Multiple sequence alignment - TraesCS5D01G174200

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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 TraesCS5D01G174200 chr5D 100.000 3826 0 0 1 3826 273059408 273063233 0.000000e+00 7066.0
1 TraesCS5D01G174200 chr5D 74.114 649 122 33 1243 1865 81736776 81736148 3.850000e-55 226.0
2 TraesCS5D01G174200 chr5D 88.966 145 16 0 1244 1388 44488974 44489118 3.040000e-41 180.0
3 TraesCS5D01G174200 chr5D 71.951 738 156 31 2097 2820 80300591 80301291 6.570000e-38 169.0
4 TraesCS5D01G174200 chr5B 95.614 2645 95 14 340 2973 308790520 308793154 0.000000e+00 4222.0
5 TraesCS5D01G174200 chr5B 91.362 903 32 16 2959 3826 308793296 308794187 0.000000e+00 1194.0
6 TraesCS5D01G174200 chr5B 89.655 348 36 0 2 349 308757589 308757936 9.750000e-121 444.0
7 TraesCS5D01G174200 chr5B 88.966 145 16 0 1244 1388 43884298 43884442 3.040000e-41 180.0
8 TraesCS5D01G174200 chr5B 87.261 157 20 0 1244 1400 44231459 44231303 3.040000e-41 180.0
9 TraesCS5D01G174200 chr5A 96.416 2288 72 5 896 3177 362376540 362378823 0.000000e+00 3762.0
10 TraesCS5D01G174200 chr5A 89.137 626 34 15 3176 3773 362378911 362379530 0.000000e+00 749.0
11 TraesCS5D01G174200 chr5A 88.276 145 17 0 1244 1388 34903678 34903822 1.410000e-39 174.0
12 TraesCS5D01G174200 chr5A 85.263 95 9 4 480 572 31282944 31283035 4.070000e-15 93.5
13 TraesCS5D01G174200 chr5A 95.652 46 1 1 754 798 362376143 362376188 5.300000e-09 73.1
14 TraesCS5D01G174200 chr7B 79.583 240 43 6 1247 1486 699372091 699372324 2.360000e-37 167.0
15 TraesCS5D01G174200 chr7D 79.167 240 44 6 1247 1486 610782548 610782315 1.100000e-35 161.0
16 TraesCS5D01G174200 chr7D 82.540 126 15 7 481 602 611359746 611359868 1.880000e-18 104.0
17 TraesCS5D01G174200 chr2D 81.159 207 32 7 430 633 545846594 545846392 3.960000e-35 159.0
18 TraesCS5D01G174200 chr2A 78.652 178 33 5 433 607 549981939 549981764 3.120000e-21 113.0


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 TraesCS5D01G174200 chr5D 273059408 273063233 3825 False 7066.000000 7066 100.000 1 3826 1 chr5D.!!$F3 3825
1 TraesCS5D01G174200 chr5D 81736148 81736776 628 True 226.000000 226 74.114 1243 1865 1 chr5D.!!$R1 622
2 TraesCS5D01G174200 chr5B 308790520 308794187 3667 False 2708.000000 4222 93.488 340 3826 2 chr5B.!!$F3 3486
3 TraesCS5D01G174200 chr5A 362376143 362379530 3387 False 1528.033333 3762 93.735 754 3773 3 chr5A.!!$F3 3019

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
235 236 0.033504 GCCCTATTTGCGGAGATCGA 59.966 55.000 0.0 0.00 42.43 3.59 F
428 432 0.035152 GCATGTCTGGTGTCCCATGA 60.035 55.000 0.0 0.00 40.90 3.07 F
671 677 0.320374 CGGCTTCCCTAACACTGTCA 59.680 55.000 0.0 0.00 0.00 3.58 F
2160 2455 1.065851 TCAATTGCAGTGCTGTGTGTG 59.934 47.619 17.6 6.12 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 1966 0.036388 GAAGCCCTTGGACGATGTCA 60.036 55.000 0.00 0.0 33.68 3.58 R
1857 2152 1.004610 CAATAGCATTCAGGACGCACG 60.005 52.381 0.00 0.0 0.00 5.34 R
2226 2522 1.128692 GTCAGCTTATCAACACGTGGC 59.871 52.381 21.57 11.5 0.00 5.01 R
3531 4110 0.106719 GGATCCCGGATTCTTTGCCA 60.107 55.000 0.73 0.0 0.00 4.92 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 3.771798 GAGGACGAACACTACAATCTCC 58.228 50.000 0.00 0.00 0.00 3.71
22 23 3.162666 AGGACGAACACTACAATCTCCA 58.837 45.455 0.00 0.00 0.00 3.86
23 24 3.193691 AGGACGAACACTACAATCTCCAG 59.806 47.826 0.00 0.00 0.00 3.86
24 25 2.924290 GACGAACACTACAATCTCCAGC 59.076 50.000 0.00 0.00 0.00 4.85
25 26 2.563179 ACGAACACTACAATCTCCAGCT 59.437 45.455 0.00 0.00 0.00 4.24
26 27 3.182967 CGAACACTACAATCTCCAGCTC 58.817 50.000 0.00 0.00 0.00 4.09
27 28 3.119316 CGAACACTACAATCTCCAGCTCT 60.119 47.826 0.00 0.00 0.00 4.09
28 29 4.619394 CGAACACTACAATCTCCAGCTCTT 60.619 45.833 0.00 0.00 0.00 2.85
29 30 4.464069 ACACTACAATCTCCAGCTCTTC 57.536 45.455 0.00 0.00 0.00 2.87
30 31 3.119316 ACACTACAATCTCCAGCTCTTCG 60.119 47.826 0.00 0.00 0.00 3.79
31 32 3.129462 CACTACAATCTCCAGCTCTTCGA 59.871 47.826 0.00 0.00 0.00 3.71
32 33 2.663826 ACAATCTCCAGCTCTTCGAC 57.336 50.000 0.00 0.00 0.00 4.20
33 34 1.135257 ACAATCTCCAGCTCTTCGACG 60.135 52.381 0.00 0.00 0.00 5.12
34 35 1.133216 CAATCTCCAGCTCTTCGACGA 59.867 52.381 0.00 0.00 0.00 4.20
35 36 1.021202 ATCTCCAGCTCTTCGACGAG 58.979 55.000 14.25 14.25 0.00 4.18
41 42 2.868196 CTCTTCGACGAGCACCGA 59.132 61.111 5.94 0.00 41.76 4.69
42 43 1.512310 CTCTTCGACGAGCACCGAC 60.512 63.158 5.94 0.00 41.76 4.79
43 44 1.913451 CTCTTCGACGAGCACCGACT 61.913 60.000 5.94 0.00 41.76 4.18
44 45 1.512310 CTTCGACGAGCACCGACTC 60.512 63.158 5.53 0.00 41.76 3.36
50 51 2.649034 GAGCACCGACTCGTGGAA 59.351 61.111 0.00 0.00 34.16 3.53
51 52 1.006571 GAGCACCGACTCGTGGAAA 60.007 57.895 0.00 0.00 34.16 3.13
52 53 1.006102 AGCACCGACTCGTGGAAAG 60.006 57.895 0.00 0.00 34.16 2.62
53 54 1.006571 GCACCGACTCGTGGAAAGA 60.007 57.895 0.00 0.00 34.16 2.52
54 55 1.282930 GCACCGACTCGTGGAAAGAC 61.283 60.000 0.00 0.00 34.16 3.01
55 56 0.666577 CACCGACTCGTGGAAAGACC 60.667 60.000 0.00 0.00 39.54 3.85
69 70 2.785258 GACCAATTGTCGGCGAGC 59.215 61.111 11.20 6.16 33.49 5.03
70 71 2.031919 ACCAATTGTCGGCGAGCA 59.968 55.556 11.20 9.09 0.00 4.26
71 72 1.970917 GACCAATTGTCGGCGAGCAG 61.971 60.000 11.20 2.63 33.49 4.24
72 73 2.753966 CCAATTGTCGGCGAGCAGG 61.754 63.158 11.20 4.49 0.00 4.85
73 74 3.127533 AATTGTCGGCGAGCAGGC 61.128 61.111 11.20 0.00 42.76 4.85
82 83 4.753877 CGAGCAGGCGAACGACGA 62.754 66.667 0.00 0.00 45.77 4.20
83 84 2.202623 GAGCAGGCGAACGACGAT 60.203 61.111 0.00 0.00 45.77 3.73
84 85 2.507102 AGCAGGCGAACGACGATG 60.507 61.111 0.00 8.72 45.77 3.84
85 86 4.210304 GCAGGCGAACGACGATGC 62.210 66.667 0.00 15.61 45.77 3.91
88 89 2.890474 GGCGAACGACGATGCCAT 60.890 61.111 19.52 0.00 46.76 4.40
89 90 2.621000 GCGAACGACGATGCCATC 59.379 61.111 0.00 0.00 45.77 3.51
90 91 2.164663 GCGAACGACGATGCCATCA 61.165 57.895 0.00 0.00 45.77 3.07
91 92 1.631072 CGAACGACGATGCCATCAC 59.369 57.895 0.00 0.00 45.77 3.06
92 93 1.631072 GAACGACGATGCCATCACG 59.369 57.895 15.99 15.99 35.77 4.35
93 94 1.752501 GAACGACGATGCCATCACGG 61.753 60.000 19.75 5.57 34.63 4.94
109 110 4.467084 GGCCATGGTCGCGAAGGA 62.467 66.667 12.06 0.00 0.00 3.36
110 111 2.203070 GCCATGGTCGCGAAGGAT 60.203 61.111 12.06 0.00 0.00 3.24
111 112 2.247437 GCCATGGTCGCGAAGGATC 61.247 63.158 12.06 0.00 0.00 3.36
112 113 1.443407 CCATGGTCGCGAAGGATCT 59.557 57.895 12.06 0.00 0.00 2.75
113 114 0.673985 CCATGGTCGCGAAGGATCTA 59.326 55.000 12.06 0.00 0.00 1.98
114 115 1.336332 CCATGGTCGCGAAGGATCTAG 60.336 57.143 12.06 0.00 0.00 2.43
115 116 0.962489 ATGGTCGCGAAGGATCTAGG 59.038 55.000 12.06 0.00 0.00 3.02
116 117 1.007154 GGTCGCGAAGGATCTAGGC 60.007 63.158 12.06 0.00 0.00 3.93
117 118 1.457009 GGTCGCGAAGGATCTAGGCT 61.457 60.000 12.06 0.00 0.00 4.58
118 119 0.386113 GTCGCGAAGGATCTAGGCTT 59.614 55.000 12.06 0.00 0.00 4.35
119 120 0.669077 TCGCGAAGGATCTAGGCTTC 59.331 55.000 6.20 0.00 0.00 3.86
120 121 0.319125 CGCGAAGGATCTAGGCTTCC 60.319 60.000 0.00 0.00 0.00 3.46
121 122 1.044611 GCGAAGGATCTAGGCTTCCT 58.955 55.000 0.18 0.18 44.35 3.36
122 123 2.240279 GCGAAGGATCTAGGCTTCCTA 58.760 52.381 6.66 0.00 41.58 2.94
132 133 2.998316 AGGCTTCCTAGATGAGCAAC 57.002 50.000 12.08 0.00 38.14 4.17
133 134 1.137872 AGGCTTCCTAGATGAGCAACG 59.862 52.381 12.08 0.00 38.14 4.10
134 135 1.137086 GGCTTCCTAGATGAGCAACGA 59.863 52.381 12.08 0.00 38.14 3.85
135 136 2.468831 GCTTCCTAGATGAGCAACGAG 58.531 52.381 0.00 0.00 36.45 4.18
136 137 2.468831 CTTCCTAGATGAGCAACGAGC 58.531 52.381 0.00 0.00 46.19 5.03
145 146 4.178861 GCAACGAGCGATGTACCA 57.821 55.556 0.00 0.00 0.00 3.25
146 147 1.999051 GCAACGAGCGATGTACCAG 59.001 57.895 0.00 0.00 0.00 4.00
147 148 0.736325 GCAACGAGCGATGTACCAGT 60.736 55.000 0.00 0.00 0.00 4.00
148 149 1.269166 CAACGAGCGATGTACCAGTC 58.731 55.000 0.00 0.00 0.00 3.51
149 150 0.172803 AACGAGCGATGTACCAGTCC 59.827 55.000 0.00 0.00 0.00 3.85
150 151 0.963856 ACGAGCGATGTACCAGTCCA 60.964 55.000 0.00 0.00 0.00 4.02
151 152 0.385751 CGAGCGATGTACCAGTCCAT 59.614 55.000 0.00 0.00 0.00 3.41
152 153 1.858091 GAGCGATGTACCAGTCCATG 58.142 55.000 0.00 0.00 0.00 3.66
153 154 1.137086 GAGCGATGTACCAGTCCATGT 59.863 52.381 0.00 0.00 0.00 3.21
154 155 1.134699 AGCGATGTACCAGTCCATGTG 60.135 52.381 0.00 0.00 0.00 3.21
155 156 1.405526 GCGATGTACCAGTCCATGTGT 60.406 52.381 0.00 0.00 0.00 3.72
156 157 2.159156 GCGATGTACCAGTCCATGTGTA 60.159 50.000 0.00 0.00 0.00 2.90
157 158 3.706698 CGATGTACCAGTCCATGTGTAG 58.293 50.000 0.00 0.00 0.00 2.74
158 159 3.458189 GATGTACCAGTCCATGTGTAGC 58.542 50.000 0.00 0.00 0.00 3.58
159 160 1.203758 TGTACCAGTCCATGTGTAGCG 59.796 52.381 0.00 0.00 0.00 4.26
160 161 0.174845 TACCAGTCCATGTGTAGCGC 59.825 55.000 0.00 0.00 0.00 5.92
161 162 1.815421 CCAGTCCATGTGTAGCGCC 60.815 63.158 2.29 0.00 0.00 6.53
162 163 1.815421 CAGTCCATGTGTAGCGCCC 60.815 63.158 2.29 0.00 0.00 6.13
163 164 2.267642 GTCCATGTGTAGCGCCCA 59.732 61.111 2.29 0.00 0.00 5.36
164 165 2.106683 GTCCATGTGTAGCGCCCAC 61.107 63.158 18.14 18.14 0.00 4.61
165 166 3.195002 CCATGTGTAGCGCCCACG 61.195 66.667 19.23 8.82 44.07 4.94
166 167 2.125713 CATGTGTAGCGCCCACGA 60.126 61.111 19.23 11.15 43.93 4.35
167 168 2.125673 ATGTGTAGCGCCCACGAC 60.126 61.111 19.23 12.04 43.93 4.34
168 169 2.938086 ATGTGTAGCGCCCACGACA 61.938 57.895 19.23 16.00 43.93 4.35
169 170 2.125673 GTGTAGCGCCCACGACAT 60.126 61.111 2.29 0.00 43.93 3.06
170 171 2.165301 GTGTAGCGCCCACGACATC 61.165 63.158 2.29 0.00 43.93 3.06
171 172 2.348104 TGTAGCGCCCACGACATCT 61.348 57.895 2.29 0.00 43.93 2.90
172 173 1.878522 GTAGCGCCCACGACATCTG 60.879 63.158 2.29 0.00 43.93 2.90
173 174 3.716539 TAGCGCCCACGACATCTGC 62.717 63.158 2.29 0.00 43.93 4.26
175 176 4.758251 CGCCCACGACATCTGCCA 62.758 66.667 0.00 0.00 43.93 4.92
176 177 2.359850 GCCCACGACATCTGCCAA 60.360 61.111 0.00 0.00 0.00 4.52
177 178 2.401766 GCCCACGACATCTGCCAAG 61.402 63.158 0.00 0.00 0.00 3.61
178 179 1.296392 CCCACGACATCTGCCAAGA 59.704 57.895 0.00 0.00 36.69 3.02
179 180 0.742281 CCCACGACATCTGCCAAGAG 60.742 60.000 0.00 0.00 35.37 2.85
180 181 1.364626 CCACGACATCTGCCAAGAGC 61.365 60.000 0.00 0.00 44.14 4.09
190 191 2.270205 CCAAGAGCGATGGTGGCT 59.730 61.111 0.00 0.00 45.00 4.75
191 192 2.110967 CCAAGAGCGATGGTGGCTG 61.111 63.158 0.00 0.00 41.72 4.85
192 193 2.437359 AAGAGCGATGGTGGCTGC 60.437 61.111 0.00 0.00 41.72 5.25
193 194 4.827087 AGAGCGATGGTGGCTGCG 62.827 66.667 0.00 0.00 41.72 5.18
201 202 4.752879 GGTGGCTGCGCGTCCTAA 62.753 66.667 17.01 0.00 0.00 2.69
202 203 3.188786 GTGGCTGCGCGTCCTAAG 61.189 66.667 17.01 2.70 0.00 2.18
203 204 4.451150 TGGCTGCGCGTCCTAAGG 62.451 66.667 17.01 0.00 0.00 2.69
209 210 4.570663 CGCGTCCTAAGGGCGGAG 62.571 72.222 7.89 0.00 45.69 4.63
210 211 3.145551 GCGTCCTAAGGGCGGAGA 61.146 66.667 0.00 0.00 34.44 3.71
211 212 3.121019 CGTCCTAAGGGCGGAGAG 58.879 66.667 0.00 0.00 0.00 3.20
212 213 1.753463 CGTCCTAAGGGCGGAGAGT 60.753 63.158 0.00 0.00 0.00 3.24
213 214 1.817209 GTCCTAAGGGCGGAGAGTG 59.183 63.158 0.00 0.00 0.00 3.51
214 215 0.683504 GTCCTAAGGGCGGAGAGTGA 60.684 60.000 0.00 0.00 0.00 3.41
215 216 0.683504 TCCTAAGGGCGGAGAGTGAC 60.684 60.000 0.00 0.00 0.00 3.67
216 217 1.433879 CTAAGGGCGGAGAGTGACG 59.566 63.158 0.00 0.00 0.00 4.35
222 223 3.843304 CGGAGAGTGACGCCCTAT 58.157 61.111 0.00 0.00 34.98 2.57
223 224 2.116383 CGGAGAGTGACGCCCTATT 58.884 57.895 0.00 0.00 34.98 1.73
224 225 0.460311 CGGAGAGTGACGCCCTATTT 59.540 55.000 0.00 0.00 34.98 1.40
225 226 1.802880 CGGAGAGTGACGCCCTATTTG 60.803 57.143 0.00 0.00 34.98 2.32
226 227 1.291132 GAGAGTGACGCCCTATTTGC 58.709 55.000 0.00 0.00 0.00 3.68
234 235 2.533318 GCCCTATTTGCGGAGATCG 58.467 57.895 0.00 0.00 42.76 3.69
235 236 0.033504 GCCCTATTTGCGGAGATCGA 59.966 55.000 0.00 0.00 42.43 3.59
236 237 1.784525 CCCTATTTGCGGAGATCGAC 58.215 55.000 0.00 0.00 42.43 4.20
237 238 1.409412 CCTATTTGCGGAGATCGACG 58.591 55.000 7.58 7.58 42.43 5.12
242 243 4.965858 GCGGAGATCGACGCGGAG 62.966 72.222 18.46 3.43 46.58 4.63
243 244 4.315122 CGGAGATCGACGCGGAGG 62.315 72.222 12.47 0.00 42.43 4.30
244 245 4.632458 GGAGATCGACGCGGAGGC 62.632 72.222 12.47 0.00 0.00 4.70
245 246 3.889044 GAGATCGACGCGGAGGCA 61.889 66.667 12.47 0.00 39.92 4.75
246 247 3.815569 GAGATCGACGCGGAGGCAG 62.816 68.421 12.47 0.00 39.92 4.85
247 248 3.889044 GATCGACGCGGAGGCAGA 61.889 66.667 12.47 0.07 39.92 4.26
248 249 4.194720 ATCGACGCGGAGGCAGAC 62.195 66.667 12.47 0.00 39.92 3.51
251 252 3.807538 GACGCGGAGGCAGACGTA 61.808 66.667 12.47 0.00 39.16 3.57
252 253 3.736482 GACGCGGAGGCAGACGTAG 62.736 68.421 12.47 0.00 39.16 3.51
253 254 3.506096 CGCGGAGGCAGACGTAGA 61.506 66.667 0.00 0.00 39.92 2.59
254 255 2.409651 GCGGAGGCAGACGTAGAG 59.590 66.667 0.00 0.00 39.62 2.43
255 256 3.111939 CGGAGGCAGACGTAGAGG 58.888 66.667 0.00 0.00 0.00 3.69
256 257 1.451567 CGGAGGCAGACGTAGAGGA 60.452 63.158 0.00 0.00 0.00 3.71
257 258 1.440938 CGGAGGCAGACGTAGAGGAG 61.441 65.000 0.00 0.00 0.00 3.69
258 259 1.104577 GGAGGCAGACGTAGAGGAGG 61.105 65.000 0.00 0.00 0.00 4.30
259 260 1.730451 GAGGCAGACGTAGAGGAGGC 61.730 65.000 0.00 0.00 0.00 4.70
260 261 2.052690 GGCAGACGTAGAGGAGGCA 61.053 63.158 0.00 0.00 0.00 4.75
261 262 1.395826 GGCAGACGTAGAGGAGGCAT 61.396 60.000 0.00 0.00 0.00 4.40
262 263 1.319541 GCAGACGTAGAGGAGGCATA 58.680 55.000 0.00 0.00 0.00 3.14
263 264 1.268352 GCAGACGTAGAGGAGGCATAG 59.732 57.143 0.00 0.00 0.00 2.23
264 265 1.883275 CAGACGTAGAGGAGGCATAGG 59.117 57.143 0.00 0.00 0.00 2.57
265 266 0.599060 GACGTAGAGGAGGCATAGGC 59.401 60.000 0.00 0.00 40.13 3.93
266 267 1.173444 ACGTAGAGGAGGCATAGGCG 61.173 60.000 0.00 0.00 42.47 5.52
267 268 0.889638 CGTAGAGGAGGCATAGGCGA 60.890 60.000 0.00 0.00 42.47 5.54
268 269 1.551452 GTAGAGGAGGCATAGGCGAT 58.449 55.000 0.00 0.00 42.47 4.58
269 270 1.203523 GTAGAGGAGGCATAGGCGATG 59.796 57.143 2.94 2.94 42.47 3.84
270 271 1.190833 AGAGGAGGCATAGGCGATGG 61.191 60.000 9.68 0.00 42.47 3.51
275 276 3.647824 GCATAGGCGATGGCAGAC 58.352 61.111 9.68 0.00 42.47 3.51
276 277 2.313172 GCATAGGCGATGGCAGACG 61.313 63.158 9.68 11.49 42.47 4.18
277 278 1.068083 CATAGGCGATGGCAGACGT 59.932 57.895 15.80 0.00 42.47 4.34
278 279 0.941463 CATAGGCGATGGCAGACGTC 60.941 60.000 7.70 7.70 42.47 4.34
306 307 4.440127 CGTTTGCCATGCTGCCCC 62.440 66.667 0.00 0.00 0.00 5.80
307 308 4.086547 GTTTGCCATGCTGCCCCC 62.087 66.667 0.00 0.00 0.00 5.40
308 309 4.635312 TTTGCCATGCTGCCCCCA 62.635 61.111 0.00 0.00 0.00 4.96
309 310 3.927817 TTTGCCATGCTGCCCCCAT 62.928 57.895 0.00 0.00 0.00 4.00
313 314 2.364579 CATGCTGCCCCCATGGTT 60.365 61.111 11.73 0.00 37.12 3.67
314 315 2.042639 ATGCTGCCCCCATGGTTC 60.043 61.111 11.73 0.00 36.04 3.62
315 316 3.684369 ATGCTGCCCCCATGGTTCC 62.684 63.158 11.73 0.00 36.04 3.62
317 318 4.820744 CTGCCCCCATGGTTCCCG 62.821 72.222 11.73 0.00 36.04 5.14
324 325 4.820744 CATGGTTCCCGCCCCCTG 62.821 72.222 0.00 0.00 0.00 4.45
326 327 3.954740 ATGGTTCCCGCCCCCTGTA 62.955 63.158 0.00 0.00 0.00 2.74
327 328 3.332385 GGTTCCCGCCCCCTGTAA 61.332 66.667 0.00 0.00 0.00 2.41
328 329 2.686572 GGTTCCCGCCCCCTGTAAT 61.687 63.158 0.00 0.00 0.00 1.89
329 330 1.453197 GTTCCCGCCCCCTGTAATG 60.453 63.158 0.00 0.00 0.00 1.90
330 331 1.926489 TTCCCGCCCCCTGTAATGT 60.926 57.895 0.00 0.00 0.00 2.71
331 332 1.917336 TTCCCGCCCCCTGTAATGTC 61.917 60.000 0.00 0.00 0.00 3.06
332 333 2.192175 CCGCCCCCTGTAATGTCC 59.808 66.667 0.00 0.00 0.00 4.02
333 334 2.675242 CCGCCCCCTGTAATGTCCA 61.675 63.158 0.00 0.00 0.00 4.02
334 335 1.531748 CGCCCCCTGTAATGTCCAT 59.468 57.895 0.00 0.00 0.00 3.41
335 336 0.819259 CGCCCCCTGTAATGTCCATG 60.819 60.000 0.00 0.00 0.00 3.66
336 337 0.550914 GCCCCCTGTAATGTCCATGA 59.449 55.000 0.00 0.00 0.00 3.07
337 338 1.477558 GCCCCCTGTAATGTCCATGAG 60.478 57.143 0.00 0.00 0.00 2.90
338 339 1.143684 CCCCCTGTAATGTCCATGAGG 59.856 57.143 0.00 0.00 0.00 3.86
339 340 1.477558 CCCCTGTAATGTCCATGAGGC 60.478 57.143 0.00 0.00 33.74 4.70
340 341 1.477558 CCCTGTAATGTCCATGAGGCC 60.478 57.143 0.00 0.00 33.74 5.19
341 342 1.586422 CTGTAATGTCCATGAGGCCG 58.414 55.000 0.00 0.00 33.74 6.13
342 343 1.138859 CTGTAATGTCCATGAGGCCGA 59.861 52.381 0.00 0.00 33.74 5.54
343 344 1.134521 TGTAATGTCCATGAGGCCGAC 60.135 52.381 0.00 0.00 33.74 4.79
366 367 1.206811 TCCACATCCAGCACCATCCA 61.207 55.000 0.00 0.00 0.00 3.41
367 368 0.106369 CCACATCCAGCACCATCCAT 60.106 55.000 0.00 0.00 0.00 3.41
368 369 1.143481 CCACATCCAGCACCATCCATA 59.857 52.381 0.00 0.00 0.00 2.74
369 370 2.224942 CCACATCCAGCACCATCCATAT 60.225 50.000 0.00 0.00 0.00 1.78
379 381 3.316308 GCACCATCCATATGACAAACTCC 59.684 47.826 3.65 0.00 34.84 3.85
396 398 2.027377 ACTCCGACGAGAAAGAGTAGGA 60.027 50.000 0.00 0.00 39.30 2.94
399 401 2.486982 CCGACGAGAAAGAGTAGGACAA 59.513 50.000 0.00 0.00 35.54 3.18
400 402 3.426426 CCGACGAGAAAGAGTAGGACAAG 60.426 52.174 0.00 0.00 35.54 3.16
401 403 3.426426 CGACGAGAAAGAGTAGGACAAGG 60.426 52.174 0.00 0.00 0.00 3.61
414 418 2.034066 CAAGGGACGTGGGCATGT 59.966 61.111 0.00 0.00 33.25 3.21
428 432 0.035152 GCATGTCTGGTGTCCCATGA 60.035 55.000 0.00 0.00 40.90 3.07
432 436 1.704628 TGTCTGGTGTCCCATGAACAT 59.295 47.619 0.00 0.00 40.90 2.71
490 494 6.020599 CACAACCGACGAAGATTTAGACTATG 60.021 42.308 0.00 0.00 0.00 2.23
493 497 7.325660 ACCGACGAAGATTTAGACTATGTTA 57.674 36.000 0.00 0.00 0.00 2.41
494 498 7.765307 ACCGACGAAGATTTAGACTATGTTAA 58.235 34.615 0.00 0.00 0.00 2.01
533 537 8.213812 CCGCTTTTGTTTAGTTGAAATATGTTG 58.786 33.333 0.00 0.00 0.00 3.33
595 601 3.979101 ATTTGCATGAAATTTCCCGGT 57.021 38.095 15.48 0.00 29.22 5.28
598 604 3.037431 TGCATGAAATTTCCCGGTTTG 57.963 42.857 15.48 5.20 0.00 2.93
602 608 3.357166 TGAAATTTCCCGGTTTGTTCG 57.643 42.857 15.48 0.00 0.00 3.95
657 663 1.304134 GGGGTTGAATGTCCGGCTT 60.304 57.895 0.00 0.00 0.00 4.35
671 677 0.320374 CGGCTTCCCTAACACTGTCA 59.680 55.000 0.00 0.00 0.00 3.58
673 679 1.623811 GGCTTCCCTAACACTGTCAGA 59.376 52.381 6.91 0.00 0.00 3.27
721 727 1.571215 CCGTTTTAGGGGTGTGCGTC 61.571 60.000 0.00 0.00 0.00 5.19
735 741 2.892640 CGTCGGAGATGCCCTGAA 59.107 61.111 0.00 0.00 40.67 3.02
814 823 3.209318 CCATGGGGCAAATGGTCG 58.791 61.111 2.85 0.00 39.87 4.79
823 961 1.632422 GCAAATGGTCGAATGCCTTG 58.368 50.000 0.00 0.00 32.73 3.61
962 1226 4.484872 GCACCGCCCTACCCCTTC 62.485 72.222 0.00 0.00 0.00 3.46
963 1227 2.687566 CACCGCCCTACCCCTTCT 60.688 66.667 0.00 0.00 0.00 2.85
964 1228 2.687566 ACCGCCCTACCCCTTCTG 60.688 66.667 0.00 0.00 0.00 3.02
1055 1326 2.282180 GCCGGCCAAGGAGACAAA 60.282 61.111 18.11 0.00 0.00 2.83
1131 1402 2.338620 CGTGAAGAGGTGCCGACA 59.661 61.111 0.00 0.00 0.00 4.35
1338 1609 3.518998 ACCCAGATCCTCGCGTCG 61.519 66.667 5.77 0.00 0.00 5.12
1433 1704 2.547855 CCTACATCGATTCCCGCATTGA 60.548 50.000 0.00 0.00 38.37 2.57
1671 1966 1.687368 GGAAAATGCAGCCTCCCTGAT 60.687 52.381 0.00 0.00 44.64 2.90
1737 2032 2.436539 CGACAGTGTCCGCATCACG 61.437 63.158 17.57 0.00 40.28 4.35
1857 2152 3.507622 CCCTTAGCCTTATAAGCATTGGC 59.492 47.826 6.99 5.81 43.52 4.52
2020 2315 1.457346 CTGCCTTTCTGATGTCACCC 58.543 55.000 0.00 0.00 0.00 4.61
2160 2455 1.065851 TCAATTGCAGTGCTGTGTGTG 59.934 47.619 17.60 6.12 0.00 3.82
2182 2477 5.572511 GTGCAAAAATCGCATATCACTTGAA 59.427 36.000 0.00 0.00 42.32 2.69
2190 2485 4.571984 TCGCATATCACTTGAATTGTCCAG 59.428 41.667 0.00 0.00 0.00 3.86
2226 2522 7.895759 TGTTTCTTTCATTCTTGATAAAGGGG 58.104 34.615 0.00 0.00 0.00 4.79
2259 2555 2.633657 CTGACAACGGCAGTGTGC 59.366 61.111 0.00 0.00 44.08 4.57
2372 2668 7.009179 TGTACATTCAGGTGAAGATTCTTCT 57.991 36.000 23.29 4.68 37.48 2.85
2463 2759 7.549488 TGGTTGGTTTTTAATTTGTCGATGTTT 59.451 29.630 0.00 0.00 0.00 2.83
2504 2800 0.943835 GGGAAAACAATGTGTGGCGC 60.944 55.000 0.00 0.00 0.00 6.53
2692 2988 1.233019 GAGTTCTTTGCAGAGCAGCA 58.767 50.000 0.00 0.00 40.61 4.41
2816 3112 7.548780 CGTGATTTGGGTTTAATTGATCCATTT 59.451 33.333 0.00 0.00 0.00 2.32
2988 3441 6.951062 TCACTAGGACTGACAGATTGATAG 57.049 41.667 10.08 6.46 0.00 2.08
3097 3555 6.510746 CATGCATGCATGTGAAATTTAGAG 57.489 37.500 40.30 18.96 46.20 2.43
3099 3557 3.484649 GCATGCATGTGAAATTTAGAGCG 59.515 43.478 26.79 0.00 0.00 5.03
3121 3579 4.093408 CGTTGTATGGCAGCATATATGGAC 59.907 45.833 14.51 1.52 0.00 4.02
3157 3615 2.470821 GTCGGGAATACTTGTCCATCG 58.529 52.381 0.00 0.00 36.83 3.84
3192 3739 7.782644 ACTATGATATATACTTGAGGAGGAGGC 59.217 40.741 0.00 0.00 0.00 4.70
3194 3741 2.750141 TATACTTGAGGAGGAGGCGT 57.250 50.000 0.00 0.00 0.00 5.68
3195 3742 1.867363 ATACTTGAGGAGGAGGCGTT 58.133 50.000 0.00 0.00 0.00 4.84
3198 3745 1.975680 ACTTGAGGAGGAGGCGTTTTA 59.024 47.619 0.00 0.00 0.00 1.52
3324 3871 6.161855 TGTCCAAGAGTGTATCATATCCAC 57.838 41.667 0.00 0.00 0.00 4.02
3432 3986 2.091541 ACACCCGTAATTTCCTGCATG 58.908 47.619 0.00 0.00 0.00 4.06
3491 4045 4.612412 GGTCGTTGGCCGTGGTCA 62.612 66.667 0.00 0.00 37.94 4.02
3513 4067 2.142292 AACCGCTGAGGCTTCCCATT 62.142 55.000 0.00 0.00 46.52 3.16
3514 4068 1.379044 CCGCTGAGGCTTCCCATTT 60.379 57.895 0.00 0.00 36.09 2.32
3515 4069 1.660560 CCGCTGAGGCTTCCCATTTG 61.661 60.000 0.00 0.00 36.09 2.32
3516 4070 1.514553 GCTGAGGCTTCCCATTTGC 59.485 57.895 0.00 0.00 35.22 3.68
3517 4071 1.953231 GCTGAGGCTTCCCATTTGCC 61.953 60.000 0.00 0.00 46.42 4.52
3559 4138 1.285280 ATCCGGGATCCAGTGAACAA 58.715 50.000 15.23 0.00 0.00 2.83
3609 4188 1.821136 GGTTCAGGCCATCTTTCCTTG 59.179 52.381 5.01 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.192844 TGGAGATTGTAGTGTTCGTCCTC 59.807 47.826 0.00 0.00 0.00 3.71
1 2 3.162666 TGGAGATTGTAGTGTTCGTCCT 58.837 45.455 0.00 0.00 0.00 3.85
3 4 2.924290 GCTGGAGATTGTAGTGTTCGTC 59.076 50.000 0.00 0.00 0.00 4.20
4 5 2.563179 AGCTGGAGATTGTAGTGTTCGT 59.437 45.455 0.00 0.00 0.00 3.85
5 6 3.119316 AGAGCTGGAGATTGTAGTGTTCG 60.119 47.826 0.00 0.00 0.00 3.95
6 7 4.464069 AGAGCTGGAGATTGTAGTGTTC 57.536 45.455 0.00 0.00 0.00 3.18
7 8 4.619394 CGAAGAGCTGGAGATTGTAGTGTT 60.619 45.833 0.00 0.00 0.00 3.32
8 9 3.119316 CGAAGAGCTGGAGATTGTAGTGT 60.119 47.826 0.00 0.00 0.00 3.55
9 10 3.129462 TCGAAGAGCTGGAGATTGTAGTG 59.871 47.826 0.00 0.00 0.00 2.74
10 11 3.129638 GTCGAAGAGCTGGAGATTGTAGT 59.870 47.826 0.00 0.00 36.95 2.73
11 12 3.701241 GTCGAAGAGCTGGAGATTGTAG 58.299 50.000 0.00 0.00 36.95 2.74
12 13 2.097629 CGTCGAAGAGCTGGAGATTGTA 59.902 50.000 0.00 0.00 36.95 2.41
13 14 1.135257 CGTCGAAGAGCTGGAGATTGT 60.135 52.381 0.00 0.00 36.95 2.71
14 15 1.133216 TCGTCGAAGAGCTGGAGATTG 59.867 52.381 0.00 0.00 36.95 2.67
15 16 1.403679 CTCGTCGAAGAGCTGGAGATT 59.596 52.381 15.39 0.00 36.95 2.40
16 17 1.021202 CTCGTCGAAGAGCTGGAGAT 58.979 55.000 15.39 0.00 36.95 2.75
17 18 2.472355 CTCGTCGAAGAGCTGGAGA 58.528 57.895 15.39 0.00 36.95 3.71
24 25 1.512310 GTCGGTGCTCGTCGAAGAG 60.512 63.158 22.11 22.11 36.95 2.85
25 26 1.909141 GAGTCGGTGCTCGTCGAAGA 61.909 60.000 0.03 0.03 40.32 2.87
26 27 1.512310 GAGTCGGTGCTCGTCGAAG 60.512 63.158 0.00 0.00 40.32 3.79
27 28 2.559840 GAGTCGGTGCTCGTCGAA 59.440 61.111 0.00 0.00 40.32 3.71
33 34 1.006571 TTTCCACGAGTCGGTGCTC 60.007 57.895 18.30 0.00 36.59 4.26
34 35 1.006102 CTTTCCACGAGTCGGTGCT 60.006 57.895 18.30 0.00 36.59 4.40
35 36 1.006571 TCTTTCCACGAGTCGGTGC 60.007 57.895 18.30 0.00 36.59 5.01
36 37 0.666577 GGTCTTTCCACGAGTCGGTG 60.667 60.000 18.30 12.17 37.66 4.94
37 38 1.111116 TGGTCTTTCCACGAGTCGGT 61.111 55.000 18.30 0.00 41.93 4.69
38 39 1.663739 TGGTCTTTCCACGAGTCGG 59.336 57.895 18.30 5.77 41.93 4.79
46 47 1.243902 GCCGACAATTGGTCTTTCCA 58.756 50.000 10.83 0.00 44.68 3.53
47 48 0.168128 CGCCGACAATTGGTCTTTCC 59.832 55.000 10.83 0.00 44.68 3.13
48 49 1.128692 CTCGCCGACAATTGGTCTTTC 59.871 52.381 10.83 0.00 44.68 2.62
49 50 1.156736 CTCGCCGACAATTGGTCTTT 58.843 50.000 10.83 0.00 44.68 2.52
50 51 1.298859 GCTCGCCGACAATTGGTCTT 61.299 55.000 10.83 0.00 44.68 3.01
51 52 1.741770 GCTCGCCGACAATTGGTCT 60.742 57.895 10.83 0.00 44.68 3.85
52 53 1.970917 CTGCTCGCCGACAATTGGTC 61.971 60.000 10.83 4.35 43.36 4.02
53 54 2.031919 TGCTCGCCGACAATTGGT 59.968 55.556 10.83 0.00 0.00 3.67
54 55 2.753966 CCTGCTCGCCGACAATTGG 61.754 63.158 10.83 0.00 0.00 3.16
55 56 2.787249 CCTGCTCGCCGACAATTG 59.213 61.111 3.24 3.24 0.00 2.32
56 57 3.127533 GCCTGCTCGCCGACAATT 61.128 61.111 0.00 0.00 0.00 2.32
65 66 4.753877 TCGTCGTTCGCCTGCTCG 62.754 66.667 0.00 0.00 39.67 5.03
66 67 2.202623 ATCGTCGTTCGCCTGCTC 60.203 61.111 0.00 0.00 39.67 4.26
67 68 2.507102 CATCGTCGTTCGCCTGCT 60.507 61.111 0.00 0.00 39.67 4.24
68 69 4.210304 GCATCGTCGTTCGCCTGC 62.210 66.667 0.00 11.27 39.32 4.85
69 70 3.554692 GGCATCGTCGTTCGCCTG 61.555 66.667 12.86 1.20 41.50 4.85
70 71 3.371097 ATGGCATCGTCGTTCGCCT 62.371 57.895 18.35 6.31 45.13 5.52
71 72 2.871427 GATGGCATCGTCGTTCGCC 61.871 63.158 12.40 13.13 45.11 5.54
72 73 2.164663 TGATGGCATCGTCGTTCGC 61.165 57.895 21.65 0.00 39.67 4.70
73 74 1.631072 GTGATGGCATCGTCGTTCG 59.369 57.895 21.65 0.00 41.41 3.95
74 75 1.631072 CGTGATGGCATCGTCGTTC 59.369 57.895 25.57 11.95 0.00 3.95
75 76 1.809619 CCGTGATGGCATCGTCGTT 60.810 57.895 28.75 0.00 0.00 3.85
76 77 2.202743 CCGTGATGGCATCGTCGT 60.203 61.111 28.75 0.39 0.00 4.34
85 86 2.896854 CGACCATGGCCGTGATGG 60.897 66.667 27.13 21.61 45.26 3.51
86 87 3.576356 GCGACCATGGCCGTGATG 61.576 66.667 27.13 15.55 0.00 3.07
92 93 3.757248 ATCCTTCGCGACCATGGCC 62.757 63.158 9.15 0.00 0.00 5.36
93 94 2.203070 ATCCTTCGCGACCATGGC 60.203 61.111 9.15 3.65 0.00 4.40
94 95 0.673985 TAGATCCTTCGCGACCATGG 59.326 55.000 9.15 11.19 0.00 3.66
95 96 1.336332 CCTAGATCCTTCGCGACCATG 60.336 57.143 9.15 0.00 0.00 3.66
96 97 0.962489 CCTAGATCCTTCGCGACCAT 59.038 55.000 9.15 0.00 0.00 3.55
97 98 1.735376 GCCTAGATCCTTCGCGACCA 61.735 60.000 9.15 0.00 0.00 4.02
98 99 1.007154 GCCTAGATCCTTCGCGACC 60.007 63.158 9.15 0.00 0.00 4.79
99 100 0.386113 AAGCCTAGATCCTTCGCGAC 59.614 55.000 9.15 0.00 0.00 5.19
100 101 0.669077 GAAGCCTAGATCCTTCGCGA 59.331 55.000 3.71 3.71 0.00 5.87
101 102 0.319125 GGAAGCCTAGATCCTTCGCG 60.319 60.000 0.00 0.00 38.62 5.87
102 103 1.044611 AGGAAGCCTAGATCCTTCGC 58.955 55.000 6.03 3.51 43.59 4.70
112 113 2.362397 CGTTGCTCATCTAGGAAGCCTA 59.638 50.000 8.73 0.00 36.04 3.93
113 114 1.137872 CGTTGCTCATCTAGGAAGCCT 59.862 52.381 8.73 0.00 36.04 4.58
114 115 1.137086 TCGTTGCTCATCTAGGAAGCC 59.863 52.381 8.73 0.00 36.04 4.35
115 116 2.468831 CTCGTTGCTCATCTAGGAAGC 58.531 52.381 5.34 5.34 36.04 3.86
116 117 2.468831 GCTCGTTGCTCATCTAGGAAG 58.531 52.381 0.00 0.00 36.04 3.46
117 118 1.202302 CGCTCGTTGCTCATCTAGGAA 60.202 52.381 0.00 0.00 40.11 3.36
118 119 0.382158 CGCTCGTTGCTCATCTAGGA 59.618 55.000 0.00 0.00 40.11 2.94
119 120 0.382158 TCGCTCGTTGCTCATCTAGG 59.618 55.000 0.00 0.00 40.11 3.02
120 121 2.049959 CATCGCTCGTTGCTCATCTAG 58.950 52.381 2.29 0.00 40.11 2.43
121 122 1.405463 ACATCGCTCGTTGCTCATCTA 59.595 47.619 0.79 0.00 40.11 1.98
122 123 0.174389 ACATCGCTCGTTGCTCATCT 59.826 50.000 0.79 0.00 40.11 2.90
123 124 1.518929 GTACATCGCTCGTTGCTCATC 59.481 52.381 0.79 0.00 40.11 2.92
124 125 1.560923 GTACATCGCTCGTTGCTCAT 58.439 50.000 0.79 0.00 40.11 2.90
125 126 0.457853 GGTACATCGCTCGTTGCTCA 60.458 55.000 0.00 0.00 40.11 4.26
126 127 0.457853 TGGTACATCGCTCGTTGCTC 60.458 55.000 0.00 0.00 40.11 4.26
127 128 0.458543 CTGGTACATCGCTCGTTGCT 60.459 55.000 0.00 0.00 38.20 3.91
128 129 0.736325 ACTGGTACATCGCTCGTTGC 60.736 55.000 0.00 0.00 38.20 4.17
129 130 1.269166 GACTGGTACATCGCTCGTTG 58.731 55.000 0.00 0.00 38.20 4.10
130 131 0.172803 GGACTGGTACATCGCTCGTT 59.827 55.000 0.00 0.00 38.20 3.85
131 132 0.963856 TGGACTGGTACATCGCTCGT 60.964 55.000 0.00 0.00 38.20 4.18
132 133 0.385751 ATGGACTGGTACATCGCTCG 59.614 55.000 0.00 0.00 38.20 5.03
133 134 1.137086 ACATGGACTGGTACATCGCTC 59.863 52.381 0.00 0.00 38.20 5.03
134 135 1.134699 CACATGGACTGGTACATCGCT 60.135 52.381 0.00 0.00 38.20 4.93
135 136 1.290203 CACATGGACTGGTACATCGC 58.710 55.000 0.00 0.00 38.20 4.58
136 137 2.672961 ACACATGGACTGGTACATCG 57.327 50.000 0.00 0.00 38.20 3.84
137 138 3.458189 GCTACACATGGACTGGTACATC 58.542 50.000 0.00 0.00 38.20 3.06
138 139 2.159099 CGCTACACATGGACTGGTACAT 60.159 50.000 0.00 0.00 38.20 2.29
139 140 1.203758 CGCTACACATGGACTGGTACA 59.796 52.381 0.00 0.00 0.00 2.90
140 141 1.922570 CGCTACACATGGACTGGTAC 58.077 55.000 0.00 0.00 0.00 3.34
141 142 0.174845 GCGCTACACATGGACTGGTA 59.825 55.000 0.00 0.00 0.00 3.25
142 143 1.079127 GCGCTACACATGGACTGGT 60.079 57.895 0.00 0.00 0.00 4.00
143 144 1.815421 GGCGCTACACATGGACTGG 60.815 63.158 7.64 0.00 0.00 4.00
144 145 1.815421 GGGCGCTACACATGGACTG 60.815 63.158 7.64 0.00 0.00 3.51
145 146 2.290287 TGGGCGCTACACATGGACT 61.290 57.895 7.64 0.00 0.00 3.85
146 147 2.106683 GTGGGCGCTACACATGGAC 61.107 63.158 23.99 2.85 38.67 4.02
147 148 2.267642 GTGGGCGCTACACATGGA 59.732 61.111 23.99 0.00 38.67 3.41
148 149 3.195002 CGTGGGCGCTACACATGG 61.195 66.667 26.62 12.98 38.74 3.66
149 150 2.125713 TCGTGGGCGCTACACATG 60.126 61.111 26.62 17.49 38.74 3.21
150 151 2.125673 GTCGTGGGCGCTACACAT 60.126 61.111 26.62 0.00 38.74 3.21
151 152 2.829043 GATGTCGTGGGCGCTACACA 62.829 60.000 26.62 20.87 38.74 3.72
152 153 2.125673 ATGTCGTGGGCGCTACAC 60.126 61.111 20.67 20.67 38.14 2.90
153 154 2.183300 GATGTCGTGGGCGCTACA 59.817 61.111 7.64 3.94 38.14 2.74
154 155 1.878522 CAGATGTCGTGGGCGCTAC 60.879 63.158 7.64 6.30 38.14 3.58
155 156 2.494445 CAGATGTCGTGGGCGCTA 59.506 61.111 7.64 0.00 38.14 4.26
158 159 4.758251 TGGCAGATGTCGTGGGCG 62.758 66.667 0.00 0.00 39.92 6.13
159 160 2.359850 TTGGCAGATGTCGTGGGC 60.360 61.111 0.00 0.00 0.00 5.36
160 161 0.742281 CTCTTGGCAGATGTCGTGGG 60.742 60.000 0.00 0.00 0.00 4.61
161 162 1.364626 GCTCTTGGCAGATGTCGTGG 61.365 60.000 0.00 0.00 41.35 4.94
162 163 1.690283 CGCTCTTGGCAGATGTCGTG 61.690 60.000 0.00 0.00 41.91 4.35
163 164 1.446792 CGCTCTTGGCAGATGTCGT 60.447 57.895 0.00 0.00 41.91 4.34
164 165 0.529337 ATCGCTCTTGGCAGATGTCG 60.529 55.000 0.00 0.00 41.91 4.35
165 166 0.935898 CATCGCTCTTGGCAGATGTC 59.064 55.000 5.71 0.00 41.85 3.06
166 167 0.463295 CCATCGCTCTTGGCAGATGT 60.463 55.000 11.33 0.00 43.43 3.06
167 168 0.463295 ACCATCGCTCTTGGCAGATG 60.463 55.000 6.68 6.68 43.95 2.90
168 169 0.463295 CACCATCGCTCTTGGCAGAT 60.463 55.000 0.00 0.00 41.91 2.90
169 170 1.078918 CACCATCGCTCTTGGCAGA 60.079 57.895 0.00 0.00 41.91 4.26
170 171 2.110967 CCACCATCGCTCTTGGCAG 61.111 63.158 0.00 0.00 41.91 4.85
171 172 2.046023 CCACCATCGCTCTTGGCA 60.046 61.111 0.00 0.00 41.91 4.92
173 174 2.110967 CAGCCACCATCGCTCTTGG 61.111 63.158 0.00 0.00 40.26 3.61
174 175 2.758089 GCAGCCACCATCGCTCTTG 61.758 63.158 0.00 0.00 33.17 3.02
175 176 2.437359 GCAGCCACCATCGCTCTT 60.437 61.111 0.00 0.00 33.17 2.85
176 177 4.827087 CGCAGCCACCATCGCTCT 62.827 66.667 0.00 0.00 33.17 4.09
192 193 4.570663 CTCCGCCCTTAGGACGCG 62.571 72.222 13.60 13.60 45.32 6.01
193 194 3.140225 CTCTCCGCCCTTAGGACGC 62.140 68.421 0.26 0.00 33.58 5.19
194 195 1.753463 ACTCTCCGCCCTTAGGACG 60.753 63.158 0.00 0.00 33.58 4.79
195 196 0.683504 TCACTCTCCGCCCTTAGGAC 60.684 60.000 0.00 0.00 33.58 3.85
196 197 0.683504 GTCACTCTCCGCCCTTAGGA 60.684 60.000 0.00 0.00 36.20 2.94
197 198 1.817209 GTCACTCTCCGCCCTTAGG 59.183 63.158 0.00 0.00 0.00 2.69
198 199 1.433879 CGTCACTCTCCGCCCTTAG 59.566 63.158 0.00 0.00 0.00 2.18
199 200 2.707849 GCGTCACTCTCCGCCCTTA 61.708 63.158 0.00 0.00 43.96 2.69
200 201 4.070552 GCGTCACTCTCCGCCCTT 62.071 66.667 0.00 0.00 43.96 3.95
205 206 0.460311 AAATAGGGCGTCACTCTCCG 59.540 55.000 0.00 0.00 0.00 4.63
206 207 1.941325 CAAATAGGGCGTCACTCTCC 58.059 55.000 0.00 0.00 0.00 3.71
207 208 1.291132 GCAAATAGGGCGTCACTCTC 58.709 55.000 0.00 0.00 0.00 3.20
208 209 3.460648 GCAAATAGGGCGTCACTCT 57.539 52.632 0.00 0.00 0.00 3.24
216 217 0.033504 TCGATCTCCGCAAATAGGGC 59.966 55.000 0.00 0.00 38.37 5.19
217 218 1.784525 GTCGATCTCCGCAAATAGGG 58.215 55.000 0.00 0.00 38.37 3.53
218 219 1.409412 CGTCGATCTCCGCAAATAGG 58.591 55.000 0.00 0.00 38.37 2.57
225 226 4.965858 CTCCGCGTCGATCTCCGC 62.966 72.222 4.92 13.85 46.10 5.54
226 227 4.315122 CCTCCGCGTCGATCTCCG 62.315 72.222 4.92 0.00 40.25 4.63
227 228 4.632458 GCCTCCGCGTCGATCTCC 62.632 72.222 4.92 0.00 0.00 3.71
228 229 3.815569 CTGCCTCCGCGTCGATCTC 62.816 68.421 4.92 0.00 38.08 2.75
229 230 3.893763 CTGCCTCCGCGTCGATCT 61.894 66.667 4.92 0.00 38.08 2.75
230 231 3.889044 TCTGCCTCCGCGTCGATC 61.889 66.667 4.92 0.00 38.08 3.69
231 232 4.194720 GTCTGCCTCCGCGTCGAT 62.195 66.667 4.92 0.00 38.08 3.59
234 235 3.736482 CTACGTCTGCCTCCGCGTC 62.736 68.421 4.92 0.00 38.56 5.19
235 236 3.812019 CTACGTCTGCCTCCGCGT 61.812 66.667 4.92 0.00 40.76 6.01
236 237 3.456431 CTCTACGTCTGCCTCCGCG 62.456 68.421 0.00 0.00 38.08 6.46
237 238 2.409651 CTCTACGTCTGCCTCCGC 59.590 66.667 0.00 0.00 0.00 5.54
238 239 1.440938 CTCCTCTACGTCTGCCTCCG 61.441 65.000 0.00 0.00 0.00 4.63
239 240 1.104577 CCTCCTCTACGTCTGCCTCC 61.105 65.000 0.00 0.00 0.00 4.30
240 241 1.730451 GCCTCCTCTACGTCTGCCTC 61.730 65.000 0.00 0.00 0.00 4.70
241 242 1.755008 GCCTCCTCTACGTCTGCCT 60.755 63.158 0.00 0.00 0.00 4.75
242 243 1.395826 ATGCCTCCTCTACGTCTGCC 61.396 60.000 0.00 0.00 0.00 4.85
243 244 1.268352 CTATGCCTCCTCTACGTCTGC 59.732 57.143 0.00 0.00 0.00 4.26
244 245 1.883275 CCTATGCCTCCTCTACGTCTG 59.117 57.143 0.00 0.00 0.00 3.51
245 246 1.820090 GCCTATGCCTCCTCTACGTCT 60.820 57.143 0.00 0.00 0.00 4.18
246 247 0.599060 GCCTATGCCTCCTCTACGTC 59.401 60.000 0.00 0.00 0.00 4.34
247 248 1.173444 CGCCTATGCCTCCTCTACGT 61.173 60.000 0.00 0.00 0.00 3.57
248 249 0.889638 TCGCCTATGCCTCCTCTACG 60.890 60.000 0.00 0.00 0.00 3.51
249 250 1.203523 CATCGCCTATGCCTCCTCTAC 59.796 57.143 0.00 0.00 0.00 2.59
250 251 1.550327 CATCGCCTATGCCTCCTCTA 58.450 55.000 0.00 0.00 0.00 2.43
251 252 1.190833 CCATCGCCTATGCCTCCTCT 61.191 60.000 0.00 0.00 33.92 3.69
252 253 1.294780 CCATCGCCTATGCCTCCTC 59.705 63.158 0.00 0.00 33.92 3.71
253 254 2.888447 GCCATCGCCTATGCCTCCT 61.888 63.158 0.00 0.00 33.92 3.69
254 255 2.359230 GCCATCGCCTATGCCTCC 60.359 66.667 0.00 0.00 33.92 4.30
255 256 1.670406 CTGCCATCGCCTATGCCTC 60.670 63.158 0.00 0.00 33.92 4.70
256 257 2.142761 TCTGCCATCGCCTATGCCT 61.143 57.895 0.00 0.00 33.92 4.75
257 258 1.963338 GTCTGCCATCGCCTATGCC 60.963 63.158 0.00 0.00 33.92 4.40
258 259 2.313172 CGTCTGCCATCGCCTATGC 61.313 63.158 0.00 0.00 33.92 3.14
259 260 0.941463 GACGTCTGCCATCGCCTATG 60.941 60.000 8.70 0.00 35.15 2.23
260 261 1.364171 GACGTCTGCCATCGCCTAT 59.636 57.895 8.70 0.00 0.00 2.57
261 262 2.805546 GACGTCTGCCATCGCCTA 59.194 61.111 8.70 0.00 0.00 3.93
262 263 4.498520 CGACGTCTGCCATCGCCT 62.499 66.667 14.70 0.00 0.00 5.52
296 297 2.364579 AACCATGGGGGCAGCATG 60.365 61.111 18.09 0.00 42.05 4.06
297 298 2.042639 GAACCATGGGGGCAGCAT 60.043 61.111 18.09 0.00 42.05 3.79
298 299 4.380945 GGAACCATGGGGGCAGCA 62.381 66.667 18.09 0.00 42.05 4.41
311 312 1.453197 CATTACAGGGGGCGGGAAC 60.453 63.158 0.00 0.00 0.00 3.62
312 313 1.917336 GACATTACAGGGGGCGGGAA 61.917 60.000 0.00 0.00 0.00 3.97
313 314 2.285818 ACATTACAGGGGGCGGGA 60.286 61.111 0.00 0.00 0.00 5.14
314 315 2.192175 GACATTACAGGGGGCGGG 59.808 66.667 0.00 0.00 0.00 6.13
315 316 1.994885 ATGGACATTACAGGGGGCGG 61.995 60.000 0.00 0.00 0.00 6.13
316 317 0.819259 CATGGACATTACAGGGGGCG 60.819 60.000 0.00 0.00 0.00 6.13
317 318 0.550914 TCATGGACATTACAGGGGGC 59.449 55.000 0.00 0.00 0.00 5.80
318 319 1.143684 CCTCATGGACATTACAGGGGG 59.856 57.143 0.00 0.00 33.53 5.40
319 320 1.477558 GCCTCATGGACATTACAGGGG 60.478 57.143 0.00 0.00 34.57 4.79
320 321 1.477558 GGCCTCATGGACATTACAGGG 60.478 57.143 0.00 0.00 42.34 4.45
321 322 1.811558 CGGCCTCATGGACATTACAGG 60.812 57.143 0.00 0.00 43.17 4.00
322 323 1.138859 TCGGCCTCATGGACATTACAG 59.861 52.381 0.00 0.00 43.17 2.74
323 324 1.134521 GTCGGCCTCATGGACATTACA 60.135 52.381 0.00 0.00 43.17 2.41
324 325 1.583054 GTCGGCCTCATGGACATTAC 58.417 55.000 0.00 0.00 43.17 1.89
325 326 0.468226 GGTCGGCCTCATGGACATTA 59.532 55.000 0.00 0.00 43.17 1.90
326 327 1.224592 GGTCGGCCTCATGGACATT 59.775 57.895 0.00 0.00 43.17 2.71
327 328 2.746375 GGGTCGGCCTCATGGACAT 61.746 63.158 5.77 0.00 43.17 3.06
328 329 3.399181 GGGTCGGCCTCATGGACA 61.399 66.667 5.77 0.00 43.17 4.02
329 330 4.530857 CGGGTCGGCCTCATGGAC 62.531 72.222 5.77 0.00 38.25 4.02
331 332 4.530857 GACGGGTCGGCCTCATGG 62.531 72.222 5.77 0.00 34.45 3.66
338 339 4.832608 GGATGTGGACGGGTCGGC 62.833 72.222 0.00 0.00 0.00 5.54
339 340 3.371097 CTGGATGTGGACGGGTCGG 62.371 68.421 0.00 0.00 0.00 4.79
340 341 2.184322 CTGGATGTGGACGGGTCG 59.816 66.667 0.00 0.00 0.00 4.79
341 342 2.125106 GCTGGATGTGGACGGGTC 60.125 66.667 0.00 0.00 0.00 4.46
342 343 2.927856 TGCTGGATGTGGACGGGT 60.928 61.111 0.00 0.00 0.00 5.28
343 344 2.436646 GTGCTGGATGTGGACGGG 60.437 66.667 0.00 0.00 0.00 5.28
366 367 4.713824 TTCTCGTCGGAGTTTGTCATAT 57.286 40.909 0.00 0.00 41.26 1.78
367 368 4.216902 TCTTTCTCGTCGGAGTTTGTCATA 59.783 41.667 0.00 0.00 41.26 2.15
368 369 3.005472 TCTTTCTCGTCGGAGTTTGTCAT 59.995 43.478 0.00 0.00 41.26 3.06
369 370 2.359848 TCTTTCTCGTCGGAGTTTGTCA 59.640 45.455 0.00 0.00 41.26 3.58
379 381 3.426426 CCTTGTCCTACTCTTTCTCGTCG 60.426 52.174 0.00 0.00 0.00 5.12
396 398 2.034066 CATGCCCACGTCCCTTGT 59.966 61.111 0.00 0.00 0.00 3.16
399 401 2.607750 AGACATGCCCACGTCCCT 60.608 61.111 0.00 0.00 32.33 4.20
400 402 2.436646 CAGACATGCCCACGTCCC 60.437 66.667 0.00 0.00 32.33 4.46
401 403 2.436646 CCAGACATGCCCACGTCC 60.437 66.667 0.00 0.00 32.33 4.79
428 432 0.324943 CGTCCTGTCTTCCCCATGTT 59.675 55.000 0.00 0.00 0.00 2.71
432 436 3.691342 CGCGTCCTGTCTTCCCCA 61.691 66.667 0.00 0.00 0.00 4.96
434 438 3.358076 CTCCGCGTCCTGTCTTCCC 62.358 68.421 4.92 0.00 0.00 3.97
533 537 8.831715 AAACCAGACCAAATCAATTACATTTC 57.168 30.769 0.00 0.00 0.00 2.17
546 551 9.114952 GGAAATTTTCATTTAAACCAGACCAAA 57.885 29.630 11.09 0.00 32.35 3.28
570 575 5.395103 CCGGGAAATTTCATGCAAATTAGGA 60.395 40.000 19.49 0.00 42.86 2.94
577 582 3.181461 ACAAACCGGGAAATTTCATGCAA 60.181 39.130 19.49 0.00 0.00 4.08
622 628 1.533625 CCCACACATCAAACGTCCAT 58.466 50.000 0.00 0.00 0.00 3.41
657 663 1.202964 TCCGTCTGACAGTGTTAGGGA 60.203 52.381 14.50 11.20 0.00 4.20
690 696 4.181578 CCCTAAAACGGACACAGTATCTG 58.818 47.826 0.00 0.00 37.52 2.90
696 702 1.202722 ACACCCCTAAAACGGACACAG 60.203 52.381 0.00 0.00 0.00 3.66
710 716 3.771160 ATCTCCGACGCACACCCC 61.771 66.667 0.00 0.00 0.00 4.95
721 727 1.019673 CACATTTCAGGGCATCTCCG 58.980 55.000 0.00 0.00 34.94 4.63
814 823 3.256631 ACAAACTGGTCATCAAGGCATTC 59.743 43.478 0.00 0.00 0.00 2.67
821 959 5.654650 ACAAGGTAAACAAACTGGTCATCAA 59.345 36.000 0.00 0.00 0.00 2.57
823 961 5.767816 ACAAGGTAAACAAACTGGTCATC 57.232 39.130 0.00 0.00 0.00 2.92
955 1219 3.330720 CCGGGAAGCAGAAGGGGT 61.331 66.667 0.00 0.00 0.00 4.95
958 1222 0.960861 GTTTCCCGGGAAGCAGAAGG 60.961 60.000 36.91 2.86 35.78 3.46
959 1223 0.960861 GGTTTCCCGGGAAGCAGAAG 60.961 60.000 40.14 7.30 37.13 2.85
960 1224 1.074248 GGTTTCCCGGGAAGCAGAA 59.926 57.895 40.14 23.72 37.13 3.02
961 1225 1.710996 TTGGTTTCCCGGGAAGCAGA 61.711 55.000 40.14 28.65 37.13 4.26
962 1226 0.825840 TTTGGTTTCCCGGGAAGCAG 60.826 55.000 40.14 9.56 37.13 4.24
963 1227 1.110518 GTTTGGTTTCCCGGGAAGCA 61.111 55.000 40.14 31.96 37.13 3.91
964 1228 1.663739 GTTTGGTTTCCCGGGAAGC 59.336 57.895 35.09 35.09 35.38 3.86
1433 1704 0.532573 AAGGATGTGCGAGATGACGT 59.467 50.000 0.00 0.00 35.59 4.34
1671 1966 0.036388 GAAGCCCTTGGACGATGTCA 60.036 55.000 0.00 0.00 33.68 3.58
1737 2032 1.739562 CCTGTGCAGCGAGAACTCC 60.740 63.158 0.00 0.00 0.00 3.85
1857 2152 1.004610 CAATAGCATTCAGGACGCACG 60.005 52.381 0.00 0.00 0.00 5.34
2020 2315 1.293924 CTCTCCGCAAATGTAGGCAG 58.706 55.000 0.00 0.00 0.00 4.85
2051 2346 3.064931 GAGTTACGAAACCCACCAGAAG 58.935 50.000 0.00 0.00 36.15 2.85
2160 2455 6.817270 ATTCAAGTGATATGCGATTTTTGC 57.183 33.333 0.00 0.00 0.00 3.68
2182 2477 4.240881 ACATTACTCATGCCTGGACAAT 57.759 40.909 0.00 0.00 36.14 2.71
2190 2485 7.542025 AGAATGAAAGAAACATTACTCATGCC 58.458 34.615 0.00 0.00 37.96 4.40
2226 2522 1.128692 GTCAGCTTATCAACACGTGGC 59.871 52.381 21.57 11.50 0.00 5.01
2257 2553 3.133691 CAGCTAAAGTCTTGACTGTGCA 58.866 45.455 17.84 0.00 0.00 4.57
2259 2555 5.289595 TGTACAGCTAAAGTCTTGACTGTG 58.710 41.667 18.67 4.12 38.70 3.66
2372 2668 6.152932 AGAACACAACTAAGAGTTACCGAA 57.847 37.500 0.00 0.00 36.03 4.30
2504 2800 1.347221 GAAATCGCGGTGCTTACGG 59.653 57.895 6.13 0.00 0.00 4.02
2517 2813 9.129532 AGGGATATCAAAACTTCTGATGAAATC 57.870 33.333 4.83 0.00 45.83 2.17
2816 3112 2.358582 CTGGTTTCAGTGTCAACATGCA 59.641 45.455 0.00 0.00 36.30 3.96
2905 3202 0.955428 TTCTTTGGCTGCAGCTACCG 60.955 55.000 35.82 23.06 41.70 4.02
2988 3441 9.547753 ACCATGATAAACTACAACAGATCATAC 57.452 33.333 0.00 0.00 33.40 2.39
3082 3540 6.688385 CCATACAACGCTCTAAATTTCACATG 59.312 38.462 0.00 0.00 0.00 3.21
3083 3541 6.677920 GCCATACAACGCTCTAAATTTCACAT 60.678 38.462 0.00 0.00 0.00 3.21
3084 3542 5.391523 GCCATACAACGCTCTAAATTTCACA 60.392 40.000 0.00 0.00 0.00 3.58
3085 3543 5.028375 GCCATACAACGCTCTAAATTTCAC 58.972 41.667 0.00 0.00 0.00 3.18
3097 3555 3.181507 CCATATATGCTGCCATACAACGC 60.182 47.826 7.24 0.00 36.79 4.84
3099 3557 4.093408 CGTCCATATATGCTGCCATACAAC 59.907 45.833 7.24 0.00 36.79 3.32
3121 3579 1.652124 CCGACGAAACAACATAGGACG 59.348 52.381 0.00 0.00 0.00 4.79
3324 3871 1.130955 GCAACATGAAAACACAGCCG 58.869 50.000 0.00 0.00 0.00 5.52
3432 3986 3.059352 ACATGTTCAGTAAGGCCACTC 57.941 47.619 5.01 0.00 0.00 3.51
3491 4045 1.078143 GGAAGCCTCAGCGGTTCAT 60.078 57.895 7.21 0.00 46.67 2.57
3513 4067 1.546923 CCACAGATTCTTGCATGGCAA 59.453 47.619 3.40 3.40 46.80 4.52
3514 4068 1.179152 CCACAGATTCTTGCATGGCA 58.821 50.000 0.00 0.00 36.47 4.92
3515 4069 0.179119 GCCACAGATTCTTGCATGGC 60.179 55.000 7.86 7.86 45.26 4.40
3516 4070 1.179152 TGCCACAGATTCTTGCATGG 58.821 50.000 0.00 0.00 0.00 3.66
3517 4071 3.057104 TCTTTGCCACAGATTCTTGCATG 60.057 43.478 0.00 0.00 0.00 4.06
3518 4072 3.159472 TCTTTGCCACAGATTCTTGCAT 58.841 40.909 0.00 0.00 0.00 3.96
3519 4073 2.585330 TCTTTGCCACAGATTCTTGCA 58.415 42.857 0.00 0.00 0.00 4.08
3531 4110 0.106719 GGATCCCGGATTCTTTGCCA 60.107 55.000 0.73 0.00 0.00 4.92
3559 4138 3.767711 GGGAATTCCTTCTTGGTCAAGT 58.232 45.455 23.63 0.00 36.66 3.16
3609 4188 3.243569 CCACAAGAGATATCCGACAGACC 60.244 52.174 0.00 0.00 0.00 3.85
3667 4248 2.727123 TCTCAACAGTTTCTGGCCAA 57.273 45.000 7.01 0.00 35.51 4.52
3668 4249 2.727123 TTCTCAACAGTTTCTGGCCA 57.273 45.000 4.71 4.71 35.51 5.36
3669 4250 4.279420 AGAAATTCTCAACAGTTTCTGGCC 59.721 41.667 0.00 0.00 38.92 5.36
3670 4251 5.444663 AGAAATTCTCAACAGTTTCTGGC 57.555 39.130 0.00 0.00 38.92 4.85
3672 4253 7.068341 CGAGAAGAAATTCTCAACAGTTTCTG 58.932 38.462 15.98 0.00 45.85 3.02
3674 4255 5.848559 GCGAGAAGAAATTCTCAACAGTTTC 59.151 40.000 15.98 0.00 45.85 2.78
3676 4257 4.816385 TGCGAGAAGAAATTCTCAACAGTT 59.184 37.500 15.98 0.00 45.85 3.16
3677 4258 4.380531 TGCGAGAAGAAATTCTCAACAGT 58.619 39.130 15.98 0.00 45.85 3.55
3678 4259 4.450419 ACTGCGAGAAGAAATTCTCAACAG 59.550 41.667 23.22 23.22 46.50 3.16
3679 4260 4.380531 ACTGCGAGAAGAAATTCTCAACA 58.619 39.130 15.98 12.32 45.85 3.33
3680 4261 4.999751 ACTGCGAGAAGAAATTCTCAAC 57.000 40.909 15.98 9.08 45.85 3.18
3681 4262 8.948631 AATATACTGCGAGAAGAAATTCTCAA 57.051 30.769 15.98 5.00 45.85 3.02
3793 4374 6.183361 GGTCCAGTCCTTCAGATAAATCAGAT 60.183 42.308 0.00 0.00 0.00 2.90
3799 4380 3.526899 TGGGTCCAGTCCTTCAGATAAA 58.473 45.455 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.