Multiple sequence alignment - TraesCS6B01G318700

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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 TraesCS6B01G318700 chr6B 100.000 2897 0 0 1 2897 566534114 566537010 0.000000e+00 5350.0
1 TraesCS6B01G318700 chr6B 86.374 455 57 4 2444 2897 147962850 147962400 2.590000e-135 492.0
2 TraesCS6B01G318700 chr6D 93.001 843 52 5 2061 2897 379723207 379722366 0.000000e+00 1223.0
3 TraesCS6B01G318700 chr6D 91.046 927 45 11 939 1850 379724455 379723552 0.000000e+00 1218.0
4 TraesCS6B01G318700 chr6D 86.137 642 38 22 292 893 379725085 379724455 0.000000e+00 645.0
5 TraesCS6B01G318700 chr6D 87.500 56 3 3 243 295 379725668 379725614 8.670000e-06 62.1
6 TraesCS6B01G318700 chr6A 89.243 911 45 29 941 1817 520869454 520870345 0.000000e+00 1090.0
7 TraesCS6B01G318700 chr6A 93.121 596 28 4 2303 2897 520870960 520871543 0.000000e+00 861.0
8 TraesCS6B01G318700 chr6A 86.578 678 42 27 245 893 520868795 520869452 0.000000e+00 702.0
9 TraesCS6B01G318700 chr6A 85.591 465 64 2 2433 2897 90034061 90033600 4.340000e-133 484.0


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 TraesCS6B01G318700 chr6B 566534114 566537010 2896 False 5350.000000 5350 100.000000 1 2897 1 chr6B.!!$F1 2896
1 TraesCS6B01G318700 chr6D 379722366 379725668 3302 True 787.025000 1223 89.421000 243 2897 4 chr6D.!!$R1 2654
2 TraesCS6B01G318700 chr6A 520868795 520871543 2748 False 884.333333 1090 89.647333 245 2897 3 chr6A.!!$F1 2652

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
171 172 0.040058 AATGTCTGCTTCATGGGGCA 59.960 50.0 11.69 11.69 36.94 5.36 F
173 174 0.178967 TGTCTGCTTCATGGGGCAAA 60.179 50.0 12.88 0.00 38.02 3.68 F
1042 1657 0.037232 GTTCCGTTCCACAGCTAGCT 60.037 55.0 12.68 12.68 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1042 1657 0.177373 TCGGTCACTCGAGCTAGCTA 59.823 55.000 19.38 1.34 37.51 3.32 R
1669 2296 0.536687 CATATCACCCTGGGCAGCAG 60.537 60.000 14.08 0.00 0.00 4.24 R
2816 3687 1.079543 CAGCTCAAGGGTGTCCTCG 60.080 63.158 0.00 0.00 44.07 4.63 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 4.258935 CATCACGTGTAACATGGCTTAC 57.741 45.455 16.51 0.00 35.74 2.34
22 23 3.671008 TCACGTGTAACATGGCTTACT 57.329 42.857 16.51 0.00 35.74 2.24
23 24 4.787260 TCACGTGTAACATGGCTTACTA 57.213 40.909 16.51 0.00 35.74 1.82
24 25 4.487948 TCACGTGTAACATGGCTTACTAC 58.512 43.478 16.51 0.00 35.74 2.73
25 26 3.302434 CACGTGTAACATGGCTTACTACG 59.698 47.826 7.58 18.43 37.27 3.51
26 27 3.191162 ACGTGTAACATGGCTTACTACGA 59.809 43.478 22.54 1.60 36.16 3.43
27 28 4.168014 CGTGTAACATGGCTTACTACGAA 58.832 43.478 16.81 0.00 35.48 3.85
28 29 4.264614 CGTGTAACATGGCTTACTACGAAG 59.735 45.833 16.81 0.00 35.48 3.79
29 30 4.032558 GTGTAACATGGCTTACTACGAAGC 59.967 45.833 0.00 0.00 43.68 3.86
30 31 6.134186 GTGTAACATGGCTTACTACGAAGCT 61.134 44.000 7.96 0.00 43.80 3.74
31 32 6.898549 GTGTAACATGGCTTACTACGAAGCTA 60.899 42.308 7.96 2.53 45.54 3.32
32 33 8.314857 GTGTAACATGGCTTACTACGAAGCTAA 61.315 40.741 7.96 0.00 44.77 3.09
40 41 7.611821 GCTTACTACGAAGCTAATACTCTTG 57.388 40.000 0.94 0.00 46.85 3.02
41 42 7.416022 GCTTACTACGAAGCTAATACTCTTGA 58.584 38.462 0.94 0.00 46.85 3.02
42 43 7.376601 GCTTACTACGAAGCTAATACTCTTGAC 59.623 40.741 0.94 0.00 46.85 3.18
43 44 6.754702 ACTACGAAGCTAATACTCTTGACA 57.245 37.500 0.00 0.00 0.00 3.58
44 45 6.553524 ACTACGAAGCTAATACTCTTGACAC 58.446 40.000 0.00 0.00 0.00 3.67
45 46 4.745649 ACGAAGCTAATACTCTTGACACC 58.254 43.478 0.00 0.00 0.00 4.16
46 47 4.219944 ACGAAGCTAATACTCTTGACACCA 59.780 41.667 0.00 0.00 0.00 4.17
47 48 5.168569 CGAAGCTAATACTCTTGACACCAA 58.831 41.667 0.00 0.00 0.00 3.67
57 58 3.344904 CTTGACACCAAGCAAGTTCAG 57.655 47.619 0.00 0.00 42.72 3.02
58 59 2.708216 TGACACCAAGCAAGTTCAGA 57.292 45.000 0.00 0.00 0.00 3.27
59 60 2.997980 TGACACCAAGCAAGTTCAGAA 58.002 42.857 0.00 0.00 0.00 3.02
60 61 3.554934 TGACACCAAGCAAGTTCAGAAT 58.445 40.909 0.00 0.00 0.00 2.40
61 62 4.713553 TGACACCAAGCAAGTTCAGAATA 58.286 39.130 0.00 0.00 0.00 1.75
62 63 5.316167 TGACACCAAGCAAGTTCAGAATAT 58.684 37.500 0.00 0.00 0.00 1.28
63 64 6.472016 TGACACCAAGCAAGTTCAGAATATA 58.528 36.000 0.00 0.00 0.00 0.86
64 65 6.595326 TGACACCAAGCAAGTTCAGAATATAG 59.405 38.462 0.00 0.00 0.00 1.31
65 66 5.355350 ACACCAAGCAAGTTCAGAATATAGC 59.645 40.000 0.00 0.00 0.00 2.97
66 67 4.884164 ACCAAGCAAGTTCAGAATATAGCC 59.116 41.667 0.00 0.00 0.00 3.93
67 68 4.024556 CCAAGCAAGTTCAGAATATAGCCG 60.025 45.833 0.00 0.00 0.00 5.52
68 69 3.134458 AGCAAGTTCAGAATATAGCCGC 58.866 45.455 0.00 0.00 0.00 6.53
69 70 3.134458 GCAAGTTCAGAATATAGCCGCT 58.866 45.455 0.00 0.00 0.00 5.52
70 71 3.561725 GCAAGTTCAGAATATAGCCGCTT 59.438 43.478 0.00 0.00 0.00 4.68
71 72 4.035675 GCAAGTTCAGAATATAGCCGCTTT 59.964 41.667 0.00 0.00 0.00 3.51
72 73 5.742446 CAAGTTCAGAATATAGCCGCTTTC 58.258 41.667 0.00 0.00 0.00 2.62
73 74 5.283457 AGTTCAGAATATAGCCGCTTTCT 57.717 39.130 0.00 0.00 0.00 2.52
74 75 6.406692 AGTTCAGAATATAGCCGCTTTCTA 57.593 37.500 0.00 0.00 0.00 2.10
75 76 6.817184 AGTTCAGAATATAGCCGCTTTCTAA 58.183 36.000 0.00 0.00 0.00 2.10
76 77 6.926272 AGTTCAGAATATAGCCGCTTTCTAAG 59.074 38.462 0.00 0.00 0.00 2.18
77 78 5.784177 TCAGAATATAGCCGCTTTCTAAGG 58.216 41.667 0.00 0.00 0.00 2.69
78 79 5.304614 TCAGAATATAGCCGCTTTCTAAGGT 59.695 40.000 0.00 0.00 0.00 3.50
79 80 5.406780 CAGAATATAGCCGCTTTCTAAGGTG 59.593 44.000 0.00 0.00 0.00 4.00
80 81 2.622064 ATAGCCGCTTTCTAAGGTGG 57.378 50.000 0.00 0.33 36.31 4.61
81 82 1.563924 TAGCCGCTTTCTAAGGTGGA 58.436 50.000 8.46 0.00 35.33 4.02
82 83 0.690762 AGCCGCTTTCTAAGGTGGAA 59.309 50.000 8.46 0.00 35.33 3.53
83 84 1.282157 AGCCGCTTTCTAAGGTGGAAT 59.718 47.619 8.46 0.00 35.33 3.01
84 85 2.092323 GCCGCTTTCTAAGGTGGAATT 58.908 47.619 8.46 0.00 35.33 2.17
85 86 2.159379 GCCGCTTTCTAAGGTGGAATTG 60.159 50.000 8.46 0.00 35.33 2.32
86 87 3.081804 CCGCTTTCTAAGGTGGAATTGT 58.918 45.455 0.00 0.00 35.33 2.71
87 88 3.127030 CCGCTTTCTAAGGTGGAATTGTC 59.873 47.826 0.00 0.00 35.33 3.18
88 89 4.003648 CGCTTTCTAAGGTGGAATTGTCT 58.996 43.478 0.00 0.00 0.00 3.41
89 90 4.142816 CGCTTTCTAAGGTGGAATTGTCTG 60.143 45.833 0.00 0.00 0.00 3.51
90 91 5.003804 GCTTTCTAAGGTGGAATTGTCTGA 58.996 41.667 0.00 0.00 0.00 3.27
91 92 5.473504 GCTTTCTAAGGTGGAATTGTCTGAA 59.526 40.000 0.00 0.00 0.00 3.02
92 93 6.151817 GCTTTCTAAGGTGGAATTGTCTGAAT 59.848 38.462 0.00 0.00 0.00 2.57
93 94 7.627300 GCTTTCTAAGGTGGAATTGTCTGAATC 60.627 40.741 0.00 0.00 0.00 2.52
94 95 6.627087 TCTAAGGTGGAATTGTCTGAATCT 57.373 37.500 0.00 0.00 0.00 2.40
95 96 7.733773 TCTAAGGTGGAATTGTCTGAATCTA 57.266 36.000 0.00 0.00 0.00 1.98
96 97 7.556844 TCTAAGGTGGAATTGTCTGAATCTAC 58.443 38.462 0.00 0.00 0.00 2.59
97 98 6.380079 AAGGTGGAATTGTCTGAATCTACT 57.620 37.500 0.00 0.00 0.00 2.57
98 99 5.983540 AGGTGGAATTGTCTGAATCTACTC 58.016 41.667 0.00 0.00 0.00 2.59
99 100 4.806247 GGTGGAATTGTCTGAATCTACTCG 59.194 45.833 0.00 0.00 0.00 4.18
100 101 4.268884 GTGGAATTGTCTGAATCTACTCGC 59.731 45.833 0.00 0.00 0.00 5.03
101 102 4.081697 TGGAATTGTCTGAATCTACTCGCA 60.082 41.667 0.00 0.00 0.00 5.10
102 103 4.870426 GGAATTGTCTGAATCTACTCGCAA 59.130 41.667 0.00 0.00 0.00 4.85
103 104 5.351465 GGAATTGTCTGAATCTACTCGCAAA 59.649 40.000 0.00 0.00 0.00 3.68
104 105 6.128282 GGAATTGTCTGAATCTACTCGCAAAA 60.128 38.462 0.00 0.00 0.00 2.44
105 106 6.801539 ATTGTCTGAATCTACTCGCAAAAA 57.198 33.333 0.00 0.00 0.00 1.94
132 133 6.560253 AAAAATTGTCTGAATCACTACGCT 57.440 33.333 0.00 0.00 0.00 5.07
133 134 5.786401 AAATTGTCTGAATCACTACGCTC 57.214 39.130 0.00 0.00 0.00 5.03
134 135 2.941453 TGTCTGAATCACTACGCTCC 57.059 50.000 0.00 0.00 0.00 4.70
135 136 1.476891 TGTCTGAATCACTACGCTCCC 59.523 52.381 0.00 0.00 0.00 4.30
136 137 0.738975 TCTGAATCACTACGCTCCCG 59.261 55.000 0.00 0.00 41.14 5.14
137 138 0.738975 CTGAATCACTACGCTCCCGA 59.261 55.000 0.00 0.00 38.29 5.14
138 139 1.338337 CTGAATCACTACGCTCCCGAT 59.662 52.381 0.00 0.00 38.29 4.18
139 140 2.552743 CTGAATCACTACGCTCCCGATA 59.447 50.000 0.00 0.00 38.29 2.92
140 141 2.292569 TGAATCACTACGCTCCCGATAC 59.707 50.000 0.00 0.00 38.29 2.24
141 142 1.245732 ATCACTACGCTCCCGATACC 58.754 55.000 0.00 0.00 38.29 2.73
142 143 0.182061 TCACTACGCTCCCGATACCT 59.818 55.000 0.00 0.00 38.29 3.08
143 144 0.311165 CACTACGCTCCCGATACCTG 59.689 60.000 0.00 0.00 38.29 4.00
144 145 0.822532 ACTACGCTCCCGATACCTGG 60.823 60.000 0.00 0.00 38.29 4.45
145 146 2.143594 CTACGCTCCCGATACCTGGC 62.144 65.000 0.00 0.00 38.29 4.85
146 147 2.914756 TACGCTCCCGATACCTGGCA 62.915 60.000 0.00 0.00 38.29 4.92
147 148 2.908015 GCTCCCGATACCTGGCAA 59.092 61.111 0.00 0.00 0.00 4.52
148 149 1.223487 GCTCCCGATACCTGGCAAA 59.777 57.895 0.00 0.00 0.00 3.68
149 150 0.393808 GCTCCCGATACCTGGCAAAA 60.394 55.000 0.00 0.00 0.00 2.44
150 151 1.379527 CTCCCGATACCTGGCAAAAC 58.620 55.000 0.00 0.00 0.00 2.43
151 152 0.988832 TCCCGATACCTGGCAAAACT 59.011 50.000 0.00 0.00 0.00 2.66
152 153 2.169769 CTCCCGATACCTGGCAAAACTA 59.830 50.000 0.00 0.00 0.00 2.24
153 154 2.572556 TCCCGATACCTGGCAAAACTAA 59.427 45.455 0.00 0.00 0.00 2.24
154 155 3.201266 TCCCGATACCTGGCAAAACTAAT 59.799 43.478 0.00 0.00 0.00 1.73
155 156 3.315191 CCCGATACCTGGCAAAACTAATG 59.685 47.826 0.00 0.00 0.00 1.90
156 157 3.945285 CCGATACCTGGCAAAACTAATGT 59.055 43.478 0.00 0.00 0.00 2.71
157 158 4.035208 CCGATACCTGGCAAAACTAATGTC 59.965 45.833 0.00 0.00 0.00 3.06
158 159 4.876107 CGATACCTGGCAAAACTAATGTCT 59.124 41.667 0.00 0.00 0.00 3.41
159 160 5.220662 CGATACCTGGCAAAACTAATGTCTG 60.221 44.000 0.00 0.00 0.00 3.51
160 161 2.558359 ACCTGGCAAAACTAATGTCTGC 59.442 45.455 0.00 0.00 0.00 4.26
161 162 2.821969 CCTGGCAAAACTAATGTCTGCT 59.178 45.455 0.00 0.00 33.49 4.24
162 163 3.256631 CCTGGCAAAACTAATGTCTGCTT 59.743 43.478 0.00 0.00 33.49 3.91
163 164 4.479619 CTGGCAAAACTAATGTCTGCTTC 58.520 43.478 0.00 0.00 33.49 3.86
164 165 3.888323 TGGCAAAACTAATGTCTGCTTCA 59.112 39.130 0.00 0.00 33.49 3.02
165 166 4.523943 TGGCAAAACTAATGTCTGCTTCAT 59.476 37.500 0.00 0.00 33.49 2.57
166 167 4.860907 GGCAAAACTAATGTCTGCTTCATG 59.139 41.667 0.00 0.00 33.49 3.07
167 168 4.860907 GCAAAACTAATGTCTGCTTCATGG 59.139 41.667 0.00 0.00 0.00 3.66
168 169 5.404946 CAAAACTAATGTCTGCTTCATGGG 58.595 41.667 0.00 0.00 0.00 4.00
169 170 3.287867 ACTAATGTCTGCTTCATGGGG 57.712 47.619 0.00 0.00 0.00 4.96
170 171 1.952296 CTAATGTCTGCTTCATGGGGC 59.048 52.381 0.00 0.00 0.00 5.80
171 172 0.040058 AATGTCTGCTTCATGGGGCA 59.960 50.000 11.69 11.69 36.94 5.36
172 173 0.040058 ATGTCTGCTTCATGGGGCAA 59.960 50.000 12.88 1.92 38.02 4.52
173 174 0.178967 TGTCTGCTTCATGGGGCAAA 60.179 50.000 12.88 0.00 38.02 3.68
174 175 0.968405 GTCTGCTTCATGGGGCAAAA 59.032 50.000 12.88 4.13 38.02 2.44
175 176 1.551883 GTCTGCTTCATGGGGCAAAAT 59.448 47.619 12.88 0.00 38.02 1.82
176 177 1.551430 TCTGCTTCATGGGGCAAAATG 59.449 47.619 12.88 4.12 38.02 2.32
177 178 1.276989 CTGCTTCATGGGGCAAAATGT 59.723 47.619 12.88 0.00 38.02 2.71
178 179 1.275856 TGCTTCATGGGGCAAAATGTC 59.724 47.619 10.24 0.00 35.40 3.06
179 180 1.275856 GCTTCATGGGGCAAAATGTCA 59.724 47.619 0.00 0.00 0.00 3.58
180 181 2.675889 GCTTCATGGGGCAAAATGTCAG 60.676 50.000 0.00 0.00 0.00 3.51
181 182 2.601240 TCATGGGGCAAAATGTCAGA 57.399 45.000 0.00 0.00 0.00 3.27
182 183 2.170166 TCATGGGGCAAAATGTCAGAC 58.830 47.619 0.00 0.00 0.00 3.51
183 184 2.173519 CATGGGGCAAAATGTCAGACT 58.826 47.619 1.31 0.00 0.00 3.24
184 185 1.619654 TGGGGCAAAATGTCAGACTG 58.380 50.000 1.31 0.00 0.00 3.51
185 186 0.244721 GGGGCAAAATGTCAGACTGC 59.755 55.000 1.31 3.02 0.00 4.40
186 187 0.961019 GGGCAAAATGTCAGACTGCA 59.039 50.000 13.03 0.00 34.66 4.41
187 188 1.336240 GGGCAAAATGTCAGACTGCAC 60.336 52.381 13.03 6.88 34.66 4.57
188 189 1.337703 GGCAAAATGTCAGACTGCACA 59.662 47.619 13.03 4.03 34.66 4.57
189 190 2.606308 GGCAAAATGTCAGACTGCACAG 60.606 50.000 13.03 0.00 34.66 3.66
190 191 2.291465 GCAAAATGTCAGACTGCACAGA 59.709 45.455 4.31 0.00 33.19 3.41
191 192 3.851105 GCAAAATGTCAGACTGCACAGAC 60.851 47.826 4.31 0.00 33.19 3.51
192 193 2.916702 AATGTCAGACTGCACAGACA 57.083 45.000 4.31 5.25 44.16 3.41
193 194 2.916702 ATGTCAGACTGCACAGACAA 57.083 45.000 4.31 0.00 43.38 3.18
194 195 2.916702 TGTCAGACTGCACAGACAAT 57.083 45.000 4.31 0.00 37.99 2.71
195 196 4.541973 ATGTCAGACTGCACAGACAATA 57.458 40.909 4.31 0.00 43.38 1.90
196 197 4.335400 TGTCAGACTGCACAGACAATAA 57.665 40.909 4.31 0.00 37.99 1.40
197 198 4.702831 TGTCAGACTGCACAGACAATAAA 58.297 39.130 4.31 0.00 37.99 1.40
198 199 5.122519 TGTCAGACTGCACAGACAATAAAA 58.877 37.500 4.31 0.00 37.99 1.52
199 200 5.588246 TGTCAGACTGCACAGACAATAAAAA 59.412 36.000 4.31 0.00 37.99 1.94
223 224 2.928416 GTTCTCTGGAACCCAACCG 58.072 57.895 0.00 0.00 44.24 4.44
224 225 0.395312 GTTCTCTGGAACCCAACCGA 59.605 55.000 0.00 0.00 44.24 4.69
225 226 0.395312 TTCTCTGGAACCCAACCGAC 59.605 55.000 0.00 0.00 30.80 4.79
226 227 0.761323 TCTCTGGAACCCAACCGACA 60.761 55.000 0.00 0.00 30.80 4.35
227 228 0.320771 CTCTGGAACCCAACCGACAG 60.321 60.000 0.00 0.00 30.80 3.51
228 229 1.052124 TCTGGAACCCAACCGACAGT 61.052 55.000 0.00 0.00 30.80 3.55
229 230 0.179029 CTGGAACCCAACCGACAGTT 60.179 55.000 0.00 0.00 40.16 3.16
240 241 3.067684 ACCGACAGTTGGATAAAAGGG 57.932 47.619 14.52 0.00 0.00 3.95
241 242 2.374170 ACCGACAGTTGGATAAAAGGGT 59.626 45.455 14.52 0.00 0.00 4.34
283 284 1.620822 ATGGGGTTTTGTGAGCTGAC 58.379 50.000 0.00 0.00 0.00 3.51
386 921 2.445525 ACCCACAACAGACCAACCTAAT 59.554 45.455 0.00 0.00 0.00 1.73
435 970 1.083242 GCTGCTTGAGCTCTCCTTCG 61.083 60.000 16.19 0.41 45.21 3.79
471 1006 3.369997 GGAACCCTAGAAGAAGGCAAGAG 60.370 52.174 0.00 0.00 35.09 2.85
477 1012 2.777094 AGAAGAAGGCAAGAGCAACTC 58.223 47.619 0.00 0.00 44.61 3.01
494 1029 0.721718 CTCTGCCCGAAAACGATGAC 59.278 55.000 0.00 0.00 0.00 3.06
499 1034 1.076332 CCCGAAAACGATGACCTGAC 58.924 55.000 0.00 0.00 0.00 3.51
512 1047 2.427095 TGACCTGACCATGTCTCATACG 59.573 50.000 6.91 0.00 33.15 3.06
513 1048 2.427453 GACCTGACCATGTCTCATACGT 59.573 50.000 0.00 0.00 33.15 3.57
516 1051 3.131223 CCTGACCATGTCTCATACGTTCT 59.869 47.826 0.00 0.00 33.15 3.01
517 1052 4.338400 CCTGACCATGTCTCATACGTTCTA 59.662 45.833 0.00 0.00 33.15 2.10
518 1053 5.010112 CCTGACCATGTCTCATACGTTCTAT 59.990 44.000 0.00 0.00 33.15 1.98
519 1054 6.206829 CCTGACCATGTCTCATACGTTCTATA 59.793 42.308 0.00 0.00 33.15 1.31
520 1055 6.967135 TGACCATGTCTCATACGTTCTATAC 58.033 40.000 0.00 0.00 33.15 1.47
573 1110 1.312815 GCTCTTTCAAGCCACACACT 58.687 50.000 0.00 0.00 36.22 3.55
592 1131 9.106070 CACACACTAGTAGTATAGATGTACACA 57.894 37.037 1.57 0.00 30.08 3.72
705 1276 4.473520 CGGCGCCTCATTCCACCT 62.474 66.667 26.68 0.00 0.00 4.00
720 1291 7.965718 TCATTCCACCTTTTTCATTTTGATCT 58.034 30.769 0.00 0.00 0.00 2.75
863 1452 4.581824 TCCCATGTCGTTATGTAGGAGTAC 59.418 45.833 0.00 0.00 0.00 2.73
886 1482 6.043411 ACTACTATGTGCAAGCTAAGCTAAC 58.957 40.000 11.76 4.15 38.25 2.34
898 1494 3.432517 AGCTAACGCTCTGCTTCAG 57.567 52.632 0.00 0.00 45.15 3.02
899 1495 0.605589 AGCTAACGCTCTGCTTCAGT 59.394 50.000 0.00 0.00 45.15 3.41
900 1496 1.819288 AGCTAACGCTCTGCTTCAGTA 59.181 47.619 0.00 0.00 45.15 2.74
901 1497 2.428890 AGCTAACGCTCTGCTTCAGTAT 59.571 45.455 0.00 0.00 45.15 2.12
902 1498 3.632604 AGCTAACGCTCTGCTTCAGTATA 59.367 43.478 0.00 0.00 45.15 1.47
903 1499 4.279671 AGCTAACGCTCTGCTTCAGTATAT 59.720 41.667 0.00 0.00 45.15 0.86
904 1500 4.619336 GCTAACGCTCTGCTTCAGTATATC 59.381 45.833 0.00 0.00 32.61 1.63
905 1501 3.651803 ACGCTCTGCTTCAGTATATCC 57.348 47.619 0.00 0.00 32.61 2.59
906 1502 2.959030 ACGCTCTGCTTCAGTATATCCA 59.041 45.455 0.00 0.00 32.61 3.41
907 1503 3.384789 ACGCTCTGCTTCAGTATATCCAA 59.615 43.478 0.00 0.00 32.61 3.53
908 1504 3.986572 CGCTCTGCTTCAGTATATCCAAG 59.013 47.826 0.00 0.00 32.61 3.61
909 1505 4.261783 CGCTCTGCTTCAGTATATCCAAGA 60.262 45.833 0.00 0.00 32.61 3.02
910 1506 5.605534 GCTCTGCTTCAGTATATCCAAGAA 58.394 41.667 0.00 0.00 32.61 2.52
911 1507 5.695816 GCTCTGCTTCAGTATATCCAAGAAG 59.304 44.000 0.00 0.00 38.88 2.85
916 1512 5.674525 CTTCAGTATATCCAAGAAGCACCA 58.325 41.667 0.00 0.00 30.64 4.17
917 1513 5.023533 TCAGTATATCCAAGAAGCACCAC 57.976 43.478 0.00 0.00 0.00 4.16
918 1514 3.804325 CAGTATATCCAAGAAGCACCACG 59.196 47.826 0.00 0.00 0.00 4.94
919 1515 1.668419 ATATCCAAGAAGCACCACGC 58.332 50.000 0.00 0.00 42.91 5.34
920 1516 0.323302 TATCCAAGAAGCACCACGCA 59.677 50.000 0.00 0.00 46.13 5.24
921 1517 0.957395 ATCCAAGAAGCACCACGCAG 60.957 55.000 0.00 0.00 46.13 5.18
922 1518 2.253452 CAAGAAGCACCACGCAGC 59.747 61.111 0.00 0.00 46.13 5.25
923 1519 2.203195 AAGAAGCACCACGCAGCA 60.203 55.556 0.00 0.00 46.13 4.41
924 1520 2.256591 AAGAAGCACCACGCAGCAG 61.257 57.895 0.00 0.00 46.13 4.24
925 1521 2.665008 AAGAAGCACCACGCAGCAGA 62.665 55.000 0.00 0.00 46.13 4.26
926 1522 2.203195 AAGCACCACGCAGCAGAA 60.203 55.556 0.00 0.00 46.13 3.02
927 1523 1.785041 GAAGCACCACGCAGCAGAAA 61.785 55.000 0.00 0.00 46.13 2.52
928 1524 1.383456 AAGCACCACGCAGCAGAAAA 61.383 50.000 0.00 0.00 46.13 2.29
929 1525 1.370900 GCACCACGCAGCAGAAAAG 60.371 57.895 0.00 0.00 41.79 2.27
930 1526 1.283793 CACCACGCAGCAGAAAAGG 59.716 57.895 0.00 0.00 0.00 3.11
931 1527 2.256461 CCACGCAGCAGAAAAGGC 59.744 61.111 0.00 0.00 0.00 4.35
932 1528 2.554636 CCACGCAGCAGAAAAGGCA 61.555 57.895 0.00 0.00 0.00 4.75
933 1529 1.359833 CACGCAGCAGAAAAGGCAA 59.640 52.632 0.00 0.00 0.00 4.52
934 1530 0.936297 CACGCAGCAGAAAAGGCAAC 60.936 55.000 0.00 0.00 0.00 4.17
1009 1613 2.787994 CCTCCATAATCACAGGCCATC 58.212 52.381 5.01 0.00 0.00 3.51
1029 1633 1.884444 GCTCTCTTCTCCGTTCCGT 59.116 57.895 0.00 0.00 0.00 4.69
1041 1656 1.352156 CGTTCCGTTCCACAGCTAGC 61.352 60.000 6.62 6.62 0.00 3.42
1042 1657 0.037232 GTTCCGTTCCACAGCTAGCT 60.037 55.000 12.68 12.68 0.00 3.32
1043 1658 1.203994 GTTCCGTTCCACAGCTAGCTA 59.796 52.381 18.86 0.00 0.00 3.32
1044 1659 1.103803 TCCGTTCCACAGCTAGCTAG 58.896 55.000 18.86 16.84 0.00 3.42
1109 1724 4.814294 GCCAGCGTCCCGTACCTG 62.814 72.222 0.00 0.00 0.00 4.00
1154 1769 2.561209 TCAGGCCTCATTACCAGGTA 57.439 50.000 0.00 0.00 32.98 3.08
1160 1775 2.398588 CCTCATTACCAGGTAGCTCCA 58.601 52.381 0.00 0.00 39.02 3.86
1163 1778 3.900601 CTCATTACCAGGTAGCTCCAGAT 59.099 47.826 0.00 0.00 39.02 2.90
1217 1832 2.504244 GTTCCTCAGGCGACGTCG 60.504 66.667 32.57 32.57 43.27 5.12
1656 2283 4.493747 CCGTCGAGGAAGCGGGAC 62.494 72.222 6.70 0.00 45.00 4.46
1867 2518 3.004752 AGTGCTGAGTTGTCCAGTTTT 57.995 42.857 0.00 0.00 34.29 2.43
1868 2519 2.684881 AGTGCTGAGTTGTCCAGTTTTG 59.315 45.455 0.00 0.00 34.29 2.44
1869 2520 1.405105 TGCTGAGTTGTCCAGTTTTGC 59.595 47.619 0.00 0.00 34.29 3.68
1870 2521 1.269257 GCTGAGTTGTCCAGTTTTGCC 60.269 52.381 0.00 0.00 34.29 4.52
1871 2522 2.023673 CTGAGTTGTCCAGTTTTGCCA 58.976 47.619 0.00 0.00 0.00 4.92
1875 2535 3.561143 AGTTGTCCAGTTTTGCCATGTA 58.439 40.909 0.00 0.00 0.00 2.29
1876 2536 3.317993 AGTTGTCCAGTTTTGCCATGTAC 59.682 43.478 0.00 0.00 0.00 2.90
1887 2547 7.280876 CAGTTTTGCCATGTACTCATGTACTAT 59.719 37.037 7.67 0.00 46.99 2.12
1888 2548 8.482943 AGTTTTGCCATGTACTCATGTACTATA 58.517 33.333 7.67 0.00 46.99 1.31
1889 2549 9.104965 GTTTTGCCATGTACTCATGTACTATAA 57.895 33.333 7.67 0.00 46.99 0.98
1891 2551 7.354751 TGCCATGTACTCATGTACTATAACA 57.645 36.000 7.67 0.00 46.99 2.41
1893 2553 8.261522 TGCCATGTACTCATGTACTATAACAAA 58.738 33.333 7.67 0.00 46.99 2.83
1991 2769 9.710979 TTTAAAAACTCGTCACAGAAATACAAG 57.289 29.630 0.00 0.00 0.00 3.16
1992 2770 4.992381 AACTCGTCACAGAAATACAAGC 57.008 40.909 0.00 0.00 0.00 4.01
1994 2772 3.990469 ACTCGTCACAGAAATACAAGCAG 59.010 43.478 0.00 0.00 0.00 4.24
2003 2781 8.481314 TCACAGAAATACAAGCAGAATCTATCT 58.519 33.333 0.00 0.00 39.68 1.98
2013 2791 8.270744 ACAAGCAGAATCTATCTAGGTGATTTT 58.729 33.333 0.00 0.00 36.32 1.82
2014 2792 8.557864 CAAGCAGAATCTATCTAGGTGATTTTG 58.442 37.037 13.81 13.81 36.32 2.44
2055 2833 7.155655 TGCACAATCAACATTAGCTGATAAA 57.844 32.000 0.00 0.00 30.66 1.40
2067 2882 2.724349 GCTGATAAAATGAAGGCAGCG 58.276 47.619 0.00 0.00 39.23 5.18
2068 2883 2.724349 CTGATAAAATGAAGGCAGCGC 58.276 47.619 0.00 0.00 0.00 5.92
2072 2887 0.038892 AAAATGAAGGCAGCGCTGTG 60.039 50.000 35.80 15.92 0.00 3.66
2098 2913 7.458397 ACTGGAAAATCAACATTACCTGTCTA 58.542 34.615 0.00 0.00 36.98 2.59
2130 2947 7.067859 CCATGAGATTTCTGGATAAGCAAAAGA 59.932 37.037 0.00 0.00 31.38 2.52
2134 2951 8.585471 AGATTTCTGGATAAGCAAAAGATTCA 57.415 30.769 0.00 0.00 0.00 2.57
2155 2972 1.811965 AGCATGCAACTCAATAACGCA 59.188 42.857 21.98 0.00 36.95 5.24
2163 2980 7.078011 TGCAACTCAATAACGCATATAACAA 57.922 32.000 0.00 0.00 0.00 2.83
2211 3032 9.836864 AAACTTGATATAACAGCATCTCACATA 57.163 29.630 0.00 0.00 0.00 2.29
2247 3068 6.481954 ACGTAGTTTCAATGAAAGATGACC 57.518 37.500 8.88 0.00 37.78 4.02
2277 3098 1.968017 AGGCACACCAGATGCAACG 60.968 57.895 0.00 0.00 45.27 4.10
2290 3111 3.641436 AGATGCAACGGACCAGACATATA 59.359 43.478 0.00 0.00 0.00 0.86
2311 3135 4.297299 AGTCGTTCGTTTAACTGACTCA 57.703 40.909 0.00 0.00 42.73 3.41
2341 3165 6.705825 AGAAATAACCAAAAACTCAATGGTGC 59.294 34.615 0.00 0.00 46.46 5.01
2360 3229 2.058057 GCAAACAACAGGCAAATACGG 58.942 47.619 0.00 0.00 0.00 4.02
2436 3307 1.523938 GGTGGTAGGGAATCGCAGC 60.524 63.158 0.00 0.00 0.00 5.25
2559 3430 4.941263 GCTTCATTGTACCACTGGACAATA 59.059 41.667 18.10 9.02 42.89 1.90
2700 3571 3.197790 CCTTCATCAGGCACCGCG 61.198 66.667 0.00 0.00 35.13 6.46
2739 3610 0.319555 TCTTCACCACTTCCTTCGCG 60.320 55.000 0.00 0.00 0.00 5.87
2799 3670 0.392863 CATGCATCACGTCCTTGGGA 60.393 55.000 0.00 0.00 0.00 4.37
2816 3687 2.041405 AGGTAGGGCTGAGGAGGC 60.041 66.667 0.00 0.00 44.21 4.70
2841 3712 2.350134 CCCTTGAGCTGAGCTGCA 59.650 61.111 13.71 7.12 39.88 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.932710 AGTAAGCCATGTTACACGTGATG 59.067 43.478 25.01 14.96 37.29 3.07
1 2 4.202245 AGTAAGCCATGTTACACGTGAT 57.798 40.909 25.01 9.25 37.29 3.06
2 3 3.671008 AGTAAGCCATGTTACACGTGA 57.329 42.857 25.01 2.68 37.29 4.35
3 4 3.302434 CGTAGTAAGCCATGTTACACGTG 59.698 47.826 15.48 15.48 35.65 4.49
4 5 3.191162 TCGTAGTAAGCCATGTTACACGT 59.809 43.478 18.80 0.00 37.92 4.49
5 6 3.761657 TCGTAGTAAGCCATGTTACACG 58.238 45.455 16.23 16.23 37.98 4.49
6 7 4.032558 GCTTCGTAGTAAGCCATGTTACAC 59.967 45.833 8.45 4.75 44.98 2.90
7 8 4.178540 GCTTCGTAGTAAGCCATGTTACA 58.821 43.478 8.45 0.00 44.98 2.41
8 9 4.773742 GCTTCGTAGTAAGCCATGTTAC 57.226 45.455 0.00 0.00 44.98 2.50
17 18 8.396390 TGTCAAGAGTATTAGCTTCGTAGTAAG 58.604 37.037 0.00 0.00 0.00 2.34
18 19 8.180267 GTGTCAAGAGTATTAGCTTCGTAGTAA 58.820 37.037 0.00 0.00 0.00 2.24
19 20 7.201679 GGTGTCAAGAGTATTAGCTTCGTAGTA 60.202 40.741 0.00 0.00 0.00 1.82
20 21 6.404513 GGTGTCAAGAGTATTAGCTTCGTAGT 60.405 42.308 0.00 0.00 0.00 2.73
21 22 5.972382 GGTGTCAAGAGTATTAGCTTCGTAG 59.028 44.000 0.00 0.00 0.00 3.51
22 23 5.416639 TGGTGTCAAGAGTATTAGCTTCGTA 59.583 40.000 0.00 0.00 0.00 3.43
23 24 4.219944 TGGTGTCAAGAGTATTAGCTTCGT 59.780 41.667 0.00 0.00 0.00 3.85
24 25 4.744570 TGGTGTCAAGAGTATTAGCTTCG 58.255 43.478 0.00 0.00 0.00 3.79
38 39 2.997980 TCTGAACTTGCTTGGTGTCAA 58.002 42.857 0.00 0.00 0.00 3.18
39 40 2.708216 TCTGAACTTGCTTGGTGTCA 57.292 45.000 0.00 0.00 0.00 3.58
40 41 5.886960 ATATTCTGAACTTGCTTGGTGTC 57.113 39.130 0.00 0.00 0.00 3.67
41 42 5.355350 GCTATATTCTGAACTTGCTTGGTGT 59.645 40.000 0.00 0.00 0.00 4.16
42 43 5.220931 GGCTATATTCTGAACTTGCTTGGTG 60.221 44.000 0.00 0.00 0.00 4.17
43 44 4.884164 GGCTATATTCTGAACTTGCTTGGT 59.116 41.667 0.00 0.00 0.00 3.67
44 45 4.024556 CGGCTATATTCTGAACTTGCTTGG 60.025 45.833 0.00 0.00 0.00 3.61
45 46 4.553547 GCGGCTATATTCTGAACTTGCTTG 60.554 45.833 0.00 0.00 0.00 4.01
46 47 3.561725 GCGGCTATATTCTGAACTTGCTT 59.438 43.478 0.00 0.00 0.00 3.91
47 48 3.134458 GCGGCTATATTCTGAACTTGCT 58.866 45.455 0.00 0.00 0.00 3.91
48 49 3.134458 AGCGGCTATATTCTGAACTTGC 58.866 45.455 0.00 0.00 0.00 4.01
49 50 5.525378 AGAAAGCGGCTATATTCTGAACTTG 59.475 40.000 13.16 0.00 31.25 3.16
50 51 5.675538 AGAAAGCGGCTATATTCTGAACTT 58.324 37.500 13.16 0.00 31.25 2.66
51 52 5.283457 AGAAAGCGGCTATATTCTGAACT 57.717 39.130 13.16 0.00 31.25 3.01
52 53 6.146347 CCTTAGAAAGCGGCTATATTCTGAAC 59.854 42.308 20.31 0.00 34.24 3.18
53 54 6.183360 ACCTTAGAAAGCGGCTATATTCTGAA 60.183 38.462 20.31 11.98 34.24 3.02
54 55 5.304614 ACCTTAGAAAGCGGCTATATTCTGA 59.695 40.000 20.31 13.74 34.24 3.27
55 56 5.406780 CACCTTAGAAAGCGGCTATATTCTG 59.593 44.000 20.31 10.03 34.24 3.02
56 57 5.511545 CCACCTTAGAAAGCGGCTATATTCT 60.512 44.000 16.93 16.93 36.24 2.40
57 58 4.691216 CCACCTTAGAAAGCGGCTATATTC 59.309 45.833 1.35 3.64 0.00 1.75
58 59 4.347000 TCCACCTTAGAAAGCGGCTATATT 59.653 41.667 1.35 0.00 0.00 1.28
59 60 3.901844 TCCACCTTAGAAAGCGGCTATAT 59.098 43.478 1.35 0.00 0.00 0.86
60 61 3.302161 TCCACCTTAGAAAGCGGCTATA 58.698 45.455 1.35 0.00 0.00 1.31
61 62 2.116238 TCCACCTTAGAAAGCGGCTAT 58.884 47.619 1.35 0.00 0.00 2.97
62 63 1.563924 TCCACCTTAGAAAGCGGCTA 58.436 50.000 1.35 0.00 0.00 3.93
63 64 0.690762 TTCCACCTTAGAAAGCGGCT 59.309 50.000 0.00 0.00 0.00 5.52
64 65 1.751437 ATTCCACCTTAGAAAGCGGC 58.249 50.000 0.00 0.00 0.00 6.53
65 66 3.081804 ACAATTCCACCTTAGAAAGCGG 58.918 45.455 0.00 0.00 0.00 5.52
66 67 4.003648 AGACAATTCCACCTTAGAAAGCG 58.996 43.478 0.00 0.00 0.00 4.68
67 68 5.003804 TCAGACAATTCCACCTTAGAAAGC 58.996 41.667 0.00 0.00 0.00 3.51
68 69 7.609532 AGATTCAGACAATTCCACCTTAGAAAG 59.390 37.037 0.00 0.00 0.00 2.62
69 70 7.461749 AGATTCAGACAATTCCACCTTAGAAA 58.538 34.615 0.00 0.00 0.00 2.52
70 71 7.020827 AGATTCAGACAATTCCACCTTAGAA 57.979 36.000 0.00 0.00 0.00 2.10
71 72 6.627087 AGATTCAGACAATTCCACCTTAGA 57.373 37.500 0.00 0.00 0.00 2.10
72 73 7.560368 AGTAGATTCAGACAATTCCACCTTAG 58.440 38.462 0.00 0.00 0.00 2.18
73 74 7.496346 AGTAGATTCAGACAATTCCACCTTA 57.504 36.000 0.00 0.00 0.00 2.69
74 75 6.380079 AGTAGATTCAGACAATTCCACCTT 57.620 37.500 0.00 0.00 0.00 3.50
75 76 5.394663 CGAGTAGATTCAGACAATTCCACCT 60.395 44.000 0.00 0.00 0.00 4.00
76 77 4.806247 CGAGTAGATTCAGACAATTCCACC 59.194 45.833 0.00 0.00 0.00 4.61
77 78 4.268884 GCGAGTAGATTCAGACAATTCCAC 59.731 45.833 0.00 0.00 0.00 4.02
78 79 4.081697 TGCGAGTAGATTCAGACAATTCCA 60.082 41.667 0.00 0.00 0.00 3.53
79 80 4.433615 TGCGAGTAGATTCAGACAATTCC 58.566 43.478 0.00 0.00 0.00 3.01
80 81 6.408858 TTTGCGAGTAGATTCAGACAATTC 57.591 37.500 0.00 0.00 0.00 2.17
81 82 6.801539 TTTTGCGAGTAGATTCAGACAATT 57.198 33.333 0.00 0.00 0.00 2.32
82 83 6.801539 TTTTTGCGAGTAGATTCAGACAAT 57.198 33.333 0.00 0.00 0.00 2.71
109 110 6.348540 GGAGCGTAGTGATTCAGACAATTTTT 60.349 38.462 0.00 0.00 0.00 1.94
110 111 5.122396 GGAGCGTAGTGATTCAGACAATTTT 59.878 40.000 0.00 0.00 0.00 1.82
111 112 4.631813 GGAGCGTAGTGATTCAGACAATTT 59.368 41.667 0.00 0.00 0.00 1.82
112 113 4.184629 GGAGCGTAGTGATTCAGACAATT 58.815 43.478 0.00 0.00 0.00 2.32
113 114 3.430929 GGGAGCGTAGTGATTCAGACAAT 60.431 47.826 0.00 0.00 0.00 2.71
114 115 2.094182 GGGAGCGTAGTGATTCAGACAA 60.094 50.000 0.00 0.00 0.00 3.18
115 116 1.476891 GGGAGCGTAGTGATTCAGACA 59.523 52.381 0.00 0.00 0.00 3.41
116 117 1.534175 CGGGAGCGTAGTGATTCAGAC 60.534 57.143 0.00 0.00 0.00 3.51
117 118 0.738975 CGGGAGCGTAGTGATTCAGA 59.261 55.000 0.00 0.00 0.00 3.27
118 119 0.738975 TCGGGAGCGTAGTGATTCAG 59.261 55.000 0.00 0.00 0.00 3.02
119 120 1.399714 ATCGGGAGCGTAGTGATTCA 58.600 50.000 0.00 0.00 0.00 2.57
120 121 2.351544 GGTATCGGGAGCGTAGTGATTC 60.352 54.545 0.00 0.00 0.00 2.52
121 122 1.612463 GGTATCGGGAGCGTAGTGATT 59.388 52.381 0.00 0.00 0.00 2.57
122 123 1.202903 AGGTATCGGGAGCGTAGTGAT 60.203 52.381 0.00 0.00 0.00 3.06
123 124 0.182061 AGGTATCGGGAGCGTAGTGA 59.818 55.000 0.00 0.00 0.00 3.41
124 125 0.311165 CAGGTATCGGGAGCGTAGTG 59.689 60.000 0.00 0.00 0.00 2.74
125 126 0.822532 CCAGGTATCGGGAGCGTAGT 60.823 60.000 0.00 0.00 0.00 2.73
126 127 1.957562 CCAGGTATCGGGAGCGTAG 59.042 63.158 0.00 0.00 0.00 3.51
127 128 2.198287 GCCAGGTATCGGGAGCGTA 61.198 63.158 0.00 0.00 0.00 4.42
128 129 3.537874 GCCAGGTATCGGGAGCGT 61.538 66.667 0.00 0.00 0.00 5.07
129 130 2.587322 TTTGCCAGGTATCGGGAGCG 62.587 60.000 0.00 0.00 0.00 5.03
130 131 0.393808 TTTTGCCAGGTATCGGGAGC 60.394 55.000 0.00 0.00 0.00 4.70
131 132 1.065418 AGTTTTGCCAGGTATCGGGAG 60.065 52.381 0.00 0.00 0.00 4.30
132 133 0.988832 AGTTTTGCCAGGTATCGGGA 59.011 50.000 0.00 0.00 0.00 5.14
133 134 2.702592 TAGTTTTGCCAGGTATCGGG 57.297 50.000 0.00 0.00 0.00 5.14
134 135 3.945285 ACATTAGTTTTGCCAGGTATCGG 59.055 43.478 0.00 0.00 0.00 4.18
135 136 4.876107 AGACATTAGTTTTGCCAGGTATCG 59.124 41.667 0.00 0.00 0.00 2.92
136 137 5.449177 GCAGACATTAGTTTTGCCAGGTATC 60.449 44.000 0.00 0.00 34.50 2.24
137 138 4.399303 GCAGACATTAGTTTTGCCAGGTAT 59.601 41.667 0.00 0.00 34.50 2.73
138 139 3.756434 GCAGACATTAGTTTTGCCAGGTA 59.244 43.478 0.00 0.00 34.50 3.08
139 140 2.558359 GCAGACATTAGTTTTGCCAGGT 59.442 45.455 0.00 0.00 34.50 4.00
140 141 2.821969 AGCAGACATTAGTTTTGCCAGG 59.178 45.455 0.00 0.00 38.58 4.45
141 142 4.022935 TGAAGCAGACATTAGTTTTGCCAG 60.023 41.667 0.00 0.00 38.58 4.85
142 143 3.888323 TGAAGCAGACATTAGTTTTGCCA 59.112 39.130 0.00 0.00 38.58 4.92
143 144 4.503741 TGAAGCAGACATTAGTTTTGCC 57.496 40.909 0.00 0.00 38.58 4.52
144 145 4.860907 CCATGAAGCAGACATTAGTTTTGC 59.139 41.667 0.00 0.00 38.28 3.68
145 146 5.404946 CCCATGAAGCAGACATTAGTTTTG 58.595 41.667 0.00 0.00 0.00 2.44
146 147 4.463891 CCCCATGAAGCAGACATTAGTTTT 59.536 41.667 0.00 0.00 0.00 2.43
147 148 4.019174 CCCCATGAAGCAGACATTAGTTT 58.981 43.478 0.00 0.00 0.00 2.66
148 149 3.624777 CCCCATGAAGCAGACATTAGTT 58.375 45.455 0.00 0.00 0.00 2.24
149 150 2.684927 GCCCCATGAAGCAGACATTAGT 60.685 50.000 0.00 0.00 0.00 2.24
150 151 1.952296 GCCCCATGAAGCAGACATTAG 59.048 52.381 0.00 0.00 0.00 1.73
151 152 1.284491 TGCCCCATGAAGCAGACATTA 59.716 47.619 5.61 0.00 33.08 1.90
152 153 0.040058 TGCCCCATGAAGCAGACATT 59.960 50.000 5.61 0.00 33.08 2.71
153 154 0.040058 TTGCCCCATGAAGCAGACAT 59.960 50.000 9.19 0.00 40.73 3.06
154 155 0.178967 TTTGCCCCATGAAGCAGACA 60.179 50.000 9.19 0.00 40.73 3.41
155 156 0.968405 TTTTGCCCCATGAAGCAGAC 59.032 50.000 9.19 0.00 40.73 3.51
156 157 1.551430 CATTTTGCCCCATGAAGCAGA 59.449 47.619 9.19 3.42 40.73 4.26
157 158 1.276989 ACATTTTGCCCCATGAAGCAG 59.723 47.619 9.19 2.20 40.73 4.24
158 159 1.275856 GACATTTTGCCCCATGAAGCA 59.724 47.619 5.61 5.61 37.18 3.91
159 160 1.275856 TGACATTTTGCCCCATGAAGC 59.724 47.619 0.00 0.00 0.00 3.86
160 161 2.827322 TCTGACATTTTGCCCCATGAAG 59.173 45.455 0.00 0.00 0.00 3.02
161 162 2.562298 GTCTGACATTTTGCCCCATGAA 59.438 45.455 2.24 0.00 0.00 2.57
162 163 2.170166 GTCTGACATTTTGCCCCATGA 58.830 47.619 2.24 0.00 0.00 3.07
163 164 2.094390 CAGTCTGACATTTTGCCCCATG 60.094 50.000 10.88 0.00 0.00 3.66
164 165 2.173519 CAGTCTGACATTTTGCCCCAT 58.826 47.619 10.88 0.00 0.00 4.00
165 166 1.619654 CAGTCTGACATTTTGCCCCA 58.380 50.000 10.88 0.00 0.00 4.96
166 167 0.244721 GCAGTCTGACATTTTGCCCC 59.755 55.000 10.88 0.00 0.00 5.80
167 168 0.961019 TGCAGTCTGACATTTTGCCC 59.039 50.000 10.88 0.00 33.98 5.36
168 169 1.337703 TGTGCAGTCTGACATTTTGCC 59.662 47.619 10.88 6.06 33.98 4.52
169 170 2.291465 TCTGTGCAGTCTGACATTTTGC 59.709 45.455 10.88 11.24 35.42 3.68
170 171 3.313249 TGTCTGTGCAGTCTGACATTTTG 59.687 43.478 10.88 0.43 39.85 2.44
171 172 3.544684 TGTCTGTGCAGTCTGACATTTT 58.455 40.909 10.88 0.00 39.85 1.82
172 173 3.198409 TGTCTGTGCAGTCTGACATTT 57.802 42.857 10.88 0.00 39.85 2.32
173 174 2.916702 TGTCTGTGCAGTCTGACATT 57.083 45.000 10.88 0.00 39.85 2.71
174 175 2.916702 TTGTCTGTGCAGTCTGACAT 57.083 45.000 14.86 0.00 42.56 3.06
175 176 2.916702 ATTGTCTGTGCAGTCTGACA 57.083 45.000 10.88 11.44 41.81 3.58
176 177 5.673337 TTTTATTGTCTGTGCAGTCTGAC 57.327 39.130 3.32 0.00 37.00 3.51
206 207 0.395312 GTCGGTTGGGTTCCAGAGAA 59.605 55.000 0.00 0.00 33.81 2.87
207 208 0.761323 TGTCGGTTGGGTTCCAGAGA 60.761 55.000 0.00 0.00 33.81 3.10
208 209 0.320771 CTGTCGGTTGGGTTCCAGAG 60.321 60.000 0.00 0.00 33.81 3.35
209 210 1.052124 ACTGTCGGTTGGGTTCCAGA 61.052 55.000 0.00 0.00 33.81 3.86
210 211 0.179029 AACTGTCGGTTGGGTTCCAG 60.179 55.000 0.00 0.00 36.70 3.86
211 212 1.916738 AACTGTCGGTTGGGTTCCA 59.083 52.632 0.00 0.00 36.70 3.53
212 213 4.892002 AACTGTCGGTTGGGTTCC 57.108 55.556 0.00 0.00 36.70 3.62
219 220 3.181437 ACCCTTTTATCCAACTGTCGGTT 60.181 43.478 0.00 0.00 38.93 4.44
220 221 2.374170 ACCCTTTTATCCAACTGTCGGT 59.626 45.455 0.00 0.00 0.00 4.69
221 222 3.007635 GACCCTTTTATCCAACTGTCGG 58.992 50.000 0.00 0.00 0.00 4.79
222 223 2.671396 CGACCCTTTTATCCAACTGTCG 59.329 50.000 0.00 0.00 38.42 4.35
223 224 3.671716 ACGACCCTTTTATCCAACTGTC 58.328 45.455 0.00 0.00 0.00 3.51
224 225 3.782656 ACGACCCTTTTATCCAACTGT 57.217 42.857 0.00 0.00 0.00 3.55
225 226 4.630069 CAGTACGACCCTTTTATCCAACTG 59.370 45.833 0.00 0.00 0.00 3.16
226 227 4.828829 CAGTACGACCCTTTTATCCAACT 58.171 43.478 0.00 0.00 0.00 3.16
227 228 3.373130 GCAGTACGACCCTTTTATCCAAC 59.627 47.826 0.00 0.00 0.00 3.77
228 229 3.602483 GCAGTACGACCCTTTTATCCAA 58.398 45.455 0.00 0.00 0.00 3.53
229 230 2.093341 GGCAGTACGACCCTTTTATCCA 60.093 50.000 0.00 0.00 0.00 3.41
230 231 2.558378 GGCAGTACGACCCTTTTATCC 58.442 52.381 0.00 0.00 0.00 2.59
231 232 2.558378 GGGCAGTACGACCCTTTTATC 58.442 52.381 16.62 0.00 43.36 1.75
232 233 2.704464 GGGCAGTACGACCCTTTTAT 57.296 50.000 16.62 0.00 43.36 1.40
240 241 1.334243 CACTAGCTAGGGCAGTACGAC 59.666 57.143 24.35 0.00 41.70 4.34
241 242 1.676746 CACTAGCTAGGGCAGTACGA 58.323 55.000 24.35 0.00 41.70 3.43
283 284 3.181516 GCAACTTGCCACTAATTCTCTCG 60.182 47.826 1.95 0.00 37.42 4.04
316 851 3.265489 TGGATAAAGGGAAGGTGGAACT 58.735 45.455 0.00 0.00 36.74 3.01
344 879 0.849094 TTACTGTGGCCCAGGGGAAT 60.849 55.000 20.97 6.42 46.06 3.01
435 970 4.317530 AGGGTTCCTACCAGAAATTTCC 57.682 45.455 14.61 0.00 46.96 3.13
471 1006 1.503818 TCGTTTTCGGGCAGAGTTGC 61.504 55.000 0.00 0.00 45.00 4.17
477 1012 0.673644 AGGTCATCGTTTTCGGGCAG 60.674 55.000 0.00 0.00 44.25 4.85
494 1029 3.131223 AGAACGTATGAGACATGGTCAGG 59.869 47.826 0.00 0.00 34.60 3.86
499 1034 6.307915 CGAGTATAGAACGTATGAGACATGG 58.692 44.000 0.00 0.00 0.00 3.66
512 1047 5.687770 GGTTCCTCTACCGAGTATAGAAC 57.312 47.826 0.00 0.00 35.64 3.01
530 1067 0.808755 CTGTAAACATGGCCCGGTTC 59.191 55.000 9.32 0.10 0.00 3.62
537 1074 5.567138 AAGAGCAATACTGTAAACATGGC 57.433 39.130 0.00 0.00 0.00 4.40
573 1110 9.910267 TCAAAGGTGTGTACATCTATACTACTA 57.090 33.333 0.00 0.00 36.03 1.82
592 1131 1.144093 TCCGGGTGAATTGTCAAAGGT 59.856 47.619 0.00 0.00 34.87 3.50
705 1276 4.757799 TCGCCGAGATCAAAATGAAAAA 57.242 36.364 0.00 0.00 0.00 1.94
720 1291 2.281831 TGCCCATTTGTTCGCCGA 60.282 55.556 0.00 0.00 0.00 5.54
769 1344 5.127693 TGCAACGTTGTTTTATTATGGCT 57.872 34.783 27.78 0.00 0.00 4.75
770 1345 5.574830 TCATGCAACGTTGTTTTATTATGGC 59.425 36.000 27.78 10.63 0.00 4.40
863 1452 5.174035 CGTTAGCTTAGCTTGCACATAGTAG 59.826 44.000 13.44 0.00 40.44 2.57
866 1462 3.302740 GCGTTAGCTTAGCTTGCACATAG 60.303 47.826 13.44 0.00 40.44 2.23
886 1482 3.650070 TGGATATACTGAAGCAGAGCG 57.350 47.619 0.82 0.00 35.18 5.03
893 1489 5.525378 GTGGTGCTTCTTGGATATACTGAAG 59.475 44.000 13.48 13.48 37.69 3.02
894 1490 5.428253 GTGGTGCTTCTTGGATATACTGAA 58.572 41.667 0.00 0.00 0.00 3.02
895 1491 4.441495 CGTGGTGCTTCTTGGATATACTGA 60.441 45.833 0.00 0.00 0.00 3.41
896 1492 3.804325 CGTGGTGCTTCTTGGATATACTG 59.196 47.826 0.00 0.00 0.00 2.74
897 1493 3.741388 GCGTGGTGCTTCTTGGATATACT 60.741 47.826 0.00 0.00 41.73 2.12
898 1494 2.544267 GCGTGGTGCTTCTTGGATATAC 59.456 50.000 0.00 0.00 41.73 1.47
899 1495 2.169561 TGCGTGGTGCTTCTTGGATATA 59.830 45.455 0.00 0.00 46.63 0.86
900 1496 1.065491 TGCGTGGTGCTTCTTGGATAT 60.065 47.619 0.00 0.00 46.63 1.63
901 1497 0.323302 TGCGTGGTGCTTCTTGGATA 59.677 50.000 0.00 0.00 46.63 2.59
902 1498 0.957395 CTGCGTGGTGCTTCTTGGAT 60.957 55.000 0.00 0.00 46.63 3.41
903 1499 1.597854 CTGCGTGGTGCTTCTTGGA 60.598 57.895 0.00 0.00 46.63 3.53
904 1500 2.949106 CTGCGTGGTGCTTCTTGG 59.051 61.111 0.00 0.00 46.63 3.61
905 1501 2.253452 GCTGCGTGGTGCTTCTTG 59.747 61.111 0.00 0.00 46.63 3.02
906 1502 2.203195 TGCTGCGTGGTGCTTCTT 60.203 55.556 0.00 0.00 46.63 2.52
907 1503 2.665008 TTCTGCTGCGTGGTGCTTCT 62.665 55.000 0.00 0.00 46.63 2.85
908 1504 1.785041 TTTCTGCTGCGTGGTGCTTC 61.785 55.000 0.00 0.00 46.63 3.86
909 1505 1.383456 TTTTCTGCTGCGTGGTGCTT 61.383 50.000 0.00 0.00 46.63 3.91
910 1506 1.789078 CTTTTCTGCTGCGTGGTGCT 61.789 55.000 0.00 0.00 46.63 4.40
911 1507 1.370900 CTTTTCTGCTGCGTGGTGC 60.371 57.895 0.00 0.00 46.70 5.01
912 1508 1.283793 CCTTTTCTGCTGCGTGGTG 59.716 57.895 0.00 0.00 0.00 4.17
913 1509 2.555547 GCCTTTTCTGCTGCGTGGT 61.556 57.895 0.00 0.00 0.00 4.16
914 1510 2.074230 TTGCCTTTTCTGCTGCGTGG 62.074 55.000 0.00 0.00 0.00 4.94
915 1511 0.936297 GTTGCCTTTTCTGCTGCGTG 60.936 55.000 0.00 0.00 0.00 5.34
916 1512 1.103398 AGTTGCCTTTTCTGCTGCGT 61.103 50.000 0.00 0.00 0.00 5.24
917 1513 0.031178 AAGTTGCCTTTTCTGCTGCG 59.969 50.000 0.00 0.00 0.00 5.18
918 1514 1.775869 GAAGTTGCCTTTTCTGCTGC 58.224 50.000 0.00 0.00 0.00 5.25
919 1515 1.603802 TCGAAGTTGCCTTTTCTGCTG 59.396 47.619 0.00 0.00 0.00 4.41
920 1516 1.604278 GTCGAAGTTGCCTTTTCTGCT 59.396 47.619 0.00 0.00 0.00 4.24
921 1517 1.660333 CGTCGAAGTTGCCTTTTCTGC 60.660 52.381 0.00 0.00 0.00 4.26
922 1518 1.864711 TCGTCGAAGTTGCCTTTTCTG 59.135 47.619 0.00 0.00 0.00 3.02
923 1519 1.865340 GTCGTCGAAGTTGCCTTTTCT 59.135 47.619 0.00 0.00 0.00 2.52
924 1520 1.396815 CGTCGTCGAAGTTGCCTTTTC 60.397 52.381 0.00 0.00 39.71 2.29
925 1521 0.580104 CGTCGTCGAAGTTGCCTTTT 59.420 50.000 0.00 0.00 39.71 2.27
926 1522 0.529119 ACGTCGTCGAAGTTGCCTTT 60.529 50.000 9.47 0.00 40.62 3.11
927 1523 1.066918 ACGTCGTCGAAGTTGCCTT 59.933 52.632 9.47 0.00 40.62 4.35
928 1524 1.660575 CACGTCGTCGAAGTTGCCT 60.661 57.895 11.24 0.00 40.62 4.75
929 1525 2.654912 CCACGTCGTCGAAGTTGCC 61.655 63.158 11.24 0.00 40.62 4.52
930 1526 2.654912 CCCACGTCGTCGAAGTTGC 61.655 63.158 11.24 0.00 40.62 4.17
931 1527 1.273455 GACCCACGTCGTCGAAGTTG 61.273 60.000 11.24 8.15 40.62 3.16
932 1528 1.008079 GACCCACGTCGTCGAAGTT 60.008 57.895 11.24 0.00 40.62 2.66
933 1529 2.641559 GACCCACGTCGTCGAAGT 59.358 61.111 9.47 8.06 40.62 3.01
934 1530 2.126580 GGACCCACGTCGTCGAAG 60.127 66.667 9.47 6.63 40.17 3.79
935 1531 2.595463 AGGACCCACGTCGTCGAA 60.595 61.111 9.47 0.00 40.17 3.71
936 1532 2.730066 TACAGGACCCACGTCGTCGA 62.730 60.000 9.47 0.00 40.17 4.20
937 1533 2.249557 CTACAGGACCCACGTCGTCG 62.250 65.000 0.00 0.00 40.17 5.12
1009 1613 1.139947 GGAACGGAGAAGAGAGCGG 59.860 63.158 0.00 0.00 0.00 5.52
1041 1656 0.584396 CGGTCACTCGAGCTAGCTAG 59.416 60.000 19.38 18.55 37.51 3.42
1042 1657 0.177373 TCGGTCACTCGAGCTAGCTA 59.823 55.000 19.38 1.34 37.51 3.32
1043 1658 1.078356 TCGGTCACTCGAGCTAGCT 60.078 57.895 19.45 19.45 37.51 3.32
1044 1659 3.499050 TCGGTCACTCGAGCTAGC 58.501 61.111 13.61 6.62 37.51 3.42
1054 1669 2.355837 TTGCTCGTGCTCGGTCAC 60.356 61.111 11.19 0.00 40.48 3.67
1055 1670 2.049156 CTTGCTCGTGCTCGGTCA 60.049 61.111 11.19 3.94 40.48 4.02
1154 1769 2.548464 AGAGGAAGTCATCTGGAGCT 57.452 50.000 0.00 0.00 35.47 4.09
1160 1775 4.678256 TGTACTGGAAGAGGAAGTCATCT 58.322 43.478 0.00 0.00 38.83 2.90
1163 1778 3.005472 CGTTGTACTGGAAGAGGAAGTCA 59.995 47.826 0.00 0.00 37.43 3.41
1640 2267 3.277211 TTGTCCCGCTTCCTCGACG 62.277 63.158 0.00 0.00 0.00 5.12
1643 2270 1.004918 AACTTGTCCCGCTTCCTCG 60.005 57.895 0.00 0.00 0.00 4.63
1649 2276 1.451936 AAGCTCAACTTGTCCCGCT 59.548 52.632 0.00 0.00 37.17 5.52
1669 2296 0.536687 CATATCACCCTGGGCAGCAG 60.537 60.000 14.08 0.00 0.00 4.24
1718 2351 8.364894 AGGTACAAAAATGGTAATTCAAGTTCC 58.635 33.333 0.00 0.00 0.00 3.62
1851 2502 2.023673 TGGCAAAACTGGACAACTCAG 58.976 47.619 0.00 0.00 38.16 3.35
1855 2506 2.888834 ACATGGCAAAACTGGACAAC 57.111 45.000 0.00 0.00 0.00 3.32
1856 2507 3.561143 AGTACATGGCAAAACTGGACAA 58.439 40.909 4.14 0.00 0.00 3.18
1974 2744 4.251543 TCTGCTTGTATTTCTGTGACGA 57.748 40.909 0.00 0.00 0.00 4.20
1975 2745 4.990543 TTCTGCTTGTATTTCTGTGACG 57.009 40.909 0.00 0.00 0.00 4.35
1976 2746 6.734104 AGATTCTGCTTGTATTTCTGTGAC 57.266 37.500 0.00 0.00 0.00 3.67
1991 2769 8.719648 CATCAAAATCACCTAGATAGATTCTGC 58.280 37.037 0.00 0.00 35.39 4.26
1992 2770 9.993454 TCATCAAAATCACCTAGATAGATTCTG 57.007 33.333 0.00 0.00 35.39 3.02
2003 2781 4.736126 TCGCTCTCATCAAAATCACCTA 57.264 40.909 0.00 0.00 0.00 3.08
2013 2791 3.557185 GTGCAATTACATCGCTCTCATCA 59.443 43.478 0.00 0.00 0.00 3.07
2014 2792 3.557185 TGTGCAATTACATCGCTCTCATC 59.443 43.478 0.00 0.00 0.00 2.92
2019 2797 4.277257 TGATTGTGCAATTACATCGCTC 57.723 40.909 0.00 0.00 0.00 5.03
2055 2833 1.302752 TCACAGCGCTGCCTTCATT 60.303 52.632 36.28 13.25 0.00 2.57
2067 2882 3.988379 TGTTGATTTTCCAGTCACAGC 57.012 42.857 0.00 0.00 0.00 4.40
2068 2883 6.207417 AGGTAATGTTGATTTTCCAGTCACAG 59.793 38.462 0.00 0.00 0.00 3.66
2072 2887 6.431234 AGACAGGTAATGTTGATTTTCCAGTC 59.569 38.462 0.00 0.00 44.17 3.51
2130 2947 5.097529 CGTTATTGAGTTGCATGCTTGAAT 58.902 37.500 20.33 12.27 0.00 2.57
2134 2951 2.228582 TGCGTTATTGAGTTGCATGCTT 59.771 40.909 20.33 4.32 0.00 3.91
2181 2999 7.611467 TGAGATGCTGTTATATCAAGTTTTGGT 59.389 33.333 0.00 0.00 0.00 3.67
2183 3001 8.453320 TGTGAGATGCTGTTATATCAAGTTTTG 58.547 33.333 0.00 0.00 30.88 2.44
2184 3002 8.565896 TGTGAGATGCTGTTATATCAAGTTTT 57.434 30.769 0.00 0.00 30.88 2.43
2235 3056 7.111247 TGTTTGTTTTCTGGTCATCTTTCAT 57.889 32.000 0.00 0.00 0.00 2.57
2236 3057 6.405731 CCTGTTTGTTTTCTGGTCATCTTTCA 60.406 38.462 0.00 0.00 0.00 2.69
2245 3066 2.094234 GTGTGCCTGTTTGTTTTCTGGT 60.094 45.455 0.00 0.00 0.00 4.00
2247 3068 2.094286 TGGTGTGCCTGTTTGTTTTCTG 60.094 45.455 0.00 0.00 35.27 3.02
2277 3098 3.314635 ACGAACGACTATATGTCTGGTCC 59.685 47.826 0.14 0.00 43.25 4.46
2290 3111 4.297299 TGAGTCAGTTAAACGAACGACT 57.703 40.909 11.79 11.79 45.81 4.18
2341 3165 3.634568 TCCGTATTTGCCTGTTGTTTG 57.365 42.857 0.00 0.00 0.00 2.93
2436 3307 1.154131 CGACGAGTGAGAGGCAGTG 60.154 63.158 0.00 0.00 0.00 3.66
2700 3571 2.180432 ACAAGAAGTACCTTTCCGCC 57.820 50.000 0.00 0.00 0.00 6.13
2739 3610 3.076916 GGCATGGGCAAGGGGTTC 61.077 66.667 0.00 0.00 43.71 3.62
2753 3624 3.499406 AGGCACTCTTCCATGGCA 58.501 55.556 6.96 0.00 43.55 4.92
2799 3670 2.041405 GCCTCCTCAGCCCTACCT 60.041 66.667 0.00 0.00 0.00 3.08
2816 3687 1.079543 CAGCTCAAGGGTGTCCTCG 60.080 63.158 0.00 0.00 44.07 4.63


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

AutoCloner maintained by Alex Coulton.