Multiple sequence alignment - TraesCS7D01G298000

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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 TraesCS7D01G298000 chr7D 100.000 3821 0 0 1 3821 376950387 376946567 0.000000e+00 7057.0
1 TraesCS7D01G298000 chr7D 93.333 105 5 2 3206 3309 588735168 588735065 1.840000e-33 154.0
2 TraesCS7D01G298000 chr7B 94.110 3226 148 10 292 3484 372040107 372036891 0.000000e+00 4867.0
3 TraesCS7D01G298000 chr7B 91.065 291 26 0 3531 3821 372036016 372035726 9.950000e-106 394.0
4 TraesCS7D01G298000 chr7B 88.353 249 20 3 1 242 372045965 372045719 1.340000e-74 291.0
5 TraesCS7D01G298000 chr7A 95.151 2557 90 10 899 3436 424551332 424548791 0.000000e+00 4004.0
6 TraesCS7D01G298000 chr7A 91.892 296 19 3 3531 3821 424548006 424547711 3.550000e-110 409.0
7 TraesCS7D01G298000 chr3D 82.553 705 77 17 2647 3332 524731969 524732646 2.560000e-161 579.0
8 TraesCS7D01G298000 chr4A 94.872 39 2 0 2672 2710 435613045 435613007 1.150000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G298000 chr7D 376946567 376950387 3820 True 7057.0 7057 100.0000 1 3821 1 chr7D.!!$R1 3820
1 TraesCS7D01G298000 chr7B 372035726 372040107 4381 True 2630.5 4867 92.5875 292 3821 2 chr7B.!!$R2 3529
2 TraesCS7D01G298000 chr7A 424547711 424551332 3621 True 2206.5 4004 93.5215 899 3821 2 chr7A.!!$R1 2922
3 TraesCS7D01G298000 chr3D 524731969 524732646 677 False 579.0 579 82.5530 2647 3332 1 chr3D.!!$F1 685

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
738 740 0.036765 TGCCCGTCGTTTCTAGCATT 60.037 50.0 0.0 0.0 0.00 3.56 F
944 962 0.179018 ACAGCAAAGAGGGTGTGGAC 60.179 55.0 0.0 0.0 46.76 4.02 F
1961 1982 0.531532 CACGGGCAGGAAGCTATCAG 60.532 60.0 0.0 0.0 44.79 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 1662 0.773644 ACACCCTCAAAGCATCACCT 59.226 50.0 0.0 0.0 0.0 4.00 R
2025 2046 0.956633 CAGTGTGGATGCAAGCAGTT 59.043 50.0 0.0 0.0 0.0 3.16 R
3726 4665 0.546122 AGTGGTGTGCTTTGAGGTCA 59.454 50.0 0.0 0.0 0.0 4.02 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 4.212213 CATTTGGCACATGTGGTTTTTG 57.788 40.909 26.55 0.09 39.30 2.44
22 23 3.340814 TTTGGCACATGTGGTTTTTGT 57.659 38.095 26.55 0.00 39.30 2.83
23 24 4.471904 TTTGGCACATGTGGTTTTTGTA 57.528 36.364 26.55 0.00 39.30 2.41
24 25 4.679373 TTGGCACATGTGGTTTTTGTAT 57.321 36.364 26.55 0.00 39.30 2.29
25 26 3.987547 TGGCACATGTGGTTTTTGTATG 58.012 40.909 26.55 0.00 0.00 2.39
26 27 3.244009 TGGCACATGTGGTTTTTGTATGG 60.244 43.478 26.55 0.00 0.00 2.74
27 28 2.736192 GCACATGTGGTTTTTGTATGGC 59.264 45.455 26.55 4.10 0.00 4.40
28 29 3.324993 CACATGTGGTTTTTGTATGGCC 58.675 45.455 18.51 0.00 0.00 5.36
29 30 2.968574 ACATGTGGTTTTTGTATGGCCA 59.031 40.909 8.56 8.56 0.00 5.36
30 31 3.389329 ACATGTGGTTTTTGTATGGCCAA 59.611 39.130 10.96 0.00 0.00 4.52
31 32 4.041444 ACATGTGGTTTTTGTATGGCCAAT 59.959 37.500 10.96 0.36 0.00 3.16
32 33 4.000331 TGTGGTTTTTGTATGGCCAATG 58.000 40.909 10.96 0.00 0.00 2.82
33 34 2.741517 GTGGTTTTTGTATGGCCAATGC 59.258 45.455 10.96 3.17 0.00 3.56
34 35 2.636893 TGGTTTTTGTATGGCCAATGCT 59.363 40.909 10.96 0.00 37.74 3.79
35 36 3.261580 GGTTTTTGTATGGCCAATGCTC 58.738 45.455 10.96 0.00 37.74 4.26
36 37 2.923020 GTTTTTGTATGGCCAATGCTCG 59.077 45.455 10.96 0.00 37.74 5.03
37 38 0.455410 TTTGTATGGCCAATGCTCGC 59.545 50.000 10.96 0.00 37.74 5.03
38 39 1.383456 TTGTATGGCCAATGCTCGCC 61.383 55.000 10.96 0.00 45.92 5.54
42 43 3.211963 GGCCAATGCTCGCCGATT 61.212 61.111 0.00 0.00 34.94 3.34
43 44 2.025156 GCCAATGCTCGCCGATTG 59.975 61.111 0.00 0.00 33.53 2.67
44 45 2.472059 GCCAATGCTCGCCGATTGA 61.472 57.895 0.73 0.00 32.24 2.57
45 46 1.353103 CCAATGCTCGCCGATTGAC 59.647 57.895 0.73 0.00 32.24 3.18
46 47 1.353103 CAATGCTCGCCGATTGACC 59.647 57.895 0.00 0.00 32.24 4.02
47 48 1.078497 AATGCTCGCCGATTGACCA 60.078 52.632 0.00 0.00 0.00 4.02
48 49 1.091771 AATGCTCGCCGATTGACCAG 61.092 55.000 0.00 0.00 0.00 4.00
49 50 3.567797 GCTCGCCGATTGACCAGC 61.568 66.667 0.00 0.00 0.00 4.85
50 51 2.892425 CTCGCCGATTGACCAGCC 60.892 66.667 0.00 0.00 0.00 4.85
51 52 4.467084 TCGCCGATTGACCAGCCC 62.467 66.667 0.00 0.00 0.00 5.19
52 53 4.776322 CGCCGATTGACCAGCCCA 62.776 66.667 0.00 0.00 0.00 5.36
53 54 2.361104 GCCGATTGACCAGCCCAA 60.361 61.111 0.00 0.00 0.00 4.12
54 55 2.700773 GCCGATTGACCAGCCCAAC 61.701 63.158 0.00 0.00 0.00 3.77
55 56 1.002134 CCGATTGACCAGCCCAACT 60.002 57.895 0.00 0.00 0.00 3.16
56 57 0.609131 CCGATTGACCAGCCCAACTT 60.609 55.000 0.00 0.00 0.00 2.66
57 58 1.247567 CGATTGACCAGCCCAACTTT 58.752 50.000 0.00 0.00 0.00 2.66
58 59 1.200020 CGATTGACCAGCCCAACTTTC 59.800 52.381 0.00 0.00 0.00 2.62
59 60 1.200020 GATTGACCAGCCCAACTTTCG 59.800 52.381 0.00 0.00 0.00 3.46
60 61 0.821711 TTGACCAGCCCAACTTTCGG 60.822 55.000 0.00 0.00 0.00 4.30
61 62 2.597510 ACCAGCCCAACTTTCGGC 60.598 61.111 0.00 0.00 46.09 5.54
66 67 3.053896 CCCAACTTTCGGCCGGTC 61.054 66.667 27.83 0.00 0.00 4.79
67 68 3.419759 CCAACTTTCGGCCGGTCG 61.420 66.667 25.52 25.52 0.00 4.79
68 69 4.084888 CAACTTTCGGCCGGTCGC 62.085 66.667 26.77 0.00 0.00 5.19
69 70 4.612412 AACTTTCGGCCGGTCGCA 62.612 61.111 26.77 11.43 40.31 5.10
70 71 3.894547 AACTTTCGGCCGGTCGCAT 62.895 57.895 26.77 5.57 40.31 4.73
71 72 3.564027 CTTTCGGCCGGTCGCATC 61.564 66.667 26.77 0.00 40.31 3.91
95 96 3.723348 GGCCGTTGCGTTGTCCTC 61.723 66.667 0.00 0.00 38.85 3.71
96 97 3.723348 GCCGTTGCGTTGTCCTCC 61.723 66.667 0.00 0.00 0.00 4.30
97 98 2.280524 CCGTTGCGTTGTCCTCCA 60.281 61.111 0.00 0.00 0.00 3.86
98 99 1.890041 CCGTTGCGTTGTCCTCCAA 60.890 57.895 0.00 0.00 0.00 3.53
104 105 3.946907 GTTGTCCTCCAACCGTCG 58.053 61.111 0.00 0.00 46.39 5.12
105 106 1.666872 GTTGTCCTCCAACCGTCGG 60.667 63.158 10.48 10.48 46.39 4.79
106 107 1.833492 TTGTCCTCCAACCGTCGGA 60.833 57.895 20.51 0.00 0.00 4.55
107 108 1.189524 TTGTCCTCCAACCGTCGGAT 61.190 55.000 20.51 2.18 0.00 4.18
108 109 1.189524 TGTCCTCCAACCGTCGGATT 61.190 55.000 20.51 5.75 0.00 3.01
109 110 0.819582 GTCCTCCAACCGTCGGATTA 59.180 55.000 20.51 0.00 0.00 1.75
110 111 1.108776 TCCTCCAACCGTCGGATTAG 58.891 55.000 20.51 9.26 0.00 1.73
111 112 0.104304 CCTCCAACCGTCGGATTAGG 59.896 60.000 20.51 14.36 0.00 2.69
112 113 0.104304 CTCCAACCGTCGGATTAGGG 59.896 60.000 20.51 11.24 0.00 3.53
113 114 1.523032 CCAACCGTCGGATTAGGGC 60.523 63.158 20.51 0.00 0.00 5.19
114 115 1.523032 CAACCGTCGGATTAGGGCC 60.523 63.158 20.51 0.00 0.00 5.80
115 116 2.738938 AACCGTCGGATTAGGGCCC 61.739 63.158 20.51 16.46 0.00 5.80
116 117 3.158648 CCGTCGGATTAGGGCCCA 61.159 66.667 27.56 3.72 0.00 5.36
117 118 2.516888 CCGTCGGATTAGGGCCCAT 61.517 63.158 27.56 10.04 0.00 4.00
118 119 1.450211 CGTCGGATTAGGGCCCATT 59.550 57.895 27.56 6.67 0.00 3.16
119 120 0.602905 CGTCGGATTAGGGCCCATTC 60.603 60.000 27.56 17.09 0.00 2.67
120 121 0.765510 GTCGGATTAGGGCCCATTCT 59.234 55.000 27.56 5.28 0.00 2.40
121 122 1.143073 GTCGGATTAGGGCCCATTCTT 59.857 52.381 27.56 4.81 0.00 2.52
122 123 1.420138 TCGGATTAGGGCCCATTCTTC 59.580 52.381 27.56 12.88 0.00 2.87
123 124 1.142870 CGGATTAGGGCCCATTCTTCA 59.857 52.381 27.56 0.00 0.00 3.02
124 125 2.224867 CGGATTAGGGCCCATTCTTCAT 60.225 50.000 27.56 2.06 0.00 2.57
125 126 3.425659 GGATTAGGGCCCATTCTTCATC 58.574 50.000 27.56 13.15 0.00 2.92
126 127 3.425659 GATTAGGGCCCATTCTTCATCC 58.574 50.000 27.56 0.00 0.00 3.51
127 128 1.905839 TAGGGCCCATTCTTCATCCA 58.094 50.000 27.56 0.00 0.00 3.41
128 129 1.238615 AGGGCCCATTCTTCATCCAT 58.761 50.000 27.56 0.00 0.00 3.41
129 130 1.577242 AGGGCCCATTCTTCATCCATT 59.423 47.619 27.56 0.00 0.00 3.16
130 131 2.022722 AGGGCCCATTCTTCATCCATTT 60.023 45.455 27.56 0.00 0.00 2.32
131 132 2.366590 GGGCCCATTCTTCATCCATTTC 59.633 50.000 19.95 0.00 0.00 2.17
132 133 2.035066 GGCCCATTCTTCATCCATTTCG 59.965 50.000 0.00 0.00 0.00 3.46
133 134 2.689983 GCCCATTCTTCATCCATTTCGT 59.310 45.455 0.00 0.00 0.00 3.85
134 135 3.489738 GCCCATTCTTCATCCATTTCGTG 60.490 47.826 0.00 0.00 0.00 4.35
163 164 4.582701 TTTTCTCAAATCATGCAACCGT 57.417 36.364 0.00 0.00 0.00 4.83
164 165 3.557577 TTCTCAAATCATGCAACCGTG 57.442 42.857 0.00 0.00 0.00 4.94
165 166 2.503331 TCTCAAATCATGCAACCGTGT 58.497 42.857 0.00 0.00 0.00 4.49
166 167 2.226200 TCTCAAATCATGCAACCGTGTG 59.774 45.455 0.00 0.00 0.00 3.82
167 168 1.952990 TCAAATCATGCAACCGTGTGT 59.047 42.857 0.00 0.00 0.00 3.72
168 169 3.142174 TCAAATCATGCAACCGTGTGTA 58.858 40.909 0.00 0.00 0.00 2.90
169 170 3.188254 TCAAATCATGCAACCGTGTGTAG 59.812 43.478 0.00 0.00 0.00 2.74
170 171 1.737838 ATCATGCAACCGTGTGTAGG 58.262 50.000 0.00 0.00 0.00 3.18
171 172 0.682292 TCATGCAACCGTGTGTAGGA 59.318 50.000 0.00 0.00 0.00 2.94
172 173 1.078709 CATGCAACCGTGTGTAGGAG 58.921 55.000 0.00 0.00 0.00 3.69
173 174 0.973632 ATGCAACCGTGTGTAGGAGA 59.026 50.000 0.00 0.00 0.00 3.71
174 175 0.317160 TGCAACCGTGTGTAGGAGAG 59.683 55.000 0.00 0.00 0.00 3.20
175 176 0.389948 GCAACCGTGTGTAGGAGAGG 60.390 60.000 0.00 0.00 0.00 3.69
176 177 0.246635 CAACCGTGTGTAGGAGAGGG 59.753 60.000 0.00 0.00 0.00 4.30
177 178 0.113776 AACCGTGTGTAGGAGAGGGA 59.886 55.000 0.00 0.00 0.00 4.20
178 179 0.113776 ACCGTGTGTAGGAGAGGGAA 59.886 55.000 0.00 0.00 0.00 3.97
179 180 1.263356 CCGTGTGTAGGAGAGGGAAA 58.737 55.000 0.00 0.00 0.00 3.13
180 181 1.204941 CCGTGTGTAGGAGAGGGAAAG 59.795 57.143 0.00 0.00 0.00 2.62
181 182 2.168496 CGTGTGTAGGAGAGGGAAAGA 58.832 52.381 0.00 0.00 0.00 2.52
182 183 2.164624 CGTGTGTAGGAGAGGGAAAGAG 59.835 54.545 0.00 0.00 0.00 2.85
183 184 3.166679 GTGTGTAGGAGAGGGAAAGAGT 58.833 50.000 0.00 0.00 0.00 3.24
184 185 3.056465 GTGTGTAGGAGAGGGAAAGAGTG 60.056 52.174 0.00 0.00 0.00 3.51
185 186 3.181422 TGTGTAGGAGAGGGAAAGAGTGA 60.181 47.826 0.00 0.00 0.00 3.41
186 187 3.193903 GTGTAGGAGAGGGAAAGAGTGAC 59.806 52.174 0.00 0.00 0.00 3.67
187 188 2.704190 AGGAGAGGGAAAGAGTGACA 57.296 50.000 0.00 0.00 0.00 3.58
188 189 2.977808 AGGAGAGGGAAAGAGTGACAA 58.022 47.619 0.00 0.00 0.00 3.18
189 190 3.525862 AGGAGAGGGAAAGAGTGACAAT 58.474 45.455 0.00 0.00 0.00 2.71
190 191 3.262915 AGGAGAGGGAAAGAGTGACAATG 59.737 47.826 0.00 0.00 0.00 2.82
191 192 3.261897 GGAGAGGGAAAGAGTGACAATGA 59.738 47.826 0.00 0.00 0.00 2.57
192 193 4.502962 GAGAGGGAAAGAGTGACAATGAG 58.497 47.826 0.00 0.00 0.00 2.90
193 194 3.006247 GAGGGAAAGAGTGACAATGAGC 58.994 50.000 0.00 0.00 0.00 4.26
194 195 1.734465 GGGAAAGAGTGACAATGAGCG 59.266 52.381 0.00 0.00 0.00 5.03
195 196 1.129437 GGAAAGAGTGACAATGAGCGC 59.871 52.381 0.00 0.00 0.00 5.92
196 197 1.129437 GAAAGAGTGACAATGAGCGCC 59.871 52.381 2.29 0.00 0.00 6.53
197 198 1.016130 AAGAGTGACAATGAGCGCCG 61.016 55.000 2.29 0.00 0.00 6.46
198 199 3.088500 GAGTGACAATGAGCGCCGC 62.089 63.158 2.29 0.00 0.00 6.53
199 200 3.121030 GTGACAATGAGCGCCGCT 61.121 61.111 13.40 13.40 43.88 5.52
200 201 3.120385 TGACAATGAGCGCCGCTG 61.120 61.111 20.07 5.17 39.88 5.18
201 202 2.815211 GACAATGAGCGCCGCTGA 60.815 61.111 20.07 9.32 39.88 4.26
202 203 3.088500 GACAATGAGCGCCGCTGAC 62.089 63.158 20.07 2.84 39.88 3.51
203 204 3.869272 CAATGAGCGCCGCTGACC 61.869 66.667 20.07 1.91 39.88 4.02
215 216 3.402681 CTGACCGTCCTGGCCCAT 61.403 66.667 0.00 0.00 43.94 4.00
216 217 3.391665 CTGACCGTCCTGGCCCATC 62.392 68.421 0.00 0.00 43.94 3.51
217 218 4.176752 GACCGTCCTGGCCCATCC 62.177 72.222 0.00 0.00 43.94 3.51
219 220 3.492353 CCGTCCTGGCCCATCCAT 61.492 66.667 0.00 0.00 45.50 3.41
220 221 2.203252 CGTCCTGGCCCATCCATG 60.203 66.667 0.00 0.00 45.50 3.66
221 222 2.196776 GTCCTGGCCCATCCATGG 59.803 66.667 4.97 4.97 45.50 3.66
230 231 4.131376 CATCCATGGACACGAGGC 57.869 61.111 18.99 0.00 0.00 4.70
231 232 1.524621 CATCCATGGACACGAGGCC 60.525 63.158 18.99 0.00 0.00 5.19
232 233 1.690633 ATCCATGGACACGAGGCCT 60.691 57.895 18.99 3.86 0.00 5.19
233 234 1.690219 ATCCATGGACACGAGGCCTC 61.690 60.000 23.79 23.79 0.00 4.70
242 243 3.550656 CGAGGCCTCGTTGTTGAC 58.449 61.111 40.77 9.64 46.99 3.18
243 244 1.300620 CGAGGCCTCGTTGTTGACA 60.301 57.895 40.77 0.00 46.99 3.58
244 245 0.878523 CGAGGCCTCGTTGTTGACAA 60.879 55.000 40.77 0.00 46.99 3.18
245 246 1.523758 GAGGCCTCGTTGTTGACAAT 58.476 50.000 19.06 0.00 38.24 2.71
246 247 1.464997 GAGGCCTCGTTGTTGACAATC 59.535 52.381 19.06 0.00 38.24 2.67
247 248 1.202758 AGGCCTCGTTGTTGACAATCA 60.203 47.619 0.00 0.00 38.24 2.57
248 249 1.812571 GGCCTCGTTGTTGACAATCAT 59.187 47.619 0.00 0.00 38.24 2.45
249 250 2.414559 GGCCTCGTTGTTGACAATCATG 60.415 50.000 0.00 0.00 38.24 3.07
250 251 2.855180 CCTCGTTGTTGACAATCATGC 58.145 47.619 0.00 0.00 38.24 4.06
251 252 2.226200 CCTCGTTGTTGACAATCATGCA 59.774 45.455 0.00 0.00 38.24 3.96
252 253 3.304592 CCTCGTTGTTGACAATCATGCAA 60.305 43.478 0.00 0.00 38.24 4.08
253 254 3.626977 TCGTTGTTGACAATCATGCAAC 58.373 40.909 12.75 12.75 40.67 4.17
254 255 3.314913 TCGTTGTTGACAATCATGCAACT 59.685 39.130 17.11 0.00 40.78 3.16
255 256 3.422876 CGTTGTTGACAATCATGCAACTG 59.577 43.478 17.11 11.04 40.78 3.16
256 257 4.362279 GTTGTTGACAATCATGCAACTGT 58.638 39.130 12.42 0.00 40.78 3.55
257 258 3.967401 TGTTGACAATCATGCAACTGTG 58.033 40.909 12.42 0.00 40.78 3.66
258 259 3.243468 TGTTGACAATCATGCAACTGTGG 60.243 43.478 12.42 0.00 40.78 4.17
259 260 2.861274 TGACAATCATGCAACTGTGGA 58.139 42.857 0.00 0.00 0.00 4.02
260 261 3.423749 TGACAATCATGCAACTGTGGAT 58.576 40.909 0.00 0.00 35.97 3.41
271 272 4.637483 CAACTGTGGATGAGTTGTTGTT 57.363 40.909 0.00 0.00 43.55 2.83
272 273 4.601019 CAACTGTGGATGAGTTGTTGTTC 58.399 43.478 0.00 0.00 43.55 3.18
273 274 3.214328 ACTGTGGATGAGTTGTTGTTCC 58.786 45.455 0.00 0.00 0.00 3.62
274 275 2.217750 TGTGGATGAGTTGTTGTTCCG 58.782 47.619 0.00 0.00 0.00 4.30
275 276 2.158885 TGTGGATGAGTTGTTGTTCCGA 60.159 45.455 0.00 0.00 0.00 4.55
276 277 2.223377 GTGGATGAGTTGTTGTTCCGAC 59.777 50.000 0.00 0.00 0.00 4.79
277 278 2.158885 TGGATGAGTTGTTGTTCCGACA 60.159 45.455 0.00 0.00 0.00 4.35
278 279 3.074412 GGATGAGTTGTTGTTCCGACAT 58.926 45.455 0.00 0.00 35.29 3.06
279 280 3.502211 GGATGAGTTGTTGTTCCGACATT 59.498 43.478 0.00 0.00 35.29 2.71
280 281 3.961477 TGAGTTGTTGTTCCGACATTG 57.039 42.857 0.00 0.00 35.29 2.82
281 282 2.032799 TGAGTTGTTGTTCCGACATTGC 59.967 45.455 0.00 0.00 35.29 3.56
282 283 2.020720 AGTTGTTGTTCCGACATTGCA 58.979 42.857 0.00 0.00 35.29 4.08
283 284 2.622942 AGTTGTTGTTCCGACATTGCAT 59.377 40.909 0.00 0.00 35.29 3.96
284 285 3.818210 AGTTGTTGTTCCGACATTGCATA 59.182 39.130 0.00 0.00 35.29 3.14
285 286 4.277174 AGTTGTTGTTCCGACATTGCATAA 59.723 37.500 0.00 0.00 35.29 1.90
286 287 4.153958 TGTTGTTCCGACATTGCATAAC 57.846 40.909 0.00 0.00 35.29 1.89
287 288 3.160545 GTTGTTCCGACATTGCATAACG 58.839 45.455 0.00 0.00 35.29 3.18
288 289 2.418692 TGTTCCGACATTGCATAACGT 58.581 42.857 0.00 0.00 0.00 3.99
289 290 3.586892 TGTTCCGACATTGCATAACGTA 58.413 40.909 0.00 0.00 0.00 3.57
290 291 3.615056 TGTTCCGACATTGCATAACGTAG 59.385 43.478 0.00 0.00 0.00 3.51
294 295 3.002246 CCGACATTGCATAACGTAGCATT 59.998 43.478 10.46 5.39 40.94 3.56
302 303 2.357327 TAACGTAGCATTGTGAGCGT 57.643 45.000 0.00 0.00 37.01 5.07
361 362 3.071206 TGCCCTCGCTCTGGTCTC 61.071 66.667 0.00 0.00 35.36 3.36
368 369 3.462678 GCTCTGGTCTCCCGGGTC 61.463 72.222 22.86 12.28 37.74 4.46
403 404 3.358707 TGAGCATCACAGCAAAACAAG 57.641 42.857 0.00 0.00 42.56 3.16
404 405 2.056577 GAGCATCACAGCAAAACAAGC 58.943 47.619 0.00 0.00 36.85 4.01
409 410 0.929824 CACAGCAAAACAAGCCGTCG 60.930 55.000 0.00 0.00 0.00 5.12
410 411 1.370414 CAGCAAAACAAGCCGTCGG 60.370 57.895 6.99 6.99 0.00 4.79
457 458 2.421314 CATCGCGATGCCACCCTA 59.579 61.111 33.70 0.00 31.39 3.53
463 464 1.739667 CGATGCCACCCTATCGTCA 59.260 57.895 0.00 0.00 40.79 4.35
466 467 1.344438 GATGCCACCCTATCGTCATCA 59.656 52.381 0.00 0.00 32.80 3.07
469 470 1.134521 GCCACCCTATCGTCATCACAA 60.135 52.381 0.00 0.00 0.00 3.33
474 475 3.450817 ACCCTATCGTCATCACAACATCA 59.549 43.478 0.00 0.00 0.00 3.07
480 481 3.066380 CGTCATCACAACATCACTTCCA 58.934 45.455 0.00 0.00 0.00 3.53
490 491 5.047802 ACAACATCACTTCCATTGGCTAAAG 60.048 40.000 0.00 0.00 0.00 1.85
493 494 5.954150 ACATCACTTCCATTGGCTAAAGAAT 59.046 36.000 9.06 1.47 0.00 2.40
498 499 8.303876 TCACTTCCATTGGCTAAAGAATAAAAC 58.696 33.333 9.06 0.00 0.00 2.43
540 541 3.622060 AACGGCTCCAACATCCCCG 62.622 63.158 0.00 0.00 44.19 5.73
552 553 2.367202 ATCCCCGTCACCGATTGCT 61.367 57.895 0.00 0.00 35.63 3.91
598 600 1.705337 AATCGCATCGCCGGTTGAAG 61.705 55.000 1.90 0.00 29.06 3.02
599 601 2.852495 ATCGCATCGCCGGTTGAAGT 62.852 55.000 1.90 0.00 0.00 3.01
607 609 1.064952 CGCCGGTTGAAGTTTTTCTGT 59.935 47.619 1.90 0.00 34.31 3.41
609 611 2.098443 GCCGGTTGAAGTTTTTCTGTCA 59.902 45.455 1.90 0.00 34.31 3.58
620 622 2.957402 TTTCTGTCACATCTTGCCCT 57.043 45.000 0.00 0.00 0.00 5.19
670 672 4.320494 CGCTACCATTTGAAGCTTTTCTGT 60.320 41.667 0.00 0.00 34.03 3.41
672 674 4.228912 ACCATTTGAAGCTTTTCTGTCG 57.771 40.909 0.00 0.00 0.00 4.35
675 677 0.586319 TTGAAGCTTTTCTGTCGCCG 59.414 50.000 0.00 0.00 0.00 6.46
676 678 0.249699 TGAAGCTTTTCTGTCGCCGA 60.250 50.000 0.00 0.00 0.00 5.54
681 683 1.730064 GCTTTTCTGTCGCCGATTACA 59.270 47.619 0.00 0.00 0.00 2.41
687 689 2.031069 TCTGTCGCCGATTACAGCTATC 60.031 50.000 0.00 0.00 42.31 2.08
690 692 1.810755 TCGCCGATTACAGCTATCGAT 59.189 47.619 16.98 2.16 45.79 3.59
696 698 4.419280 CGATTACAGCTATCGATGATGCT 58.581 43.478 11.15 11.93 45.79 3.79
712 714 1.004918 GCTAGTGGCGTGTTCCAGT 60.005 57.895 0.00 0.00 42.21 4.00
717 719 3.637273 GGCGTGTTCCAGTCCCCT 61.637 66.667 0.00 0.00 0.00 4.79
718 720 2.358737 GCGTGTTCCAGTCCCCTG 60.359 66.667 0.00 0.00 38.50 4.45
726 728 4.394712 CAGTCCCCTGTGCCCGTC 62.395 72.222 0.00 0.00 33.80 4.79
737 739 0.739813 GTGCCCGTCGTTTCTAGCAT 60.740 55.000 0.00 0.00 32.11 3.79
738 740 0.036765 TGCCCGTCGTTTCTAGCATT 60.037 50.000 0.00 0.00 0.00 3.56
753 755 5.491070 TCTAGCATTGTGAGCTGTGTAAAT 58.509 37.500 0.00 0.00 43.33 1.40
760 762 3.007290 TGTGAGCTGTGTAAATGAGAGCT 59.993 43.478 0.00 0.00 42.69 4.09
761 763 4.220602 TGTGAGCTGTGTAAATGAGAGCTA 59.779 41.667 0.00 0.00 40.09 3.32
763 765 4.220602 TGAGCTGTGTAAATGAGAGCTACA 59.779 41.667 0.00 0.00 40.09 2.74
797 799 5.107109 TCGATGCCCGATTTAAATCATTG 57.893 39.130 24.23 15.41 43.23 2.82
798 800 3.670055 CGATGCCCGATTTAAATCATTGC 59.330 43.478 24.23 21.38 41.76 3.56
840 842 4.413189 ACACCAACCATATCATCATCCTCA 59.587 41.667 0.00 0.00 0.00 3.86
862 864 4.678287 CACATGTGAGAACATTTGCTTGAC 59.322 41.667 21.64 0.00 0.00 3.18
897 899 2.828520 TCACCAAAAGCAAAGAACACCA 59.171 40.909 0.00 0.00 0.00 4.17
944 962 0.179018 ACAGCAAAGAGGGTGTGGAC 60.179 55.000 0.00 0.00 46.76 4.02
945 963 1.071471 AGCAAAGAGGGTGTGGACG 59.929 57.895 0.00 0.00 0.00 4.79
987 1008 2.043953 GTTCCCCATGCCTGTCCC 60.044 66.667 0.00 0.00 0.00 4.46
1239 1260 0.888619 TCTCCTACAACACGCTCCTG 59.111 55.000 0.00 0.00 0.00 3.86
1500 1521 3.382832 CCCGACAAGGAGGACGCT 61.383 66.667 0.00 0.00 45.00 5.07
1501 1522 2.657237 CCGACAAGGAGGACGCTT 59.343 61.111 0.00 0.00 45.00 4.68
1581 1602 1.283321 GAGTTCTTCCAGGGAATGCCT 59.717 52.381 0.39 0.00 33.28 4.75
1599 1620 2.230660 CCTGTGAGGAACTTGGTTTCC 58.769 52.381 0.00 0.00 44.96 3.13
1641 1662 2.414058 ATGTCAAAAATTCACGCGCA 57.586 40.000 5.73 0.00 0.00 6.09
1643 1664 1.052287 GTCAAAAATTCACGCGCAGG 58.948 50.000 5.73 0.00 0.00 4.85
1961 1982 0.531532 CACGGGCAGGAAGCTATCAG 60.532 60.000 0.00 0.00 44.79 2.90
1963 1984 1.228094 GGGCAGGAAGCTATCAGCC 60.228 63.158 12.30 12.30 43.77 4.85
1979 2000 5.640189 ATCAGCCTGTTTGAAAAGATGAG 57.360 39.130 0.00 0.00 0.00 2.90
2025 2046 7.172342 ACTGGATTACTTTTGTGGCAGTATTA 58.828 34.615 0.00 0.00 0.00 0.98
2106 2127 1.404391 GAAATCTACGGAGTCGAGCCA 59.596 52.381 0.00 0.00 43.93 4.75
2268 2289 2.910688 AGAACTCGGAGTTTGCTGAA 57.089 45.000 23.17 0.00 38.80 3.02
2346 2367 4.207635 CAGTTGGCAAATATTTATGCTGCG 59.792 41.667 0.00 0.00 42.20 5.18
2400 2421 3.070018 GAGGTGGATGAAGGATAATGCG 58.930 50.000 0.00 0.00 0.00 4.73
2847 2868 4.980573 AGCCAGTAACAAGGTTTGATGTA 58.019 39.130 0.00 0.00 0.00 2.29
2848 2869 5.570320 AGCCAGTAACAAGGTTTGATGTAT 58.430 37.500 0.00 0.00 0.00 2.29
2849 2870 6.717289 AGCCAGTAACAAGGTTTGATGTATA 58.283 36.000 0.00 0.00 0.00 1.47
2850 2871 6.598064 AGCCAGTAACAAGGTTTGATGTATAC 59.402 38.462 0.00 0.00 0.00 1.47
2852 2873 7.414098 GCCAGTAACAAGGTTTGATGTATACTG 60.414 40.741 4.17 14.37 38.74 2.74
2853 2874 7.065803 CCAGTAACAAGGTTTGATGTATACTGG 59.934 40.741 20.05 20.05 43.95 4.00
2854 2875 5.897377 AACAAGGTTTGATGTATACTGGC 57.103 39.130 4.17 0.00 0.00 4.85
2972 3022 5.591067 TGGTTTCTTAGTGTTGTTACTTGGG 59.409 40.000 0.00 0.00 32.19 4.12
2985 3035 1.484038 ACTTGGGCAACATGTTGTGT 58.516 45.000 33.01 21.98 44.84 3.72
3046 3096 5.209977 CACTTGACAGACACATTGTTGATG 58.790 41.667 0.00 0.00 41.71 3.07
3116 3166 7.879070 ACTGATGAAGCGCATTTGATTTATAT 58.121 30.769 11.47 0.00 37.34 0.86
3136 3186 9.944376 TTTATATTTCACATCTAGGTATCAGGC 57.056 33.333 0.00 0.00 0.00 4.85
3332 3382 2.547211 GCACTGCATGATGTAGATGGAC 59.453 50.000 17.41 0.00 34.09 4.02
3420 3472 5.928976 AGTTAACACCGGGTAAACTTAACT 58.071 37.500 6.32 17.38 32.24 2.24
3455 3507 9.520204 AAGAAAAATAGCCATTGTCATAATTCG 57.480 29.630 0.00 0.00 0.00 3.34
3484 3536 6.257630 GTGCAAATAAGCTCAAACTTTCCAAA 59.742 34.615 0.00 0.00 34.99 3.28
3486 3538 7.335422 TGCAAATAAGCTCAAACTTTCCAAAAA 59.665 29.630 0.00 0.00 34.99 1.94
3556 4495 0.598065 AAGAATGCGAGGGTTTGTGC 59.402 50.000 0.00 0.00 0.00 4.57
3568 4507 2.299867 GGGTTTGTGCAGATTTCCATGT 59.700 45.455 0.00 0.00 0.00 3.21
3571 4510 2.470983 TGTGCAGATTTCCATGTCGA 57.529 45.000 0.00 0.00 0.00 4.20
3621 4560 1.945387 CTGTAAGAGTGCATCGCCAT 58.055 50.000 0.00 0.00 34.07 4.40
3709 4648 0.247736 AACTGAAGCCTAGGCACGAG 59.752 55.000 34.70 25.89 44.88 4.18
3726 4665 2.507944 GCCACCAGCAGATCCGAT 59.492 61.111 0.00 0.00 42.97 4.18
3750 4689 1.334869 CTCAAAGCACACCACTTCCAC 59.665 52.381 0.00 0.00 0.00 4.02
3818 4762 2.418471 GGCATGTTCAGACTCCAGAGAG 60.418 54.545 0.70 0.00 46.36 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.626670 ACAAAAACCACATGTGCCAAATG 59.373 39.130 20.81 16.65 0.00 2.32
6 7 2.736192 GCCATACAAAAACCACATGTGC 59.264 45.455 20.81 0.00 0.00 4.57
7 8 3.244009 TGGCCATACAAAAACCACATGTG 60.244 43.478 19.31 19.31 0.00 3.21
8 9 2.968574 TGGCCATACAAAAACCACATGT 59.031 40.909 0.00 0.00 0.00 3.21
9 10 3.674528 TGGCCATACAAAAACCACATG 57.325 42.857 0.00 0.00 0.00 3.21
10 11 4.577875 CATTGGCCATACAAAAACCACAT 58.422 39.130 6.09 0.00 33.48 3.21
11 12 3.805108 GCATTGGCCATACAAAAACCACA 60.805 43.478 6.09 0.00 33.48 4.17
12 13 2.741517 GCATTGGCCATACAAAAACCAC 59.258 45.455 6.09 0.00 33.48 4.16
13 14 2.636893 AGCATTGGCCATACAAAAACCA 59.363 40.909 6.09 0.00 42.56 3.67
14 15 3.261580 GAGCATTGGCCATACAAAAACC 58.738 45.455 6.09 0.00 42.56 3.27
15 16 2.923020 CGAGCATTGGCCATACAAAAAC 59.077 45.455 6.09 0.00 42.56 2.43
16 17 2.673610 GCGAGCATTGGCCATACAAAAA 60.674 45.455 6.09 0.00 42.56 1.94
17 18 1.135141 GCGAGCATTGGCCATACAAAA 60.135 47.619 6.09 0.00 42.56 2.44
18 19 0.455410 GCGAGCATTGGCCATACAAA 59.545 50.000 6.09 0.00 42.56 2.83
19 20 1.383456 GGCGAGCATTGGCCATACAA 61.383 55.000 6.09 0.00 46.50 2.41
20 21 1.823470 GGCGAGCATTGGCCATACA 60.823 57.895 6.09 0.00 46.50 2.29
21 22 3.034030 GGCGAGCATTGGCCATAC 58.966 61.111 6.09 0.00 46.50 2.39
25 26 3.211963 AATCGGCGAGCATTGGCC 61.212 61.111 17.22 0.00 43.29 5.36
26 27 2.025156 CAATCGGCGAGCATTGGC 59.975 61.111 17.22 0.00 42.66 4.52
27 28 1.353103 GTCAATCGGCGAGCATTGG 59.647 57.895 17.22 0.00 31.86 3.16
28 29 1.353103 GGTCAATCGGCGAGCATTG 59.647 57.895 17.22 15.29 0.00 2.82
29 30 1.078497 TGGTCAATCGGCGAGCATT 60.078 52.632 17.22 1.31 36.04 3.56
30 31 1.522355 CTGGTCAATCGGCGAGCAT 60.522 57.895 17.22 0.63 39.91 3.79
31 32 2.125552 CTGGTCAATCGGCGAGCA 60.126 61.111 17.22 6.90 38.49 4.26
32 33 3.567797 GCTGGTCAATCGGCGAGC 61.568 66.667 17.22 7.58 0.00 5.03
33 34 2.892425 GGCTGGTCAATCGGCGAG 60.892 66.667 17.22 2.16 39.79 5.03
34 35 4.467084 GGGCTGGTCAATCGGCGA 62.467 66.667 13.87 13.87 39.79 5.54
35 36 4.776322 TGGGCTGGTCAATCGGCG 62.776 66.667 0.00 0.00 39.79 6.46
36 37 2.361104 TTGGGCTGGTCAATCGGC 60.361 61.111 0.00 0.00 38.26 5.54
37 38 0.609131 AAGTTGGGCTGGTCAATCGG 60.609 55.000 0.00 0.00 0.00 4.18
38 39 1.200020 GAAAGTTGGGCTGGTCAATCG 59.800 52.381 0.00 0.00 0.00 3.34
39 40 1.200020 CGAAAGTTGGGCTGGTCAATC 59.800 52.381 0.00 0.00 0.00 2.67
40 41 1.247567 CGAAAGTTGGGCTGGTCAAT 58.752 50.000 0.00 0.00 0.00 2.57
41 42 0.821711 CCGAAAGTTGGGCTGGTCAA 60.822 55.000 0.00 0.00 0.00 3.18
42 43 1.228124 CCGAAAGTTGGGCTGGTCA 60.228 57.895 0.00 0.00 0.00 4.02
43 44 2.626780 GCCGAAAGTTGGGCTGGTC 61.627 63.158 9.59 0.00 46.97 4.02
44 45 2.597510 GCCGAAAGTTGGGCTGGT 60.598 61.111 9.59 0.00 46.97 4.00
49 50 3.053896 GACCGGCCGAAAGTTGGG 61.054 66.667 30.73 9.82 0.00 4.12
50 51 3.419759 CGACCGGCCGAAAGTTGG 61.420 66.667 30.73 10.69 0.00 3.77
51 52 4.084888 GCGACCGGCCGAAAGTTG 62.085 66.667 30.73 20.73 34.80 3.16
52 53 3.894547 ATGCGACCGGCCGAAAGTT 62.895 57.895 30.73 4.57 42.61 2.66
53 54 4.388499 ATGCGACCGGCCGAAAGT 62.388 61.111 30.73 17.20 42.61 2.66
54 55 3.564027 GATGCGACCGGCCGAAAG 61.564 66.667 30.73 17.91 42.61 2.62
78 79 3.723348 GAGGACAACGCAACGGCC 61.723 66.667 0.00 0.00 36.38 6.13
79 80 3.723348 GGAGGACAACGCAACGGC 61.723 66.667 0.00 0.00 0.00 5.68
80 81 1.890041 TTGGAGGACAACGCAACGG 60.890 57.895 0.00 0.00 33.18 4.44
81 82 3.725819 TTGGAGGACAACGCAACG 58.274 55.556 0.00 0.00 33.18 4.10
88 89 1.189524 ATCCGACGGTTGGAGGACAA 61.190 55.000 21.22 0.00 39.30 3.18
89 90 1.189524 AATCCGACGGTTGGAGGACA 61.190 55.000 21.22 0.00 39.30 4.02
90 91 0.819582 TAATCCGACGGTTGGAGGAC 59.180 55.000 21.22 0.00 39.30 3.85
91 92 1.108776 CTAATCCGACGGTTGGAGGA 58.891 55.000 21.22 11.14 39.30 3.71
92 93 0.104304 CCTAATCCGACGGTTGGAGG 59.896 60.000 21.22 13.71 39.30 4.30
93 94 0.104304 CCCTAATCCGACGGTTGGAG 59.896 60.000 21.22 8.87 39.30 3.86
94 95 1.963464 GCCCTAATCCGACGGTTGGA 61.963 60.000 19.21 19.21 40.46 3.53
95 96 1.523032 GCCCTAATCCGACGGTTGG 60.523 63.158 14.79 8.20 0.00 3.77
96 97 1.523032 GGCCCTAATCCGACGGTTG 60.523 63.158 14.79 2.73 0.00 3.77
97 98 2.738938 GGGCCCTAATCCGACGGTT 61.739 63.158 17.04 10.09 0.00 4.44
98 99 3.159347 GGGCCCTAATCCGACGGT 61.159 66.667 17.04 0.00 0.00 4.83
99 100 2.052047 AATGGGCCCTAATCCGACGG 62.052 60.000 25.70 7.84 0.00 4.79
100 101 0.602905 GAATGGGCCCTAATCCGACG 60.603 60.000 25.70 0.00 0.00 5.12
101 102 0.765510 AGAATGGGCCCTAATCCGAC 59.234 55.000 25.70 5.80 0.00 4.79
102 103 1.420138 GAAGAATGGGCCCTAATCCGA 59.580 52.381 25.70 0.00 0.00 4.55
103 104 1.142870 TGAAGAATGGGCCCTAATCCG 59.857 52.381 25.70 0.00 0.00 4.18
104 105 3.425659 GATGAAGAATGGGCCCTAATCC 58.574 50.000 25.70 8.48 0.00 3.01
105 106 3.181429 TGGATGAAGAATGGGCCCTAATC 60.181 47.826 25.70 17.96 0.00 1.75
106 107 2.791179 TGGATGAAGAATGGGCCCTAAT 59.209 45.455 25.70 5.95 0.00 1.73
107 108 2.213310 TGGATGAAGAATGGGCCCTAA 58.787 47.619 25.70 2.97 0.00 2.69
108 109 1.905839 TGGATGAAGAATGGGCCCTA 58.094 50.000 25.70 10.18 0.00 3.53
109 110 1.238615 ATGGATGAAGAATGGGCCCT 58.761 50.000 25.70 2.15 0.00 5.19
110 111 2.092598 AATGGATGAAGAATGGGCCC 57.907 50.000 17.59 17.59 0.00 5.80
111 112 2.035066 CGAAATGGATGAAGAATGGGCC 59.965 50.000 0.00 0.00 0.00 5.80
112 113 2.689983 ACGAAATGGATGAAGAATGGGC 59.310 45.455 0.00 0.00 0.00 5.36
113 114 4.297299 CACGAAATGGATGAAGAATGGG 57.703 45.455 0.00 0.00 0.00 4.00
141 142 4.744137 CACGGTTGCATGATTTGAGAAAAA 59.256 37.500 0.00 0.00 0.00 1.94
142 143 4.202101 ACACGGTTGCATGATTTGAGAAAA 60.202 37.500 0.00 0.00 0.00 2.29
143 144 3.317711 ACACGGTTGCATGATTTGAGAAA 59.682 39.130 0.00 0.00 0.00 2.52
144 145 2.884012 ACACGGTTGCATGATTTGAGAA 59.116 40.909 0.00 0.00 0.00 2.87
145 146 2.226200 CACACGGTTGCATGATTTGAGA 59.774 45.455 0.00 0.00 0.00 3.27
146 147 2.030893 ACACACGGTTGCATGATTTGAG 60.031 45.455 0.00 0.00 0.00 3.02
147 148 1.952990 ACACACGGTTGCATGATTTGA 59.047 42.857 0.00 0.00 0.00 2.69
148 149 2.420628 ACACACGGTTGCATGATTTG 57.579 45.000 0.00 0.00 0.00 2.32
149 150 2.487762 CCTACACACGGTTGCATGATTT 59.512 45.455 0.00 0.00 0.00 2.17
150 151 2.083774 CCTACACACGGTTGCATGATT 58.916 47.619 0.00 0.00 0.00 2.57
151 152 1.277842 TCCTACACACGGTTGCATGAT 59.722 47.619 0.00 0.00 0.00 2.45
152 153 0.682292 TCCTACACACGGTTGCATGA 59.318 50.000 0.00 0.00 0.00 3.07
153 154 1.078709 CTCCTACACACGGTTGCATG 58.921 55.000 0.00 0.00 0.00 4.06
154 155 0.973632 TCTCCTACACACGGTTGCAT 59.026 50.000 0.00 0.00 0.00 3.96
155 156 0.317160 CTCTCCTACACACGGTTGCA 59.683 55.000 0.00 0.00 0.00 4.08
156 157 0.389948 CCTCTCCTACACACGGTTGC 60.390 60.000 0.00 0.00 0.00 4.17
157 158 0.246635 CCCTCTCCTACACACGGTTG 59.753 60.000 0.00 0.00 0.00 3.77
158 159 0.113776 TCCCTCTCCTACACACGGTT 59.886 55.000 0.00 0.00 0.00 4.44
159 160 0.113776 TTCCCTCTCCTACACACGGT 59.886 55.000 0.00 0.00 0.00 4.83
160 161 1.204941 CTTTCCCTCTCCTACACACGG 59.795 57.143 0.00 0.00 0.00 4.94
161 162 2.164624 CTCTTTCCCTCTCCTACACACG 59.835 54.545 0.00 0.00 0.00 4.49
162 163 3.056465 CACTCTTTCCCTCTCCTACACAC 60.056 52.174 0.00 0.00 0.00 3.82
163 164 3.165875 CACTCTTTCCCTCTCCTACACA 58.834 50.000 0.00 0.00 0.00 3.72
164 165 3.193903 GTCACTCTTTCCCTCTCCTACAC 59.806 52.174 0.00 0.00 0.00 2.90
165 166 3.181422 TGTCACTCTTTCCCTCTCCTACA 60.181 47.826 0.00 0.00 0.00 2.74
166 167 3.432378 TGTCACTCTTTCCCTCTCCTAC 58.568 50.000 0.00 0.00 0.00 3.18
167 168 3.827817 TGTCACTCTTTCCCTCTCCTA 57.172 47.619 0.00 0.00 0.00 2.94
168 169 2.704190 TGTCACTCTTTCCCTCTCCT 57.296 50.000 0.00 0.00 0.00 3.69
169 170 3.261897 TCATTGTCACTCTTTCCCTCTCC 59.738 47.826 0.00 0.00 0.00 3.71
170 171 4.502962 CTCATTGTCACTCTTTCCCTCTC 58.497 47.826 0.00 0.00 0.00 3.20
171 172 3.307339 GCTCATTGTCACTCTTTCCCTCT 60.307 47.826 0.00 0.00 0.00 3.69
172 173 3.006247 GCTCATTGTCACTCTTTCCCTC 58.994 50.000 0.00 0.00 0.00 4.30
173 174 2.613977 CGCTCATTGTCACTCTTTCCCT 60.614 50.000 0.00 0.00 0.00 4.20
174 175 1.734465 CGCTCATTGTCACTCTTTCCC 59.266 52.381 0.00 0.00 0.00 3.97
175 176 1.129437 GCGCTCATTGTCACTCTTTCC 59.871 52.381 0.00 0.00 0.00 3.13
176 177 1.129437 GGCGCTCATTGTCACTCTTTC 59.871 52.381 7.64 0.00 0.00 2.62
177 178 1.160137 GGCGCTCATTGTCACTCTTT 58.840 50.000 7.64 0.00 0.00 2.52
178 179 1.016130 CGGCGCTCATTGTCACTCTT 61.016 55.000 7.64 0.00 0.00 2.85
179 180 1.446792 CGGCGCTCATTGTCACTCT 60.447 57.895 7.64 0.00 0.00 3.24
180 181 3.084579 CGGCGCTCATTGTCACTC 58.915 61.111 7.64 0.00 0.00 3.51
181 182 3.121030 GCGGCGCTCATTGTCACT 61.121 61.111 26.86 0.00 0.00 3.41
182 183 3.121030 AGCGGCGCTCATTGTCAC 61.121 61.111 31.35 0.00 30.62 3.67
183 184 3.120385 CAGCGGCGCTCATTGTCA 61.120 61.111 34.22 0.00 36.40 3.58
184 185 2.815211 TCAGCGGCGCTCATTGTC 60.815 61.111 34.22 0.00 36.40 3.18
185 186 3.121030 GTCAGCGGCGCTCATTGT 61.121 61.111 34.22 7.49 36.40 2.71
186 187 3.869272 GGTCAGCGGCGCTCATTG 61.869 66.667 34.22 22.08 36.40 2.82
198 199 3.391665 GATGGGCCAGGACGGTCAG 62.392 68.421 13.78 1.68 43.46 3.51
199 200 3.399181 GATGGGCCAGGACGGTCA 61.399 66.667 13.78 0.00 43.46 4.02
200 201 4.176752 GGATGGGCCAGGACGGTC 62.177 72.222 13.78 2.73 39.44 4.79
213 214 1.524621 GGCCTCGTGTCCATGGATG 60.525 63.158 19.62 11.36 0.00 3.51
214 215 1.690219 GAGGCCTCGTGTCCATGGAT 61.690 60.000 19.62 0.00 0.00 3.41
215 216 2.284625 AGGCCTCGTGTCCATGGA 60.285 61.111 11.44 11.44 0.00 3.41
216 217 2.187946 GAGGCCTCGTGTCCATGG 59.812 66.667 19.06 4.97 0.00 3.66
217 218 2.202797 CGAGGCCTCGTGTCCATG 60.203 66.667 40.77 15.72 46.99 3.66
226 227 1.464997 GATTGTCAACAACGAGGCCTC 59.535 52.381 23.79 23.79 38.86 4.70
227 228 1.202758 TGATTGTCAACAACGAGGCCT 60.203 47.619 3.86 3.86 38.86 5.19
228 229 1.234821 TGATTGTCAACAACGAGGCC 58.765 50.000 0.00 0.00 38.86 5.19
229 230 2.855180 CATGATTGTCAACAACGAGGC 58.145 47.619 0.00 0.00 38.86 4.70
230 231 2.226200 TGCATGATTGTCAACAACGAGG 59.774 45.455 0.00 0.00 38.86 4.63
231 232 3.541071 TGCATGATTGTCAACAACGAG 57.459 42.857 0.00 0.00 38.86 4.18
232 233 3.314913 AGTTGCATGATTGTCAACAACGA 59.685 39.130 13.39 0.00 44.88 3.85
233 234 3.422876 CAGTTGCATGATTGTCAACAACG 59.577 43.478 13.39 11.37 44.88 4.10
234 235 4.207635 CACAGTTGCATGATTGTCAACAAC 59.792 41.667 13.39 15.61 42.70 3.32
235 236 4.361420 CACAGTTGCATGATTGTCAACAA 58.639 39.130 13.39 0.00 39.86 2.83
236 237 3.243468 CCACAGTTGCATGATTGTCAACA 60.243 43.478 13.39 0.00 39.86 3.33
237 238 3.004629 TCCACAGTTGCATGATTGTCAAC 59.995 43.478 0.00 0.50 38.77 3.18
238 239 3.220940 TCCACAGTTGCATGATTGTCAA 58.779 40.909 0.00 0.00 0.00 3.18
239 240 2.861274 TCCACAGTTGCATGATTGTCA 58.139 42.857 0.00 0.00 0.00 3.58
240 241 3.441222 TCATCCACAGTTGCATGATTGTC 59.559 43.478 0.00 0.00 0.00 3.18
241 242 3.423749 TCATCCACAGTTGCATGATTGT 58.576 40.909 0.00 0.00 0.00 2.71
242 243 3.442625 ACTCATCCACAGTTGCATGATTG 59.557 43.478 0.00 0.00 0.00 2.67
243 244 3.693807 ACTCATCCACAGTTGCATGATT 58.306 40.909 0.00 0.00 0.00 2.57
244 245 3.361281 ACTCATCCACAGTTGCATGAT 57.639 42.857 0.00 0.00 0.00 2.45
245 246 2.815503 CAACTCATCCACAGTTGCATGA 59.184 45.455 0.00 0.00 43.18 3.07
246 247 3.211803 CAACTCATCCACAGTTGCATG 57.788 47.619 0.00 0.00 43.18 4.06
251 252 3.632145 GGAACAACAACTCATCCACAGTT 59.368 43.478 0.00 0.00 34.24 3.16
252 253 3.214328 GGAACAACAACTCATCCACAGT 58.786 45.455 0.00 0.00 0.00 3.55
253 254 2.224079 CGGAACAACAACTCATCCACAG 59.776 50.000 0.00 0.00 0.00 3.66
254 255 2.158885 TCGGAACAACAACTCATCCACA 60.159 45.455 0.00 0.00 0.00 4.17
255 256 2.223377 GTCGGAACAACAACTCATCCAC 59.777 50.000 0.00 0.00 0.00 4.02
256 257 2.158885 TGTCGGAACAACAACTCATCCA 60.159 45.455 0.00 0.00 30.70 3.41
257 258 2.489971 TGTCGGAACAACAACTCATCC 58.510 47.619 0.00 0.00 30.70 3.51
258 259 4.466828 CAATGTCGGAACAACAACTCATC 58.533 43.478 0.00 0.00 39.30 2.92
259 260 3.304659 GCAATGTCGGAACAACAACTCAT 60.305 43.478 0.00 0.00 39.30 2.90
260 261 2.032799 GCAATGTCGGAACAACAACTCA 59.967 45.455 0.00 0.00 39.30 3.41
261 262 2.032799 TGCAATGTCGGAACAACAACTC 59.967 45.455 0.00 0.00 39.30 3.01
262 263 2.020720 TGCAATGTCGGAACAACAACT 58.979 42.857 0.00 0.00 39.30 3.16
263 264 2.483583 TGCAATGTCGGAACAACAAC 57.516 45.000 0.00 0.00 39.30 3.32
264 265 4.541779 GTTATGCAATGTCGGAACAACAA 58.458 39.130 0.00 0.00 39.30 2.83
265 266 3.364465 CGTTATGCAATGTCGGAACAACA 60.364 43.478 0.00 0.00 39.30 3.33
266 267 3.160545 CGTTATGCAATGTCGGAACAAC 58.839 45.455 0.00 0.00 39.30 3.32
267 268 2.809119 ACGTTATGCAATGTCGGAACAA 59.191 40.909 0.00 0.00 39.30 2.83
268 269 2.418692 ACGTTATGCAATGTCGGAACA 58.581 42.857 0.00 0.00 40.38 3.18
269 270 3.543460 GCTACGTTATGCAATGTCGGAAC 60.543 47.826 0.00 0.00 35.49 3.62
270 271 2.605818 GCTACGTTATGCAATGTCGGAA 59.394 45.455 0.00 0.00 35.49 4.30
271 272 2.198406 GCTACGTTATGCAATGTCGGA 58.802 47.619 0.00 0.00 35.49 4.55
272 273 1.930503 TGCTACGTTATGCAATGTCGG 59.069 47.619 0.00 0.00 35.49 4.79
273 274 3.859745 ATGCTACGTTATGCAATGTCG 57.140 42.857 13.03 0.00 42.74 4.35
274 275 4.730042 CACAATGCTACGTTATGCAATGTC 59.270 41.667 20.68 0.00 46.37 3.06
275 276 4.963276 ACAATGCTACGTTATGCAATGT 57.037 36.364 18.95 18.95 45.09 2.71
276 277 4.907579 TCACAATGCTACGTTATGCAATG 58.092 39.130 18.01 18.01 43.39 2.82
277 278 4.496341 GCTCACAATGCTACGTTATGCAAT 60.496 41.667 13.03 4.15 42.74 3.56
278 279 3.181511 GCTCACAATGCTACGTTATGCAA 60.182 43.478 13.03 0.00 42.74 4.08
279 280 2.351418 GCTCACAATGCTACGTTATGCA 59.649 45.455 11.77 11.77 43.67 3.96
280 281 2.597505 CGCTCACAATGCTACGTTATGC 60.598 50.000 0.00 0.00 0.00 3.14
281 282 2.603110 ACGCTCACAATGCTACGTTATG 59.397 45.455 0.00 0.00 0.00 1.90
282 283 2.888594 ACGCTCACAATGCTACGTTAT 58.111 42.857 0.00 0.00 0.00 1.89
283 284 2.357327 ACGCTCACAATGCTACGTTA 57.643 45.000 0.00 0.00 0.00 3.18
284 285 1.194547 CAACGCTCACAATGCTACGTT 59.805 47.619 0.00 0.00 43.73 3.99
285 286 0.790207 CAACGCTCACAATGCTACGT 59.210 50.000 0.00 0.00 34.85 3.57
286 287 0.519175 GCAACGCTCACAATGCTACG 60.519 55.000 0.00 0.00 35.93 3.51
287 288 0.179189 GGCAACGCTCACAATGCTAC 60.179 55.000 0.00 0.00 38.79 3.58
288 289 1.305219 GGGCAACGCTCACAATGCTA 61.305 55.000 0.00 0.00 38.79 3.49
289 290 2.629656 GGGCAACGCTCACAATGCT 61.630 57.895 0.00 0.00 38.79 3.79
290 291 2.126346 GGGCAACGCTCACAATGC 60.126 61.111 0.00 0.00 38.06 3.56
368 369 1.746615 CTCATGGGGTGAAGCGGTG 60.747 63.158 0.00 0.00 36.14 4.94
403 404 1.431496 TAAAAGCTACAACCGACGGC 58.569 50.000 15.39 0.00 0.00 5.68
404 405 3.800506 CCTATAAAAGCTACAACCGACGG 59.199 47.826 13.61 13.61 0.00 4.79
409 410 3.311596 CGGCACCTATAAAAGCTACAACC 59.688 47.826 0.00 0.00 0.00 3.77
410 411 3.311596 CCGGCACCTATAAAAGCTACAAC 59.688 47.826 0.00 0.00 0.00 3.32
447 448 1.070758 GTGATGACGATAGGGTGGCAT 59.929 52.381 0.00 0.00 43.77 4.40
457 458 3.935203 GGAAGTGATGTTGTGATGACGAT 59.065 43.478 0.00 0.00 0.00 3.73
463 464 3.194116 GCCAATGGAAGTGATGTTGTGAT 59.806 43.478 2.05 0.00 30.28 3.06
466 467 2.880443 AGCCAATGGAAGTGATGTTGT 58.120 42.857 2.05 0.00 30.28 3.32
469 470 4.922206 TCTTTAGCCAATGGAAGTGATGT 58.078 39.130 2.05 0.00 30.28 3.06
474 475 7.310423 GGGTTTTATTCTTTAGCCAATGGAAGT 60.310 37.037 2.05 0.00 0.00 3.01
480 481 4.142026 GGCGGGTTTTATTCTTTAGCCAAT 60.142 41.667 0.00 0.00 41.46 3.16
540 541 0.674895 AAGGAGCAGCAATCGGTGAC 60.675 55.000 0.00 0.00 43.56 3.67
552 553 2.747686 GACGGGGTGAAAGGAGCA 59.252 61.111 0.00 0.00 0.00 4.26
598 600 3.319122 AGGGCAAGATGTGACAGAAAAAC 59.681 43.478 0.00 0.00 36.72 2.43
599 601 3.565307 AGGGCAAGATGTGACAGAAAAA 58.435 40.909 0.00 0.00 36.72 1.94
639 641 1.191096 CAAATGGTAGCGCGATTTGC 58.809 50.000 12.10 0.00 43.00 3.68
652 654 2.982470 GCGACAGAAAAGCTTCAAATGG 59.018 45.455 0.00 0.00 33.64 3.16
672 674 3.217599 TCATCGATAGCTGTAATCGGC 57.782 47.619 15.44 0.00 44.88 5.54
675 677 6.471841 CACTAGCATCATCGATAGCTGTAATC 59.528 42.308 22.18 0.00 37.94 1.75
676 678 6.328714 CACTAGCATCATCGATAGCTGTAAT 58.671 40.000 22.18 8.01 37.94 1.89
681 683 2.094286 GCCACTAGCATCATCGATAGCT 60.094 50.000 19.01 19.01 42.97 3.32
687 689 0.528466 ACACGCCACTAGCATCATCG 60.528 55.000 0.00 0.00 44.04 3.84
690 692 0.391130 GGAACACGCCACTAGCATCA 60.391 55.000 0.00 0.00 44.04 3.07
696 698 1.669440 GGACTGGAACACGCCACTA 59.331 57.895 0.00 0.00 33.52 2.74
717 719 1.373748 GCTAGAAACGACGGGCACA 60.374 57.895 0.00 0.00 0.00 4.57
718 720 0.739813 ATGCTAGAAACGACGGGCAC 60.740 55.000 0.00 0.00 32.52 5.01
726 728 2.738846 ACAGCTCACAATGCTAGAAACG 59.261 45.455 0.00 0.00 38.92 3.60
727 729 3.499918 ACACAGCTCACAATGCTAGAAAC 59.500 43.478 0.00 0.00 38.92 2.78
729 731 3.407424 ACACAGCTCACAATGCTAGAA 57.593 42.857 0.00 0.00 38.92 2.10
737 739 3.748048 GCTCTCATTTACACAGCTCACAA 59.252 43.478 0.00 0.00 0.00 3.33
738 740 3.007290 AGCTCTCATTTACACAGCTCACA 59.993 43.478 0.00 0.00 35.46 3.58
760 762 1.065551 CATCGACCACTCGCTCATGTA 59.934 52.381 0.00 0.00 39.96 2.29
761 763 0.179127 CATCGACCACTCGCTCATGT 60.179 55.000 0.00 0.00 39.96 3.21
763 765 1.227089 GCATCGACCACTCGCTCAT 60.227 57.895 0.00 0.00 39.96 2.90
779 781 3.030291 AGGCAATGATTTAAATCGGGCA 58.970 40.909 27.12 13.62 38.26 5.36
806 808 0.601057 GGTTGGTGTGGTGGCAATAC 59.399 55.000 0.00 0.00 0.00 1.89
811 813 1.102978 GATATGGTTGGTGTGGTGGC 58.897 55.000 0.00 0.00 0.00 5.01
815 817 3.822735 GGATGATGATATGGTTGGTGTGG 59.177 47.826 0.00 0.00 0.00 4.17
816 818 4.722220 AGGATGATGATATGGTTGGTGTG 58.278 43.478 0.00 0.00 0.00 3.82
840 842 4.581824 AGTCAAGCAAATGTTCTCACATGT 59.418 37.500 0.00 0.00 43.34 3.21
862 864 8.195617 TGCTTTTGGTGAAATTTACTCAAAAG 57.804 30.769 26.93 26.93 46.38 2.27
987 1008 0.025898 CGATCATCTGTGTTGCAGCG 59.974 55.000 0.00 0.00 44.66 5.18
989 1010 1.012086 CCCGATCATCTGTGTTGCAG 58.988 55.000 0.00 0.00 46.34 4.41
1183 1204 2.107041 ATTCGGTCGAACAGGTGGCA 62.107 55.000 8.00 0.00 36.91 4.92
1574 1595 1.815003 CCAAGTTCCTCACAGGCATTC 59.185 52.381 0.00 0.00 34.61 2.67
1641 1662 0.773644 ACACCCTCAAAGCATCACCT 59.226 50.000 0.00 0.00 0.00 4.00
1643 1664 2.229792 TGAACACCCTCAAAGCATCAC 58.770 47.619 0.00 0.00 0.00 3.06
1961 1982 2.353109 GCCCTCATCTTTTCAAACAGGC 60.353 50.000 0.00 0.00 0.00 4.85
1963 1984 3.822735 TGAGCCCTCATCTTTTCAAACAG 59.177 43.478 0.00 0.00 34.14 3.16
2025 2046 0.956633 CAGTGTGGATGCAAGCAGTT 59.043 50.000 0.00 0.00 0.00 3.16
2047 2068 8.647143 AAACACTGTATTCCAAAATCACAAAG 57.353 30.769 0.00 0.00 0.00 2.77
2106 2127 2.743183 GCAAGAGTAATGATCAGCCCGT 60.743 50.000 0.09 0.00 0.00 5.28
2226 2247 6.594159 TCTTATAAACTCTACAAGCAGCCAAC 59.406 38.462 0.00 0.00 0.00 3.77
2255 2276 2.322161 CAGCAAATTCAGCAAACTCCG 58.678 47.619 5.74 0.00 0.00 4.63
2346 2367 4.467084 TCGGCCCACTGATTCGCC 62.467 66.667 0.00 0.00 38.07 5.54
2400 2421 1.480789 ACCCAGGTGTTTTGACAACC 58.519 50.000 0.00 0.00 0.00 3.77
2847 2868 5.244626 GCATCCCTATCAAATTTGCCAGTAT 59.755 40.000 13.54 4.11 0.00 2.12
2848 2869 4.584325 GCATCCCTATCAAATTTGCCAGTA 59.416 41.667 13.54 0.00 0.00 2.74
2849 2870 3.385755 GCATCCCTATCAAATTTGCCAGT 59.614 43.478 13.54 2.42 0.00 4.00
2850 2871 3.385433 TGCATCCCTATCAAATTTGCCAG 59.615 43.478 13.54 11.64 0.00 4.85
2852 2873 4.122046 GTTGCATCCCTATCAAATTTGCC 58.878 43.478 13.54 0.00 0.00 4.52
2853 2874 4.757594 TGTTGCATCCCTATCAAATTTGC 58.242 39.130 13.54 0.00 0.00 3.68
2854 2875 5.969423 ACTGTTGCATCCCTATCAAATTTG 58.031 37.500 12.15 12.15 0.00 2.32
2972 3022 1.675483 TCACAGGACACAACATGTTGC 59.325 47.619 33.23 19.52 43.56 4.17
2985 3035 2.488347 GGTTTTGCCTAACCTCACAGGA 60.488 50.000 9.24 0.00 43.44 3.86
3116 3166 4.716784 ACTGCCTGATACCTAGATGTGAAA 59.283 41.667 0.00 0.00 0.00 2.69
3136 3186 3.201290 GGAGCATACACATCTCCAACTG 58.799 50.000 2.88 0.00 44.38 3.16
3216 3266 1.678101 GAGGCTGACAAGTGCAAACTT 59.322 47.619 0.00 0.00 0.00 2.66
3332 3382 4.569966 AGCATCTGCATTTTAAGACTCTCG 59.430 41.667 4.79 0.00 45.16 4.04
3445 3497 8.122952 AGCTTATTTGCACTAACGAATTATGAC 58.877 33.333 0.00 0.00 34.99 3.06
3453 3505 5.468746 AGTTTGAGCTTATTTGCACTAACGA 59.531 36.000 0.00 0.00 41.12 3.85
3454 3506 5.689819 AGTTTGAGCTTATTTGCACTAACG 58.310 37.500 0.00 0.00 41.12 3.18
3455 3507 7.114953 GGAAAGTTTGAGCTTATTTGCACTAAC 59.885 37.037 0.00 0.00 38.58 2.34
3523 3601 7.926555 CCCTCGCATTCTTAAAGATCTTAGTTA 59.073 37.037 8.75 0.00 0.00 2.24
3525 3603 6.127026 ACCCTCGCATTCTTAAAGATCTTAGT 60.127 38.462 8.75 0.00 0.00 2.24
3526 3604 6.284459 ACCCTCGCATTCTTAAAGATCTTAG 58.716 40.000 8.75 3.52 0.00 2.18
3533 4472 4.475944 CACAAACCCTCGCATTCTTAAAG 58.524 43.478 0.00 0.00 0.00 1.85
3543 4482 0.598065 AAATCTGCACAAACCCTCGC 59.402 50.000 0.00 0.00 0.00 5.03
3556 4495 3.193263 CTGGACTCGACATGGAAATCTG 58.807 50.000 0.00 0.00 0.00 2.90
3568 4507 1.674441 CGGTGCTATAACTGGACTCGA 59.326 52.381 0.00 0.00 0.00 4.04
3571 4510 2.165845 GTGACGGTGCTATAACTGGACT 59.834 50.000 0.00 0.00 0.00 3.85
3605 4544 2.486918 CATCATGGCGATGCACTCTTA 58.513 47.619 3.45 0.00 44.95 2.10
3621 4560 2.942804 TGGTGAGAAAACTTGGCATCA 58.057 42.857 0.00 0.00 0.00 3.07
3709 4648 1.890979 CATCGGATCTGCTGGTGGC 60.891 63.158 0.00 0.00 42.22 5.01
3718 4657 1.833630 TGCTTTGAGGTCATCGGATCT 59.166 47.619 0.00 0.00 37.13 2.75
3726 4665 0.546122 AGTGGTGTGCTTTGAGGTCA 59.454 50.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.