTATGGTTTAC 58.578 40.000 0.00 0.00 0.00 2.01
249 250 5.527214 CCAGAATTGATGACGCTATGGTTTA 59.473 40.000 0.00 0.00 0.00 2.01
250 251 4.336433 CCAGAATTGATGACGCTATGGTTT 59.664 41.667 0.00 0.00 0.00 3.27
251 252 3.879295 CCAGAATTGATGACGCTATGGTT 59.121 43.478 0.00 0.00 0.00 3.67
252 253 3.134623 TCCAGAATTGATGACGCTATGGT 59.865 43.478 0.00 0.00 0.00 3.55
253 254 3.732212 TCCAGAATTGATGACGCTATGG 58.268 45.455 0.00 0.00 0.00 2.74
254 255 4.375272 ACTCCAGAATTGATGACGCTATG 58.625 43.478 0.00 0.00 0.00 2.23
255 256 4.679373 ACTCCAGAATTGATGACGCTAT 57.321 40.909 0.00 0.00 0.00 2.97
256 257 4.645136 AGTACTCCAGAATTGATGACGCTA 59.355 41.667 0.00 0.00 0.00 4.26
257 258 3.449018 AGTACTCCAGAATTGATGACGCT 59.551 43.478 0.00 0.00 0.00 5.07
258 259 3.786635 AGTACTCCAGAATTGATGACGC 58.213 45.455 0.00 0.00 0.00 5.19
259 260 5.255710 AGAGTACTCCAGAATTGATGACG 57.744 43.478 19.38 0.00 0.00 4.35
260 261 6.402222 ACAAGAGTACTCCAGAATTGATGAC 58.598 40.000 21.92 0.00 0.00 3.06
261 262 6.611613 ACAAGAGTACTCCAGAATTGATGA 57.388 37.500 21.92 0.00 0.00 2.92
262 263 6.875726 TCAACAAGAGTACTCCAGAATTGATG 59.124 38.462 21.92 19.99 0.00 3.07
263 264 6.876257 GTCAACAAGAGTACTCCAGAATTGAT 59.124 38.462 21.92 11.85 0.00 2.57
264 265 6.223852 GTCAACAAGAGTACTCCAGAATTGA 58.776 40.000 21.92 18.76 0.00 2.57
265 266 5.409826 GGTCAACAAGAGTACTCCAGAATTG 59.590 44.000 19.38 17.53 0.00 2.32
266 267 5.071788 TGGTCAACAAGAGTACTCCAGAATT 59.928 40.000 19.38 3.89 0.00 2.17
267 268 4.593206 TGGTCAACAAGAGTACTCCAGAAT 59.407 41.667 19.38 0.00 0.00 2.40
268 269 3.964688 TGGTCAACAAGAGTACTCCAGAA 59.035 43.478 19.38 0.00 0.00 3.02
269 270 3.572642 TGGTCAACAAGAGTACTCCAGA 58.427 45.455 19.38 7.61 0.00 3.86
270 271 3.574396 TCTGGTCAACAAGAGTACTCCAG 59.426 47.826 19.38 16.30 38.69 3.86
271 272 3.572642 TCTGGTCAACAAGAGTACTCCA 58.427 45.455 19.38 7.34 0.00 3.86
272 273 4.810191 ATCTGGTCAACAAGAGTACTCC 57.190 45.455 19.38 2.62 0.00 3.85
273 274 6.590677 GGTAAATCTGGTCAACAAGAGTACTC 59.409 42.308 15.41 15.41 0.00 2.59
274 275 6.042781 TGGTAAATCTGGTCAACAAGAGTACT 59.957 38.462 0.00 0.00 0.00 2.73
275 276 6.228258 TGGTAAATCTGGTCAACAAGAGTAC 58.772 40.000 0.00 0.00 0.00 2.73
276 277 6.428083 TGGTAAATCTGGTCAACAAGAGTA 57.572 37.500 0.00 0.00 0.00 2.59
277 278 5.304686 TGGTAAATCTGGTCAACAAGAGT 57.695 39.130 0.00 0.00 0.00 3.24
278 279 5.765182 ACTTGGTAAATCTGGTCAACAAGAG 59.235 40.000 5.30 0.00 37.92 2.85
279 280 5.690865 ACTTGGTAAATCTGGTCAACAAGA 58.309 37.500 5.30 0.00 37.92 3.02
280 281 6.391227 AACTTGGTAAATCTGGTCAACAAG 57.609 37.500 0.00 0.00 39.76 3.16
281 282 6.783708 AAACTTGGTAAATCTGGTCAACAA 57.216 33.333 0.00 0.00 0.00 2.83
282 283 7.227910 GTCTAAACTTGGTAAATCTGGTCAACA 59.772 37.037 0.00 0.00 0.00 3.33
283 284 7.444487 AGTCTAAACTTGGTAAATCTGGTCAAC 59.556 37.037 0.00 0.00 28.74 3.18
284 285 7.514721 AGTCTAAACTTGGTAAATCTGGTCAA 58.485 34.615 0.00 0.00 28.74 3.18
285 286 7.074653 AGTCTAAACTTGGTAAATCTGGTCA 57.925 36.000 0.00 0.00 28.74 4.02
286 287 7.981102 AAGTCTAAACTTGGTAAATCTGGTC 57.019 36.000 0.00 0.00 44.13 4.02
299 300 7.498443 ACTAGTGTAACAGCAAGTCTAAACTT 58.502 34.615 0.00 0.00 43.13 2.66
300 301 7.052142 ACTAGTGTAACAGCAAGTCTAAACT 57.948 36.000 0.00 0.00 41.43 2.66
301 302 8.295288 TCTACTAGTGTAACAGCAAGTCTAAAC 58.705 37.037 5.39 0.00 41.43 2.01
302 303 8.400184 TCTACTAGTGTAACAGCAAGTCTAAA 57.600 34.615 5.39 0.00 41.43 1.85
303 304 7.991084 TCTACTAGTGTAACAGCAAGTCTAA 57.009 36.000 5.39 0.00 41.43 2.10
304 305 7.991084 TTCTACTAGTGTAACAGCAAGTCTA 57.009 36.000 5.39 0.00 41.43 2.59
305 306 6.896021 TTCTACTAGTGTAACAGCAAGTCT 57.104 37.500 5.39 0.00 41.43 3.24
306 307 7.866393 TCTTTTCTACTAGTGTAACAGCAAGTC 59.134 37.037 5.39 0.00 41.43 3.01
307 308 7.723324 TCTTTTCTACTAGTGTAACAGCAAGT 58.277 34.615 5.39 0.00 41.43 3.16
308 309 7.329717 CCTCTTTTCTACTAGTGTAACAGCAAG 59.670 40.741 5.39 1.15 41.43 4.01
309 310 7.152645 CCTCTTTTCTACTAGTGTAACAGCAA 58.847 38.462 5.39 0.00 41.43 3.91
310 311 6.295123 CCCTCTTTTCTACTAGTGTAACAGCA 60.295 42.308 5.39 0.00 41.43 4.41
311 312 6.100668 CCCTCTTTTCTACTAGTGTAACAGC 58.899 44.000 5.39 0.00 41.43 4.40
312 313 6.071278 AGCCCTCTTTTCTACTAGTGTAACAG 60.071 42.308 5.39 2.56 41.43 3.16
313 314 5.778750 AGCCCTCTTTTCTACTAGTGTAACA 59.221 40.000 5.39 0.00 41.43 2.41
314 315 6.283544 AGCCCTCTTTTCTACTAGTGTAAC 57.716 41.667 5.39 0.00 0.00 2.50
315 316 6.930068 AAGCCCTCTTTTCTACTAGTGTAA 57.070 37.500 5.39 0.00 0.00 2.41
496 498 3.407967 GAGGCCCATTGGTCCCGA 61.408 66.667 0.00 0.00 36.69 5.14
548 550 1.752198 CTGTGGTCCCGGTTCAAGA 59.248 57.895 0.00 0.00 0.00 3.02
634 636 3.292500 CTGGAGTGCTCTGCTCGCA 62.293 63.158 8.78 0.00 34.00 5.10
1035 1038 3.371102 ACCACATCCGAATCATAGACG 57.629 47.619 0.00 0.00 0.00 4.18
1098 1101 1.735018 TCACGTTGGTCGGCATAATTG 59.265 47.619 0.00 0.00 44.69 2.32
1311 1315 4.785669 ATCTTTCTAATCTTCAAGCGCG 57.214 40.909 0.00 0.00 0.00 6.86
1375 1379 7.578571 GCAACCAAGGTAATAATTGATCCAACA 60.579 37.037 0.00 0.00 0.00 3.33
1731 1735 3.033184 CCACATTTAGGGCATGGACAAT 58.967 45.455 0.00 0.00 31.69 2.71
1885 1889 2.616960 GGCACATAGTTGTCATCGTCA 58.383 47.619 0.00 0.00 32.34 4.35
1930 1934 0.545646 GATCTTCAGCAGCTTCCCCT 59.454 55.000 0.00 0.00 0.00 4.79
1989 1993 2.570752 TCTTGATCTTCAGCAGCTTCCT 59.429 45.455 0.00 0.00 0.00 3.36
2142 2146 0.040514 TTTGTGTTGCCATCTTCGCG 60.041 50.000 0.00 0.00 0.00 5.87
2214 2218 7.765695 TCAATAGCTTCTCAAATCCTTTGTT 57.234 32.000 0.00 0.00 41.36 2.83
2307 2314 3.567902 CCTCCAATCCTAGAGGGCT 57.432 57.895 0.00 0.00 45.08 5.19
2330 2337 5.939883 GTCATTAGGGCATGCATGTATCTTA 59.060 40.000 26.79 15.42 0.00 2.10
2404 2411 1.137282 TCTTATACCGCAATGCACCGA 59.863 47.619 5.91 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.