Multiple sequence alignment - TraesCS6D01G355400

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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 TraesCS6D01G355400 chr6D 100.000 2255 0 0 1 2255 450164041 450166295 0.000000e+00 4165.0
1 TraesCS6D01G355400 chr6D 82.119 1057 83 57 278 1301 450136195 450137178 0.000000e+00 808.0
2 TraesCS6D01G355400 chr6B 88.644 1224 51 31 321 1483 682655529 682656725 0.000000e+00 1410.0
3 TraesCS6D01G355400 chr6B 81.339 1120 80 58 278 1343 682587860 682588904 0.000000e+00 791.0
4 TraesCS6D01G355400 chr6B 85.575 617 43 20 1641 2223 682656865 682657469 2.480000e-169 604.0
5 TraesCS6D01G355400 chr6A 88.526 1072 52 28 297 1339 595658360 595659389 0.000000e+00 1232.0
6 TraesCS6D01G355400 chr6A 90.238 840 27 21 1434 2243 595659639 595660453 0.000000e+00 1046.0
7 TraesCS6D01G355400 chr6A 84.826 949 74 37 297 1195 595647712 595648640 0.000000e+00 891.0
8 TraesCS6D01G355400 chr6A 90.667 75 2 2 1333 1403 595659560 595659633 6.630000e-16 95.3
9 TraesCS6D01G355400 chr6A 89.041 73 4 4 1228 1300 595648643 595648711 1.110000e-13 87.9
10 TraesCS6D01G355400 chr7A 96.774 31 1 0 8 38 139826081 139826051 4.000000e-03 52.8


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 TraesCS6D01G355400 chr6D 450164041 450166295 2254 False 4165.00 4165 100.000000 1 2255 1 chr6D.!!$F2 2254
1 TraesCS6D01G355400 chr6D 450136195 450137178 983 False 808.00 808 82.119000 278 1301 1 chr6D.!!$F1 1023
2 TraesCS6D01G355400 chr6B 682655529 682657469 1940 False 1007.00 1410 87.109500 321 2223 2 chr6B.!!$F2 1902
3 TraesCS6D01G355400 chr6B 682587860 682588904 1044 False 791.00 791 81.339000 278 1343 1 chr6B.!!$F1 1065
4 TraesCS6D01G355400 chr6A 595658360 595660453 2093 False 791.10 1232 89.810333 297 2243 3 chr6A.!!$F2 1946
5 TraesCS6D01G355400 chr6A 595647712 595648711 999 False 489.45 891 86.933500 297 1300 2 chr6A.!!$F1 1003

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
38 39 0.102481 ACAGCAACGACGACAGAAGT 59.898 50.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 2405 0.036105 TGCATGCAACCTCGAGTCAT 60.036 50.0 20.3 6.32 0.0 3.06 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
18 19 1.412226 TACTCGAACGACGACGACG 59.588 57.895 17.60 17.60 46.45 5.12
19 20 1.001745 TACTCGAACGACGACGACGA 61.002 55.000 25.15 23.14 46.45 4.20
20 21 1.852351 CTCGAACGACGACGACGAC 60.852 63.158 25.15 16.36 46.45 4.34
21 22 2.128017 CGAACGACGACGACGACA 60.128 61.111 25.15 0.00 45.77 4.35
22 23 2.130219 CGAACGACGACGACGACAG 61.130 63.158 25.15 11.60 45.77 3.51
23 24 2.415997 GAACGACGACGACGACAGC 61.416 63.158 25.15 8.11 42.66 4.40
24 25 3.172099 AACGACGACGACGACAGCA 62.172 57.895 25.15 0.00 42.66 4.41
25 26 2.426261 CGACGACGACGACAGCAA 60.426 61.111 15.32 0.00 42.66 3.91
26 27 2.694615 CGACGACGACGACAGCAAC 61.695 63.158 15.32 0.00 42.66 4.17
27 28 2.694615 GACGACGACGACAGCAACG 61.695 63.158 15.32 0.00 42.66 4.10
28 29 2.426261 CGACGACGACAGCAACGA 60.426 61.111 0.00 0.00 42.66 3.85
29 30 2.694615 CGACGACGACAGCAACGAC 61.695 63.158 0.00 0.00 42.66 4.34
31 32 2.426261 CGACGACAGCAACGACGA 60.426 61.111 0.00 0.00 46.85 4.20
32 33 2.694615 CGACGACAGCAACGACGAC 61.695 63.158 0.00 0.00 46.85 4.34
33 34 1.656263 GACGACAGCAACGACGACA 60.656 57.895 0.00 0.00 34.70 4.35
34 35 1.597700 GACGACAGCAACGACGACAG 61.598 60.000 0.00 0.00 34.70 3.51
35 36 1.370051 CGACAGCAACGACGACAGA 60.370 57.895 0.00 0.00 0.00 3.41
36 37 0.933047 CGACAGCAACGACGACAGAA 60.933 55.000 0.00 0.00 0.00 3.02
37 38 0.778815 GACAGCAACGACGACAGAAG 59.221 55.000 0.00 0.00 0.00 2.85
38 39 0.102481 ACAGCAACGACGACAGAAGT 59.898 50.000 0.00 0.00 0.00 3.01
39 40 1.209128 CAGCAACGACGACAGAAGTT 58.791 50.000 0.00 0.00 0.00 2.66
40 41 1.190323 CAGCAACGACGACAGAAGTTC 59.810 52.381 0.00 0.00 0.00 3.01
41 42 0.507358 GCAACGACGACAGAAGTTCC 59.493 55.000 0.00 0.00 0.00 3.62
42 43 1.868519 GCAACGACGACAGAAGTTCCT 60.869 52.381 0.00 0.00 0.00 3.36
43 44 2.606308 GCAACGACGACAGAAGTTCCTA 60.606 50.000 0.00 0.00 0.00 2.94
44 45 3.834610 CAACGACGACAGAAGTTCCTAT 58.165 45.455 0.00 0.00 0.00 2.57
45 46 3.489180 ACGACGACAGAAGTTCCTATG 57.511 47.619 0.00 0.00 0.00 2.23
46 47 2.163815 ACGACGACAGAAGTTCCTATGG 59.836 50.000 0.00 0.00 0.00 2.74
47 48 2.163815 CGACGACAGAAGTTCCTATGGT 59.836 50.000 0.00 0.00 0.00 3.55
48 49 3.731264 CGACGACAGAAGTTCCTATGGTC 60.731 52.174 0.00 2.04 0.00 4.02
49 50 3.162666 ACGACAGAAGTTCCTATGGTCA 58.837 45.455 0.00 0.00 0.00 4.02
50 51 3.193691 ACGACAGAAGTTCCTATGGTCAG 59.806 47.826 0.00 1.09 0.00 3.51
51 52 3.429547 CGACAGAAGTTCCTATGGTCAGG 60.430 52.174 0.00 0.00 37.00 3.86
52 53 2.840651 ACAGAAGTTCCTATGGTCAGGG 59.159 50.000 0.00 0.00 36.26 4.45
53 54 2.171448 CAGAAGTTCCTATGGTCAGGGG 59.829 54.545 0.00 0.00 36.26 4.79
54 55 1.490910 GAAGTTCCTATGGTCAGGGGG 59.509 57.143 0.00 0.00 36.26 5.40
55 56 0.421904 AGTTCCTATGGTCAGGGGGT 59.578 55.000 0.00 0.00 36.26 4.95
56 57 0.837940 GTTCCTATGGTCAGGGGGTC 59.162 60.000 0.00 0.00 36.26 4.46
57 58 0.419865 TTCCTATGGTCAGGGGGTCA 59.580 55.000 0.00 0.00 36.26 4.02
58 59 0.647738 TCCTATGGTCAGGGGGTCAT 59.352 55.000 0.00 0.00 36.26 3.06
59 60 0.767375 CCTATGGTCAGGGGGTCATG 59.233 60.000 0.00 0.00 31.47 3.07
60 61 0.109342 CTATGGTCAGGGGGTCATGC 59.891 60.000 0.00 0.00 0.00 4.06
61 62 1.695114 TATGGTCAGGGGGTCATGCG 61.695 60.000 0.00 0.00 0.00 4.73
62 63 3.717294 GGTCAGGGGGTCATGCGT 61.717 66.667 0.00 0.00 0.00 5.24
63 64 2.125106 GTCAGGGGGTCATGCGTC 60.125 66.667 0.00 0.00 0.00 5.19
64 65 3.399181 TCAGGGGGTCATGCGTCC 61.399 66.667 0.00 0.00 0.00 4.79
65 66 4.838152 CAGGGGGTCATGCGTCCG 62.838 72.222 0.00 0.00 0.00 4.79
68 69 3.463585 GGGGTCATGCGTCCGGTA 61.464 66.667 0.00 0.00 0.00 4.02
69 70 2.202837 GGGTCATGCGTCCGGTAC 60.203 66.667 0.00 0.00 0.00 3.34
70 71 2.202837 GGTCATGCGTCCGGTACC 60.203 66.667 0.16 0.16 0.00 3.34
71 72 2.718073 GGTCATGCGTCCGGTACCT 61.718 63.158 10.90 0.00 0.00 3.08
72 73 1.226888 GTCATGCGTCCGGTACCTC 60.227 63.158 10.90 0.00 0.00 3.85
73 74 2.278596 CATGCGTCCGGTACCTCG 60.279 66.667 10.90 12.72 0.00 4.63
77 78 2.514592 CGTCCGGTACCTCGCCTA 60.515 66.667 10.90 0.00 0.00 3.93
78 79 2.541120 CGTCCGGTACCTCGCCTAG 61.541 68.421 10.90 0.00 0.00 3.02
79 80 1.452833 GTCCGGTACCTCGCCTAGT 60.453 63.158 10.90 0.00 0.00 2.57
80 81 1.034292 GTCCGGTACCTCGCCTAGTT 61.034 60.000 10.90 0.00 0.00 2.24
81 82 0.323725 TCCGGTACCTCGCCTAGTTT 60.324 55.000 10.90 0.00 0.00 2.66
82 83 1.064758 TCCGGTACCTCGCCTAGTTTA 60.065 52.381 10.90 0.00 0.00 2.01
83 84 1.336125 CCGGTACCTCGCCTAGTTTAG 59.664 57.143 10.90 0.00 0.00 1.85
84 85 2.019984 CGGTACCTCGCCTAGTTTAGT 58.980 52.381 10.90 0.00 0.00 2.24
85 86 2.424956 CGGTACCTCGCCTAGTTTAGTT 59.575 50.000 10.90 0.00 0.00 2.24
86 87 3.119352 CGGTACCTCGCCTAGTTTAGTTT 60.119 47.826 10.90 0.00 0.00 2.66
87 88 4.096382 CGGTACCTCGCCTAGTTTAGTTTA 59.904 45.833 10.90 0.00 0.00 2.01
88 89 5.586339 GGTACCTCGCCTAGTTTAGTTTAG 58.414 45.833 4.06 0.00 0.00 1.85
89 90 4.120792 ACCTCGCCTAGTTTAGTTTAGC 57.879 45.455 0.00 0.00 0.00 3.09
90 91 3.768215 ACCTCGCCTAGTTTAGTTTAGCT 59.232 43.478 0.00 0.00 0.00 3.32
91 92 4.952335 ACCTCGCCTAGTTTAGTTTAGCTA 59.048 41.667 0.00 0.00 0.00 3.32
92 93 5.597594 ACCTCGCCTAGTTTAGTTTAGCTAT 59.402 40.000 0.00 0.00 0.00 2.97
93 94 6.774656 ACCTCGCCTAGTTTAGTTTAGCTATA 59.225 38.462 0.00 0.00 0.00 1.31
94 95 7.450944 ACCTCGCCTAGTTTAGTTTAGCTATAT 59.549 37.037 0.00 0.00 0.00 0.86
95 96 8.305317 CCTCGCCTAGTTTAGTTTAGCTATATT 58.695 37.037 0.00 0.00 0.00 1.28
96 97 9.694137 CTCGCCTAGTTTAGTTTAGCTATATTT 57.306 33.333 0.00 0.00 0.00 1.40
126 127 9.925268 TTTAGTCTGACTTTGTTAAATTTCGTC 57.075 29.630 16.53 0.00 0.00 4.20
127 128 6.956047 AGTCTGACTTTGTTAAATTTCGTCC 58.044 36.000 4.06 0.00 0.00 4.79
128 129 5.844396 GTCTGACTTTGTTAAATTTCGTCCG 59.156 40.000 0.00 0.00 0.00 4.79
129 130 4.529446 TGACTTTGTTAAATTTCGTCCGC 58.471 39.130 0.00 0.00 0.00 5.54
130 131 4.273969 TGACTTTGTTAAATTTCGTCCGCT 59.726 37.500 0.00 0.00 0.00 5.52
131 132 5.177725 ACTTTGTTAAATTTCGTCCGCTT 57.822 34.783 0.00 0.00 0.00 4.68
132 133 4.973663 ACTTTGTTAAATTTCGTCCGCTTG 59.026 37.500 0.00 0.00 0.00 4.01
133 134 4.815040 TTGTTAAATTTCGTCCGCTTGA 57.185 36.364 0.00 0.00 0.00 3.02
134 135 5.365403 TTGTTAAATTTCGTCCGCTTGAT 57.635 34.783 0.00 0.00 0.00 2.57
135 136 5.365403 TGTTAAATTTCGTCCGCTTGATT 57.635 34.783 0.00 0.00 0.00 2.57
136 137 5.150683 TGTTAAATTTCGTCCGCTTGATTG 58.849 37.500 0.00 0.00 0.00 2.67
137 138 3.915437 AAATTTCGTCCGCTTGATTGT 57.085 38.095 0.00 0.00 0.00 2.71
138 139 6.073167 TGTTAAATTTCGTCCGCTTGATTGTA 60.073 34.615 0.00 0.00 0.00 2.41
139 140 5.365403 AAATTTCGTCCGCTTGATTGTAA 57.635 34.783 0.00 0.00 0.00 2.41
140 141 5.365403 AATTTCGTCCGCTTGATTGTAAA 57.635 34.783 0.00 0.00 0.00 2.01
141 142 5.560966 ATTTCGTCCGCTTGATTGTAAAT 57.439 34.783 0.00 0.00 0.00 1.40
142 143 6.671614 ATTTCGTCCGCTTGATTGTAAATA 57.328 33.333 0.00 0.00 0.00 1.40
143 144 6.671614 TTTCGTCCGCTTGATTGTAAATAT 57.328 33.333 0.00 0.00 0.00 1.28
144 145 7.773864 TTTCGTCCGCTTGATTGTAAATATA 57.226 32.000 0.00 0.00 0.00 0.86
145 146 6.758593 TCGTCCGCTTGATTGTAAATATAC 57.241 37.500 0.00 0.00 0.00 1.47
146 147 5.693104 TCGTCCGCTTGATTGTAAATATACC 59.307 40.000 0.00 0.00 0.00 2.73
147 148 5.107220 CGTCCGCTTGATTGTAAATATACCC 60.107 44.000 0.00 0.00 0.00 3.69
148 149 5.180680 GTCCGCTTGATTGTAAATATACCCC 59.819 44.000 0.00 0.00 0.00 4.95
149 150 4.457949 CCGCTTGATTGTAAATATACCCCC 59.542 45.833 0.00 0.00 0.00 5.40
163 164 3.979497 CCCCCTCCCCCAACACAC 61.979 72.222 0.00 0.00 0.00 3.82
164 165 3.182263 CCCCTCCCCCAACACACA 61.182 66.667 0.00 0.00 0.00 3.72
165 166 2.115266 CCCTCCCCCAACACACAC 59.885 66.667 0.00 0.00 0.00 3.82
166 167 2.762554 CCCTCCCCCAACACACACA 61.763 63.158 0.00 0.00 0.00 3.72
167 168 1.228793 CCTCCCCCAACACACACAA 59.771 57.895 0.00 0.00 0.00 3.33
168 169 0.823356 CCTCCCCCAACACACACAAG 60.823 60.000 0.00 0.00 0.00 3.16
169 170 1.454847 TCCCCCAACACACACAAGC 60.455 57.895 0.00 0.00 0.00 4.01
170 171 1.455587 CCCCCAACACACACAAGCT 60.456 57.895 0.00 0.00 0.00 3.74
171 172 1.735360 CCCCAACACACACAAGCTG 59.265 57.895 0.00 0.00 0.00 4.24
172 173 1.037030 CCCCAACACACACAAGCTGT 61.037 55.000 0.00 0.00 0.00 4.40
173 174 0.817013 CCCAACACACACAAGCTGTT 59.183 50.000 0.00 0.00 0.00 3.16
174 175 1.202290 CCCAACACACACAAGCTGTTC 60.202 52.381 0.00 0.00 0.00 3.18
175 176 1.202290 CCAACACACACAAGCTGTTCC 60.202 52.381 0.00 0.00 0.00 3.62
176 177 1.102978 AACACACACAAGCTGTTCCC 58.897 50.000 0.00 0.00 0.00 3.97
177 178 0.751643 ACACACACAAGCTGTTCCCC 60.752 55.000 0.00 0.00 0.00 4.81
178 179 0.466189 CACACACAAGCTGTTCCCCT 60.466 55.000 0.00 0.00 0.00 4.79
179 180 0.179018 ACACACAAGCTGTTCCCCTC 60.179 55.000 0.00 0.00 0.00 4.30
180 181 0.179020 CACACAAGCTGTTCCCCTCA 60.179 55.000 0.00 0.00 0.00 3.86
181 182 0.179018 ACACAAGCTGTTCCCCTCAC 60.179 55.000 0.00 0.00 0.00 3.51
182 183 0.109342 CACAAGCTGTTCCCCTCACT 59.891 55.000 0.00 0.00 0.00 3.41
183 184 0.846693 ACAAGCTGTTCCCCTCACTT 59.153 50.000 0.00 0.00 0.00 3.16
184 185 1.215423 ACAAGCTGTTCCCCTCACTTT 59.785 47.619 0.00 0.00 0.00 2.66
185 186 1.610522 CAAGCTGTTCCCCTCACTTTG 59.389 52.381 0.00 0.00 0.00 2.77
186 187 1.140312 AGCTGTTCCCCTCACTTTGA 58.860 50.000 0.00 0.00 0.00 2.69
187 188 1.072965 AGCTGTTCCCCTCACTTTGAG 59.927 52.381 0.00 0.00 43.91 3.02
188 189 1.528129 CTGTTCCCCTCACTTTGAGC 58.472 55.000 0.00 0.00 42.98 4.26
189 190 1.072965 CTGTTCCCCTCACTTTGAGCT 59.927 52.381 0.00 0.00 42.98 4.09
190 191 2.303022 CTGTTCCCCTCACTTTGAGCTA 59.697 50.000 0.00 0.00 42.98 3.32
191 192 2.303022 TGTTCCCCTCACTTTGAGCTAG 59.697 50.000 0.00 0.00 42.98 3.42
192 193 2.303311 GTTCCCCTCACTTTGAGCTAGT 59.697 50.000 0.00 0.00 42.98 2.57
193 194 1.902508 TCCCCTCACTTTGAGCTAGTG 59.097 52.381 8.57 8.57 42.98 2.74
195 196 2.354203 CCCCTCACTTTGAGCTAGTGAC 60.354 54.545 12.78 0.00 45.15 3.67
196 197 2.564947 CCCTCACTTTGAGCTAGTGACT 59.435 50.000 12.78 0.00 45.15 3.41
197 198 3.764434 CCCTCACTTTGAGCTAGTGACTA 59.236 47.826 12.78 0.00 45.15 2.59
198 199 4.381079 CCCTCACTTTGAGCTAGTGACTAC 60.381 50.000 12.78 0.00 45.15 2.73
199 200 4.407818 CTCACTTTGAGCTAGTGACTACG 58.592 47.826 12.78 1.69 45.15 3.51
200 201 3.190744 TCACTTTGAGCTAGTGACTACGG 59.809 47.826 12.78 0.00 45.15 4.02
201 202 3.057456 CACTTTGAGCTAGTGACTACGGT 60.057 47.826 9.15 0.00 44.52 4.83
202 203 3.573110 ACTTTGAGCTAGTGACTACGGTT 59.427 43.478 0.00 0.00 0.00 4.44
203 204 3.570926 TTGAGCTAGTGACTACGGTTG 57.429 47.619 0.00 0.00 0.00 3.77
204 205 1.816835 TGAGCTAGTGACTACGGTTGG 59.183 52.381 0.00 0.00 0.00 3.77
205 206 2.089980 GAGCTAGTGACTACGGTTGGA 58.910 52.381 0.00 0.00 0.00 3.53
206 207 2.688958 GAGCTAGTGACTACGGTTGGAT 59.311 50.000 0.00 0.00 0.00 3.41
207 208 2.427453 AGCTAGTGACTACGGTTGGATG 59.573 50.000 0.00 0.00 0.00 3.51
208 209 2.426024 GCTAGTGACTACGGTTGGATGA 59.574 50.000 0.00 0.00 0.00 2.92
209 210 3.734293 GCTAGTGACTACGGTTGGATGAC 60.734 52.174 0.00 0.00 0.00 3.06
210 211 1.549170 AGTGACTACGGTTGGATGACC 59.451 52.381 0.00 0.00 36.31 4.02
216 217 4.313819 GGTTGGATGACCGGTTCC 57.686 61.111 17.13 17.13 39.42 3.62
217 218 1.743995 GGTTGGATGACCGGTTCCG 60.744 63.158 18.40 4.08 39.42 4.30
218 219 2.046700 TTGGATGACCGGTTCCGC 60.047 61.111 18.40 2.49 39.42 5.54
219 220 3.615509 TTGGATGACCGGTTCCGCC 62.616 63.158 18.40 13.62 39.42 6.13
220 221 4.851179 GGATGACCGGTTCCGCCC 62.851 72.222 9.42 2.37 0.00 6.13
234 235 4.681978 GCCCGCTGTCCACGAACT 62.682 66.667 0.00 0.00 0.00 3.01
235 236 2.432628 CCCGCTGTCCACGAACTC 60.433 66.667 0.00 0.00 0.00 3.01
236 237 2.338620 CCGCTGTCCACGAACTCA 59.661 61.111 0.00 0.00 0.00 3.41
237 238 1.079819 CCGCTGTCCACGAACTCAT 60.080 57.895 0.00 0.00 0.00 2.90
238 239 0.670546 CCGCTGTCCACGAACTCATT 60.671 55.000 0.00 0.00 0.00 2.57
239 240 1.148310 CGCTGTCCACGAACTCATTT 58.852 50.000 0.00 0.00 0.00 2.32
240 241 1.136252 CGCTGTCCACGAACTCATTTG 60.136 52.381 0.00 0.00 0.00 2.32
241 242 1.873591 GCTGTCCACGAACTCATTTGT 59.126 47.619 0.00 0.00 32.11 2.83
242 243 2.290641 GCTGTCCACGAACTCATTTGTT 59.709 45.455 0.00 0.00 29.14 2.83
243 244 3.243068 GCTGTCCACGAACTCATTTGTTT 60.243 43.478 0.00 0.00 29.14 2.83
244 245 4.733523 GCTGTCCACGAACTCATTTGTTTT 60.734 41.667 0.00 0.00 29.14 2.43
245 246 5.317733 TGTCCACGAACTCATTTGTTTTT 57.682 34.783 0.00 0.00 29.14 1.94
246 247 5.098893 TGTCCACGAACTCATTTGTTTTTG 58.901 37.500 0.00 0.00 29.14 2.44
247 248 5.106118 TGTCCACGAACTCATTTGTTTTTGA 60.106 36.000 0.00 0.00 29.14 2.69
248 249 5.977129 GTCCACGAACTCATTTGTTTTTGAT 59.023 36.000 0.00 0.00 29.14 2.57
249 250 5.976534 TCCACGAACTCATTTGTTTTTGATG 59.023 36.000 0.00 0.00 29.14 3.07
250 251 5.976534 CCACGAACTCATTTGTTTTTGATGA 59.023 36.000 0.00 0.00 29.14 2.92
251 252 6.642131 CCACGAACTCATTTGTTTTTGATGAT 59.358 34.615 0.00 0.00 29.14 2.45
252 253 7.148918 CCACGAACTCATTTGTTTTTGATGATC 60.149 37.037 0.00 0.00 29.14 2.92
253 254 6.863126 ACGAACTCATTTGTTTTTGATGATCC 59.137 34.615 0.00 0.00 0.00 3.36
254 255 6.032775 CGAACTCATTTGTTTTTGATGATCCG 59.967 38.462 0.00 0.00 0.00 4.18
255 256 6.331369 ACTCATTTGTTTTTGATGATCCGT 57.669 33.333 0.00 0.00 0.00 4.69
256 257 6.151691 ACTCATTTGTTTTTGATGATCCGTG 58.848 36.000 0.00 0.00 0.00 4.94
257 258 6.083098 TCATTTGTTTTTGATGATCCGTGT 57.917 33.333 0.00 0.00 0.00 4.49
258 259 6.511416 TCATTTGTTTTTGATGATCCGTGTT 58.489 32.000 0.00 0.00 0.00 3.32
259 260 6.420306 TCATTTGTTTTTGATGATCCGTGTTG 59.580 34.615 0.00 0.00 0.00 3.33
260 261 4.235939 TGTTTTTGATGATCCGTGTTGG 57.764 40.909 0.00 0.00 40.09 3.77
268 269 4.966123 TCCGTGTTGGAGTTGCAA 57.034 50.000 0.00 0.00 43.74 4.08
269 270 2.701587 TCCGTGTTGGAGTTGCAAG 58.298 52.632 0.00 0.00 43.74 4.01
270 271 0.817634 TCCGTGTTGGAGTTGCAAGG 60.818 55.000 0.00 0.00 43.74 3.61
271 272 0.817634 CCGTGTTGGAGTTGCAAGGA 60.818 55.000 0.00 0.00 42.00 3.36
272 273 0.307760 CGTGTTGGAGTTGCAAGGAC 59.692 55.000 0.00 0.00 0.00 3.85
273 274 1.388547 GTGTTGGAGTTGCAAGGACA 58.611 50.000 0.00 0.00 0.00 4.02
274 275 1.748493 GTGTTGGAGTTGCAAGGACAA 59.252 47.619 0.00 2.19 0.00 3.18
275 276 2.362077 GTGTTGGAGTTGCAAGGACAAT 59.638 45.455 0.00 0.00 0.00 2.71
276 277 3.568007 GTGTTGGAGTTGCAAGGACAATA 59.432 43.478 0.00 0.75 0.00 1.90
280 281 2.673368 GGAGTTGCAAGGACAATACTCG 59.327 50.000 0.00 0.00 0.00 4.18
292 293 6.527423 AGGACAATACTCGTTTTTGGACTAA 58.473 36.000 0.00 0.00 0.00 2.24
293 294 6.426025 AGGACAATACTCGTTTTTGGACTAAC 59.574 38.462 0.00 0.00 0.00 2.34
295 296 5.754890 ACAATACTCGTTTTTGGACTAACGT 59.245 36.000 0.00 0.00 45.30 3.99
481 512 1.179152 TGCGTATCTTTGGACCGAGA 58.821 50.000 0.35 0.35 0.00 4.04
482 513 1.134367 TGCGTATCTTTGGACCGAGAG 59.866 52.381 4.03 0.00 0.00 3.20
483 514 1.404391 GCGTATCTTTGGACCGAGAGA 59.596 52.381 4.03 0.00 0.00 3.10
529 563 3.588955 TCACCATCATCACACTTTCTCG 58.411 45.455 0.00 0.00 0.00 4.04
611 660 1.467734 CATTGAAGCTGTGCAGGAGAC 59.532 52.381 1.11 0.00 0.00 3.36
612 661 0.761187 TTGAAGCTGTGCAGGAGACT 59.239 50.000 1.11 0.00 46.44 3.24
653 724 2.599578 CTGCTGCTTTGCTGGGGT 60.600 61.111 0.00 0.00 0.00 4.95
753 837 4.440940 GCCTTCTTCTTCCTCTGCTACTAC 60.441 50.000 0.00 0.00 0.00 2.73
904 1022 4.537015 AGCTGTTTCTAAATCAAACGCAC 58.463 39.130 11.69 0.00 36.66 5.34
912 1034 2.132740 AATCAAACGCACGCATTTGT 57.867 40.000 10.01 0.00 37.16 2.83
913 1035 1.685302 ATCAAACGCACGCATTTGTC 58.315 45.000 10.01 0.00 37.16 3.18
914 1036 0.317436 TCAAACGCACGCATTTGTCC 60.317 50.000 10.01 0.00 37.16 4.02
928 1050 4.032786 GCATTTGTCCGAATATGTTTTGGC 59.967 41.667 0.00 0.00 0.00 4.52
984 1110 4.120755 GCTGCAGGGGGCTAGCTT 62.121 66.667 17.12 0.00 45.15 3.74
985 1111 2.746375 GCTGCAGGGGGCTAGCTTA 61.746 63.158 17.12 0.00 45.15 3.09
986 1112 1.449353 CTGCAGGGGGCTAGCTTAG 59.551 63.158 15.72 1.92 45.15 2.18
1321 1468 3.433615 AGCTGTAGTCATCTTTGCGAAAC 59.566 43.478 0.00 0.00 0.00 2.78
1350 1674 7.151308 AGCTAGTAGTAGTATGTAGTGTACGG 58.849 42.308 6.47 0.00 0.00 4.02
1423 1759 4.185059 GCAGCTAGCGCTTTGGCC 62.185 66.667 18.68 0.00 46.47 5.36
1424 1760 2.437359 CAGCTAGCGCTTTGGCCT 60.437 61.111 18.68 1.84 46.47 5.19
1425 1761 2.042831 CAGCTAGCGCTTTGGCCTT 61.043 57.895 18.68 0.25 46.47 4.35
1427 1763 1.153958 GCTAGCGCTTTGGCCTTTG 60.154 57.895 18.68 0.00 34.44 2.77
1428 1764 1.508088 CTAGCGCTTTGGCCTTTGG 59.492 57.895 18.68 0.00 34.44 3.28
1429 1765 1.937546 CTAGCGCTTTGGCCTTTGGG 61.938 60.000 18.68 3.15 34.44 4.12
1430 1766 4.377708 GCGCTTTGGCCTTTGGGG 62.378 66.667 3.32 1.26 38.36 4.96
1431 1767 3.694538 CGCTTTGGCCTTTGGGGG 61.695 66.667 3.32 0.00 35.12 5.40
1459 1795 1.138464 TGCATGGCTTTTCTTGTTGCA 59.862 42.857 0.00 0.00 36.37 4.08
1531 1867 9.715121 AAAGATTAGTTCACGTTATTCCAGTAA 57.285 29.630 0.00 0.00 0.00 2.24
1547 1883 4.873827 TCCAGTAATGTACTTGCGAAATCC 59.126 41.667 0.00 0.00 36.76 3.01
1617 1954 3.110358 CGTCATGTTTATGCAATGCCAG 58.890 45.455 1.53 0.00 34.21 4.85
1672 2039 9.591792 CTCCTTGACTGATTTTCTTTTCTTTTT 57.408 29.630 0.00 0.00 0.00 1.94
1673 2040 9.586435 TCCTTGACTGATTTTCTTTTCTTTTTC 57.414 29.630 0.00 0.00 0.00 2.29
1674 2041 8.534778 CCTTGACTGATTTTCTTTTCTTTTTCG 58.465 33.333 0.00 0.00 0.00 3.46
1695 2066 1.783250 AAAGGGGTGCCTCACAGGAG 61.783 60.000 0.00 0.00 37.67 3.69
1737 2108 3.078837 TGAAATAGGTTCCGAGTTTGCC 58.921 45.455 0.00 0.00 35.12 4.52
1836 2212 8.661352 AAATACAACTCAATTCCACCAAAAAG 57.339 30.769 0.00 0.00 0.00 2.27
1838 2214 6.293004 ACAACTCAATTCCACCAAAAAGAA 57.707 33.333 0.00 0.00 0.00 2.52
1875 2252 8.026607 TGTTTGTTTTTCTTGAAACAGAGGTAG 58.973 33.333 0.00 0.00 46.60 3.18
1888 2265 4.017808 ACAGAGGTAGTCAGATGTGGTAC 58.982 47.826 0.00 0.00 0.00 3.34
1891 2268 5.127845 CAGAGGTAGTCAGATGTGGTACATT 59.872 44.000 0.00 0.00 44.52 2.71
1898 2276 5.013079 AGTCAGATGTGGTACATTTTCCTGA 59.987 40.000 0.00 6.86 44.52 3.86
1900 2278 5.003160 CAGATGTGGTACATTTTCCTGACA 58.997 41.667 0.00 0.00 44.52 3.58
1901 2279 5.122869 CAGATGTGGTACATTTTCCTGACAG 59.877 44.000 0.00 0.00 44.52 3.51
1922 2318 7.933577 TGACAGTAAGCAGGAAATGAATATAGG 59.066 37.037 0.00 0.00 0.00 2.57
1940 2336 9.814899 GAATATAGGACAGTATTCTGATCATGG 57.185 37.037 6.32 0.00 43.76 3.66
2009 2405 0.394216 ATTGCAATGGAGGTAGCGCA 60.394 50.000 12.09 0.00 0.00 6.09
2128 2524 2.228103 TGCGTCCTATCCACATCGATAC 59.772 50.000 0.00 0.00 0.00 2.24
2129 2525 2.728225 GCGTCCTATCCACATCGATACG 60.728 54.545 0.00 2.12 0.00 3.06
2206 2612 3.118298 AGTTTCACAATGCCAGGCTTTTT 60.118 39.130 14.15 2.57 0.00 1.94
2207 2613 2.818130 TCACAATGCCAGGCTTTTTC 57.182 45.000 14.15 0.00 0.00 2.29
2208 2614 2.037901 TCACAATGCCAGGCTTTTTCA 58.962 42.857 14.15 0.00 0.00 2.69
2209 2615 2.036217 TCACAATGCCAGGCTTTTTCAG 59.964 45.455 14.15 3.37 0.00 3.02
2211 2617 2.435437 ACAATGCCAGGCTTTTTCAGTT 59.565 40.909 14.15 0.00 0.00 3.16
2212 2618 3.640967 ACAATGCCAGGCTTTTTCAGTTA 59.359 39.130 14.15 0.00 0.00 2.24
2213 2619 3.942130 ATGCCAGGCTTTTTCAGTTAC 57.058 42.857 14.15 0.00 0.00 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.168621 GTCGTCGTCGTCGTTCGA 59.831 61.111 11.41 16.14 46.83 3.71
4 5 2.128017 TGTCGTCGTCGTCGTTCG 60.128 61.111 11.41 8.65 41.41 3.95
5 6 2.415997 GCTGTCGTCGTCGTCGTTC 61.416 63.158 11.41 7.18 38.33 3.95
6 7 2.426425 GCTGTCGTCGTCGTCGTT 60.426 61.111 11.41 0.00 38.33 3.85
7 8 3.172099 TTGCTGTCGTCGTCGTCGT 62.172 57.895 11.41 0.00 38.33 4.34
8 9 2.426261 TTGCTGTCGTCGTCGTCG 60.426 61.111 5.50 5.50 38.33 5.12
9 10 2.694615 CGTTGCTGTCGTCGTCGTC 61.695 63.158 1.33 0.00 38.33 4.20
10 11 2.724721 CGTTGCTGTCGTCGTCGT 60.725 61.111 1.33 0.00 38.33 4.34
11 12 2.426261 TCGTTGCTGTCGTCGTCG 60.426 61.111 0.00 0.00 38.55 5.12
12 13 2.694615 CGTCGTTGCTGTCGTCGTC 61.695 63.158 0.00 0.00 35.85 4.20
13 14 2.724721 CGTCGTTGCTGTCGTCGT 60.725 61.111 0.00 0.00 35.85 4.34
14 15 2.426261 TCGTCGTTGCTGTCGTCG 60.426 61.111 0.00 8.31 39.95 5.12
15 16 1.597700 CTGTCGTCGTTGCTGTCGTC 61.598 60.000 0.00 0.00 0.00 4.20
16 17 1.657487 CTGTCGTCGTTGCTGTCGT 60.657 57.895 0.00 0.00 0.00 4.34
17 18 0.933047 TTCTGTCGTCGTTGCTGTCG 60.933 55.000 0.00 0.00 0.00 4.35
18 19 0.778815 CTTCTGTCGTCGTTGCTGTC 59.221 55.000 0.00 0.00 0.00 3.51
19 20 0.102481 ACTTCTGTCGTCGTTGCTGT 59.898 50.000 0.00 0.00 0.00 4.40
20 21 1.190323 GAACTTCTGTCGTCGTTGCTG 59.810 52.381 0.00 0.00 0.00 4.41
21 22 1.488527 GAACTTCTGTCGTCGTTGCT 58.511 50.000 0.00 0.00 0.00 3.91
22 23 0.507358 GGAACTTCTGTCGTCGTTGC 59.493 55.000 0.00 0.00 0.00 4.17
23 24 2.135664 AGGAACTTCTGTCGTCGTTG 57.864 50.000 0.00 0.00 27.25 4.10
24 25 3.367087 CCATAGGAACTTCTGTCGTCGTT 60.367 47.826 0.00 0.00 41.75 3.85
25 26 2.163815 CCATAGGAACTTCTGTCGTCGT 59.836 50.000 0.00 0.00 41.75 4.34
26 27 2.163815 ACCATAGGAACTTCTGTCGTCG 59.836 50.000 0.00 0.00 41.75 5.12
27 28 3.192844 TGACCATAGGAACTTCTGTCGTC 59.807 47.826 0.00 0.00 41.75 4.20
28 29 3.162666 TGACCATAGGAACTTCTGTCGT 58.837 45.455 0.00 0.00 41.75 4.34
29 30 3.429547 CCTGACCATAGGAACTTCTGTCG 60.430 52.174 0.00 0.00 40.42 4.35
30 31 3.118592 CCCTGACCATAGGAACTTCTGTC 60.119 52.174 0.00 0.00 40.42 3.51
31 32 2.840651 CCCTGACCATAGGAACTTCTGT 59.159 50.000 0.00 0.00 40.42 3.41
32 33 2.171448 CCCCTGACCATAGGAACTTCTG 59.829 54.545 0.00 0.00 40.42 3.02
33 34 2.482494 CCCCTGACCATAGGAACTTCT 58.518 52.381 0.00 0.00 40.42 2.85
34 35 1.490910 CCCCCTGACCATAGGAACTTC 59.509 57.143 0.00 0.00 40.42 3.01
35 36 1.203570 ACCCCCTGACCATAGGAACTT 60.204 52.381 0.00 0.00 40.42 2.66
36 37 0.421904 ACCCCCTGACCATAGGAACT 59.578 55.000 0.00 0.00 40.42 3.01
37 38 0.837940 GACCCCCTGACCATAGGAAC 59.162 60.000 0.00 0.00 40.42 3.62
38 39 0.419865 TGACCCCCTGACCATAGGAA 59.580 55.000 0.00 0.00 40.42 3.36
39 40 0.647738 ATGACCCCCTGACCATAGGA 59.352 55.000 0.00 0.00 40.42 2.94
40 41 0.767375 CATGACCCCCTGACCATAGG 59.233 60.000 0.00 0.00 37.59 2.57
41 42 0.109342 GCATGACCCCCTGACCATAG 59.891 60.000 0.00 0.00 0.00 2.23
42 43 1.695114 CGCATGACCCCCTGACCATA 61.695 60.000 0.00 0.00 0.00 2.74
43 44 3.010144 GCATGACCCCCTGACCAT 58.990 61.111 0.00 0.00 0.00 3.55
44 45 3.716195 CGCATGACCCCCTGACCA 61.716 66.667 0.00 0.00 0.00 4.02
45 46 3.682292 GACGCATGACCCCCTGACC 62.682 68.421 0.00 0.00 0.00 4.02
46 47 2.125106 GACGCATGACCCCCTGAC 60.125 66.667 0.00 0.00 0.00 3.51
47 48 3.399181 GGACGCATGACCCCCTGA 61.399 66.667 0.00 0.00 0.00 3.86
48 49 4.838152 CGGACGCATGACCCCCTG 62.838 72.222 0.00 0.00 0.00 4.45
51 52 3.463585 TACCGGACGCATGACCCC 61.464 66.667 9.46 0.00 0.00 4.95
52 53 2.202837 GTACCGGACGCATGACCC 60.203 66.667 9.46 0.00 0.00 4.46
53 54 2.202837 GGTACCGGACGCATGACC 60.203 66.667 9.46 0.00 0.00 4.02
54 55 1.226888 GAGGTACCGGACGCATGAC 60.227 63.158 9.46 0.00 0.00 3.06
55 56 2.767445 CGAGGTACCGGACGCATGA 61.767 63.158 9.46 0.00 0.00 3.07
56 57 2.278596 CGAGGTACCGGACGCATG 60.279 66.667 9.46 0.00 0.00 4.06
60 61 2.514592 TAGGCGAGGTACCGGACG 60.515 66.667 9.46 19.28 0.00 4.79
61 62 1.034292 AACTAGGCGAGGTACCGGAC 61.034 60.000 9.46 4.86 0.00 4.79
62 63 0.323725 AAACTAGGCGAGGTACCGGA 60.324 55.000 9.46 0.00 0.00 5.14
63 64 1.336125 CTAAACTAGGCGAGGTACCGG 59.664 57.143 6.18 0.00 0.00 5.28
64 65 2.019984 ACTAAACTAGGCGAGGTACCG 58.980 52.381 6.18 0.00 0.00 4.02
65 66 4.462508 AAACTAAACTAGGCGAGGTACC 57.537 45.455 2.73 2.73 0.00 3.34
66 67 5.039984 GCTAAACTAAACTAGGCGAGGTAC 58.960 45.833 0.00 0.00 0.00 3.34
67 68 4.952335 AGCTAAACTAAACTAGGCGAGGTA 59.048 41.667 0.00 0.00 0.00 3.08
68 69 3.768215 AGCTAAACTAAACTAGGCGAGGT 59.232 43.478 0.00 0.00 0.00 3.85
69 70 4.388378 AGCTAAACTAAACTAGGCGAGG 57.612 45.455 0.00 0.00 0.00 4.63
70 71 9.694137 AAATATAGCTAAACTAAACTAGGCGAG 57.306 33.333 0.00 0.00 33.57 5.03
100 101 9.925268 GACGAAATTTAACAAAGTCAGACTAAA 57.075 29.630 2.64 0.54 0.00 1.85
101 102 8.553696 GGACGAAATTTAACAAAGTCAGACTAA 58.446 33.333 2.64 0.00 0.00 2.24
102 103 7.095940 CGGACGAAATTTAACAAAGTCAGACTA 60.096 37.037 2.64 0.00 0.00 2.59
103 104 6.292703 CGGACGAAATTTAACAAAGTCAGACT 60.293 38.462 0.00 0.00 0.00 3.24
104 105 5.844396 CGGACGAAATTTAACAAAGTCAGAC 59.156 40.000 0.00 0.00 0.00 3.51
105 106 5.559417 GCGGACGAAATTTAACAAAGTCAGA 60.559 40.000 0.00 0.00 0.00 3.27
106 107 4.611366 GCGGACGAAATTTAACAAAGTCAG 59.389 41.667 0.00 0.00 0.00 3.51
107 108 4.273969 AGCGGACGAAATTTAACAAAGTCA 59.726 37.500 0.00 0.00 0.00 3.41
108 109 4.779987 AGCGGACGAAATTTAACAAAGTC 58.220 39.130 0.00 0.00 0.00 3.01
109 110 4.823790 AGCGGACGAAATTTAACAAAGT 57.176 36.364 0.00 0.00 0.00 2.66
110 111 5.209240 TCAAGCGGACGAAATTTAACAAAG 58.791 37.500 0.00 0.00 0.00 2.77
111 112 5.171147 TCAAGCGGACGAAATTTAACAAA 57.829 34.783 0.00 0.00 0.00 2.83
112 113 4.815040 TCAAGCGGACGAAATTTAACAA 57.185 36.364 0.00 0.00 0.00 2.83
113 114 5.150683 CAATCAAGCGGACGAAATTTAACA 58.849 37.500 0.00 0.00 0.00 2.41
114 115 5.151389 ACAATCAAGCGGACGAAATTTAAC 58.849 37.500 0.00 0.00 0.00 2.01
115 116 5.365403 ACAATCAAGCGGACGAAATTTAA 57.635 34.783 0.00 0.00 0.00 1.52
116 117 6.483385 TTACAATCAAGCGGACGAAATTTA 57.517 33.333 0.00 0.00 0.00 1.40
117 118 3.915437 ACAATCAAGCGGACGAAATTT 57.085 38.095 0.00 0.00 0.00 1.82
118 119 5.365403 TTTACAATCAAGCGGACGAAATT 57.635 34.783 0.00 0.00 0.00 1.82
119 120 5.560966 ATTTACAATCAAGCGGACGAAAT 57.439 34.783 0.00 0.00 0.00 2.17
120 121 6.671614 ATATTTACAATCAAGCGGACGAAA 57.328 33.333 0.00 0.00 0.00 3.46
121 122 6.201425 GGTATATTTACAATCAAGCGGACGAA 59.799 38.462 0.00 0.00 0.00 3.85
122 123 5.693104 GGTATATTTACAATCAAGCGGACGA 59.307 40.000 0.00 0.00 0.00 4.20
123 124 5.107220 GGGTATATTTACAATCAAGCGGACG 60.107 44.000 0.00 0.00 0.00 4.79
124 125 5.180680 GGGGTATATTTACAATCAAGCGGAC 59.819 44.000 0.00 0.00 0.00 4.79
125 126 5.310451 GGGGTATATTTACAATCAAGCGGA 58.690 41.667 0.00 0.00 0.00 5.54
126 127 4.457949 GGGGGTATATTTACAATCAAGCGG 59.542 45.833 0.00 0.00 0.00 5.52
127 128 5.622770 GGGGGTATATTTACAATCAAGCG 57.377 43.478 0.00 0.00 0.00 4.68
146 147 3.979497 GTGTGTTGGGGGAGGGGG 61.979 72.222 0.00 0.00 0.00 5.40
147 148 3.182263 TGTGTGTTGGGGGAGGGG 61.182 66.667 0.00 0.00 0.00 4.79
148 149 2.115266 GTGTGTGTTGGGGGAGGG 59.885 66.667 0.00 0.00 0.00 4.30
149 150 0.823356 CTTGTGTGTGTTGGGGGAGG 60.823 60.000 0.00 0.00 0.00 4.30
150 151 1.455383 GCTTGTGTGTGTTGGGGGAG 61.455 60.000 0.00 0.00 0.00 4.30
151 152 1.454847 GCTTGTGTGTGTTGGGGGA 60.455 57.895 0.00 0.00 0.00 4.81
152 153 1.455587 AGCTTGTGTGTGTTGGGGG 60.456 57.895 0.00 0.00 0.00 5.40
153 154 1.037030 ACAGCTTGTGTGTGTTGGGG 61.037 55.000 0.00 0.00 38.28 4.96
154 155 0.817013 AACAGCTTGTGTGTGTTGGG 59.183 50.000 0.00 0.00 40.26 4.12
155 156 1.202290 GGAACAGCTTGTGTGTGTTGG 60.202 52.381 0.00 0.00 40.26 3.77
156 157 1.202290 GGGAACAGCTTGTGTGTGTTG 60.202 52.381 0.00 0.00 40.26 3.33
157 158 1.102978 GGGAACAGCTTGTGTGTGTT 58.897 50.000 0.00 0.00 40.26 3.32
158 159 0.751643 GGGGAACAGCTTGTGTGTGT 60.752 55.000 0.00 0.00 40.26 3.72
159 160 0.466189 AGGGGAACAGCTTGTGTGTG 60.466 55.000 0.00 0.00 40.26 3.82
160 161 0.179018 GAGGGGAACAGCTTGTGTGT 60.179 55.000 0.00 0.00 40.26 3.72
161 162 0.179020 TGAGGGGAACAGCTTGTGTG 60.179 55.000 0.00 0.00 40.26 3.82
162 163 0.179018 GTGAGGGGAACAGCTTGTGT 60.179 55.000 0.00 0.00 43.24 3.72
163 164 0.109342 AGTGAGGGGAACAGCTTGTG 59.891 55.000 0.00 0.00 0.00 3.33
164 165 0.846693 AAGTGAGGGGAACAGCTTGT 59.153 50.000 0.00 0.00 0.00 3.16
165 166 1.610522 CAAAGTGAGGGGAACAGCTTG 59.389 52.381 0.00 0.00 0.00 4.01
166 167 1.494721 TCAAAGTGAGGGGAACAGCTT 59.505 47.619 0.00 0.00 0.00 3.74
167 168 1.072965 CTCAAAGTGAGGGGAACAGCT 59.927 52.381 0.00 0.00 40.71 4.24
168 169 1.528129 CTCAAAGTGAGGGGAACAGC 58.472 55.000 0.00 0.00 40.71 4.40
169 170 1.072965 AGCTCAAAGTGAGGGGAACAG 59.927 52.381 7.34 0.00 44.43 3.16
170 171 1.140312 AGCTCAAAGTGAGGGGAACA 58.860 50.000 7.34 0.00 44.43 3.18
171 172 2.303311 ACTAGCTCAAAGTGAGGGGAAC 59.697 50.000 7.34 0.00 44.43 3.62
172 173 2.303022 CACTAGCTCAAAGTGAGGGGAA 59.697 50.000 9.15 0.00 45.89 3.97
173 174 1.902508 CACTAGCTCAAAGTGAGGGGA 59.097 52.381 9.15 0.00 45.89 4.81
174 175 1.902508 TCACTAGCTCAAAGTGAGGGG 59.097 52.381 12.78 0.00 46.38 4.79
179 180 3.057456 ACCGTAGTCACTAGCTCAAAGTG 60.057 47.826 8.57 8.57 44.66 3.16
180 181 3.155501 ACCGTAGTCACTAGCTCAAAGT 58.844 45.455 0.00 0.00 0.00 2.66
181 182 3.851976 ACCGTAGTCACTAGCTCAAAG 57.148 47.619 0.00 0.00 0.00 2.77
182 183 3.305813 CCAACCGTAGTCACTAGCTCAAA 60.306 47.826 0.00 0.00 0.00 2.69
183 184 2.230508 CCAACCGTAGTCACTAGCTCAA 59.769 50.000 0.00 0.00 0.00 3.02
184 185 1.816835 CCAACCGTAGTCACTAGCTCA 59.183 52.381 0.00 0.00 0.00 4.26
185 186 2.089980 TCCAACCGTAGTCACTAGCTC 58.910 52.381 0.00 0.00 0.00 4.09
186 187 2.211250 TCCAACCGTAGTCACTAGCT 57.789 50.000 0.00 0.00 0.00 3.32
187 188 2.426024 TCATCCAACCGTAGTCACTAGC 59.574 50.000 0.00 0.00 0.00 3.42
188 189 3.181489 GGTCATCCAACCGTAGTCACTAG 60.181 52.174 0.00 0.00 0.00 2.57
189 190 2.756760 GGTCATCCAACCGTAGTCACTA 59.243 50.000 0.00 0.00 0.00 2.74
190 191 1.549170 GGTCATCCAACCGTAGTCACT 59.451 52.381 0.00 0.00 0.00 3.41
191 192 2.005971 GGTCATCCAACCGTAGTCAC 57.994 55.000 0.00 0.00 0.00 3.67
199 200 1.743995 CGGAACCGGTCATCCAACC 60.744 63.158 22.33 10.40 35.34 3.77
200 201 2.396157 GCGGAACCGGTCATCCAAC 61.396 63.158 22.33 11.70 40.19 3.77
201 202 2.046700 GCGGAACCGGTCATCCAA 60.047 61.111 22.33 0.00 40.19 3.53
202 203 4.090588 GGCGGAACCGGTCATCCA 62.091 66.667 22.33 0.00 40.19 3.41
203 204 4.851179 GGGCGGAACCGGTCATCC 62.851 72.222 8.04 12.03 40.62 3.51
217 218 4.681978 AGTTCGTGGACAGCGGGC 62.682 66.667 0.00 0.00 0.00 6.13
218 219 2.432628 GAGTTCGTGGACAGCGGG 60.433 66.667 0.00 0.00 0.00 6.13
219 220 0.670546 AATGAGTTCGTGGACAGCGG 60.671 55.000 0.00 0.00 0.00 5.52
220 221 1.136252 CAAATGAGTTCGTGGACAGCG 60.136 52.381 0.00 0.00 0.00 5.18
221 222 1.873591 ACAAATGAGTTCGTGGACAGC 59.126 47.619 0.00 0.00 0.00 4.40
222 223 4.552166 AAACAAATGAGTTCGTGGACAG 57.448 40.909 0.00 0.00 0.00 3.51
223 224 4.974368 AAAACAAATGAGTTCGTGGACA 57.026 36.364 0.00 0.00 0.00 4.02
224 225 5.336744 TCAAAAACAAATGAGTTCGTGGAC 58.663 37.500 0.00 0.00 0.00 4.02
225 226 5.568685 TCAAAAACAAATGAGTTCGTGGA 57.431 34.783 0.00 0.00 0.00 4.02
226 227 5.976534 TCATCAAAAACAAATGAGTTCGTGG 59.023 36.000 0.00 0.00 0.00 4.94
227 228 7.148918 GGATCATCAAAAACAAATGAGTTCGTG 60.149 37.037 0.00 0.00 33.24 4.35
228 229 6.863126 GGATCATCAAAAACAAATGAGTTCGT 59.137 34.615 0.00 0.00 33.24 3.85
229 230 6.032775 CGGATCATCAAAAACAAATGAGTTCG 59.967 38.462 0.00 0.00 33.24 3.95
230 231 6.863126 ACGGATCATCAAAAACAAATGAGTTC 59.137 34.615 0.00 0.00 33.24 3.01
231 232 6.642131 CACGGATCATCAAAAACAAATGAGTT 59.358 34.615 0.00 0.00 33.24 3.01
232 233 6.151691 CACGGATCATCAAAAACAAATGAGT 58.848 36.000 0.00 0.00 33.24 3.41
233 234 6.151691 ACACGGATCATCAAAAACAAATGAG 58.848 36.000 0.00 0.00 33.24 2.90
234 235 6.083098 ACACGGATCATCAAAAACAAATGA 57.917 33.333 0.00 0.00 34.17 2.57
235 236 6.346758 CCAACACGGATCATCAAAAACAAATG 60.347 38.462 0.00 0.00 36.56 2.32
236 237 5.695816 CCAACACGGATCATCAAAAACAAAT 59.304 36.000 0.00 0.00 36.56 2.32
237 238 5.046529 CCAACACGGATCATCAAAAACAAA 58.953 37.500 0.00 0.00 36.56 2.83
238 239 4.339530 TCCAACACGGATCATCAAAAACAA 59.660 37.500 0.00 0.00 39.64 2.83
239 240 3.885901 TCCAACACGGATCATCAAAAACA 59.114 39.130 0.00 0.00 39.64 2.83
240 241 4.023193 ACTCCAACACGGATCATCAAAAAC 60.023 41.667 0.00 0.00 45.19 2.43
241 242 4.141287 ACTCCAACACGGATCATCAAAAA 58.859 39.130 0.00 0.00 45.19 1.94
242 243 3.750371 ACTCCAACACGGATCATCAAAA 58.250 40.909 0.00 0.00 45.19 2.44
243 244 3.417069 ACTCCAACACGGATCATCAAA 57.583 42.857 0.00 0.00 45.19 2.69
244 245 3.073678 CAACTCCAACACGGATCATCAA 58.926 45.455 0.00 0.00 45.19 2.57
245 246 2.698803 CAACTCCAACACGGATCATCA 58.301 47.619 0.00 0.00 45.19 3.07
246 247 1.398390 GCAACTCCAACACGGATCATC 59.602 52.381 0.00 0.00 45.19 2.92
247 248 1.271325 TGCAACTCCAACACGGATCAT 60.271 47.619 0.00 0.00 45.19 2.45
248 249 0.107643 TGCAACTCCAACACGGATCA 59.892 50.000 0.00 0.00 45.19 2.92
249 250 1.197721 CTTGCAACTCCAACACGGATC 59.802 52.381 0.00 0.00 45.19 3.36
250 251 1.238439 CTTGCAACTCCAACACGGAT 58.762 50.000 0.00 0.00 45.19 4.18
251 252 0.817634 CCTTGCAACTCCAACACGGA 60.818 55.000 0.00 0.00 43.61 4.69
252 253 0.817634 TCCTTGCAACTCCAACACGG 60.818 55.000 0.00 0.00 0.00 4.94
253 254 0.307760 GTCCTTGCAACTCCAACACG 59.692 55.000 0.00 0.00 0.00 4.49
254 255 1.388547 TGTCCTTGCAACTCCAACAC 58.611 50.000 0.00 0.00 0.00 3.32
255 256 2.136298 TTGTCCTTGCAACTCCAACA 57.864 45.000 0.00 0.00 0.00 3.33
256 257 3.821033 AGTATTGTCCTTGCAACTCCAAC 59.179 43.478 0.00 0.00 0.00 3.77
257 258 4.072131 GAGTATTGTCCTTGCAACTCCAA 58.928 43.478 0.00 0.00 0.00 3.53
258 259 3.674997 GAGTATTGTCCTTGCAACTCCA 58.325 45.455 0.00 0.00 0.00 3.86
259 260 2.673368 CGAGTATTGTCCTTGCAACTCC 59.327 50.000 0.00 0.00 0.00 3.85
260 261 3.326747 ACGAGTATTGTCCTTGCAACTC 58.673 45.455 0.00 0.00 0.00 3.01
261 262 3.402628 ACGAGTATTGTCCTTGCAACT 57.597 42.857 0.00 0.00 0.00 3.16
262 263 4.483476 AAACGAGTATTGTCCTTGCAAC 57.517 40.909 0.00 0.00 0.00 4.17
263 264 5.277825 CAAAAACGAGTATTGTCCTTGCAA 58.722 37.500 0.00 0.00 0.00 4.08
264 265 4.261405 CCAAAAACGAGTATTGTCCTTGCA 60.261 41.667 0.00 0.00 0.00 4.08
265 266 4.023536 TCCAAAAACGAGTATTGTCCTTGC 60.024 41.667 0.00 0.00 0.00 4.01
266 267 5.238650 AGTCCAAAAACGAGTATTGTCCTTG 59.761 40.000 0.00 0.00 0.00 3.61
267 268 5.374071 AGTCCAAAAACGAGTATTGTCCTT 58.626 37.500 0.00 0.00 0.00 3.36
268 269 4.969484 AGTCCAAAAACGAGTATTGTCCT 58.031 39.130 0.00 0.00 0.00 3.85
269 270 6.596703 GTTAGTCCAAAAACGAGTATTGTCC 58.403 40.000 0.00 0.00 0.00 4.02
280 281 6.018016 TGGTAAGCTTACGTTAGTCCAAAAAC 60.018 38.462 26.17 10.63 34.50 2.43
292 293 2.997986 CCACGAATTGGTAAGCTTACGT 59.002 45.455 26.17 18.30 41.10 3.57
293 294 3.255725 TCCACGAATTGGTAAGCTTACG 58.744 45.455 26.17 17.71 46.97 3.18
295 296 4.811969 TCTCCACGAATTGGTAAGCTTA 57.188 40.909 0.86 0.86 46.97 3.09
319 321 4.588528 AGAATTTGTAAACCAGGTGCATGT 59.411 37.500 0.00 0.00 0.00 3.21
481 512 2.224281 TGATGACGCACTTCTGGTTTCT 60.224 45.455 0.00 0.00 0.00 2.52
482 513 2.143122 TGATGACGCACTTCTGGTTTC 58.857 47.619 0.00 0.00 0.00 2.78
483 514 2.254546 TGATGACGCACTTCTGGTTT 57.745 45.000 0.00 0.00 0.00 3.27
529 563 1.235724 GGTGGTGGTTAGCTGTCAAC 58.764 55.000 0.00 0.00 0.00 3.18
611 660 3.503827 TCGCAATGTGTACTCCAGTAG 57.496 47.619 0.00 0.00 0.00 2.57
612 661 3.181479 GGATCGCAATGTGTACTCCAGTA 60.181 47.826 0.00 0.00 0.00 2.74
653 724 1.477923 GGGTGCGAATTTATAGGCCCA 60.478 52.381 0.00 0.00 35.15 5.36
691 762 2.158755 AGTGAGGAAGAACTTGTGGTGG 60.159 50.000 0.00 0.00 0.00 4.61
753 837 1.915614 GCACGGACAGACAATGGCAG 61.916 60.000 0.00 0.00 39.54 4.85
904 1022 4.265085 CCAAAACATATTCGGACAAATGCG 59.735 41.667 0.00 0.00 41.78 4.73
912 1034 3.278574 CTCAGGCCAAAACATATTCGGA 58.721 45.455 5.01 0.00 0.00 4.55
913 1035 3.016736 ACTCAGGCCAAAACATATTCGG 58.983 45.455 5.01 0.00 0.00 4.30
914 1036 4.876107 AGTACTCAGGCCAAAACATATTCG 59.124 41.667 5.01 0.00 0.00 3.34
928 1050 6.482641 TCGATAGCAAGTTAGTAGTACTCAGG 59.517 42.308 5.96 0.00 0.00 3.86
983 1109 1.689233 ATCCTCCACGCCCTGCTAA 60.689 57.895 0.00 0.00 0.00 3.09
984 1110 2.041922 ATCCTCCACGCCCTGCTA 60.042 61.111 0.00 0.00 0.00 3.49
985 1111 3.790437 CATCCTCCACGCCCTGCT 61.790 66.667 0.00 0.00 0.00 4.24
986 1112 4.864334 CCATCCTCCACGCCCTGC 62.864 72.222 0.00 0.00 0.00 4.85
987 1113 3.083349 TCCATCCTCCACGCCCTG 61.083 66.667 0.00 0.00 0.00 4.45
1008 1134 2.126618 TACAGCTCCGTGTTCGCG 60.127 61.111 0.00 0.00 35.54 5.87
1291 1438 2.425312 AGATGACTACAGCTTCCACGAG 59.575 50.000 0.00 0.00 39.94 4.18
1350 1674 1.622811 CCAGCTCTGATGGACCTATCC 59.377 57.143 0.00 0.00 46.48 2.59
1362 1690 0.395311 AACCATCCATGCCAGCTCTG 60.395 55.000 0.00 0.00 0.00 3.35
1422 1758 4.202346 CCATGCAAATATAACCCCCAAAGG 60.202 45.833 0.00 0.00 0.00 3.11
1423 1759 4.743348 GCCATGCAAATATAACCCCCAAAG 60.743 45.833 0.00 0.00 0.00 2.77
1424 1760 3.135530 GCCATGCAAATATAACCCCCAAA 59.864 43.478 0.00 0.00 0.00 3.28
1425 1761 2.703007 GCCATGCAAATATAACCCCCAA 59.297 45.455 0.00 0.00 0.00 4.12
1427 1763 2.608623 AGCCATGCAAATATAACCCCC 58.391 47.619 0.00 0.00 0.00 5.40
1428 1764 4.687901 AAAGCCATGCAAATATAACCCC 57.312 40.909 0.00 0.00 0.00 4.95
1429 1765 5.917462 AGAAAAGCCATGCAAATATAACCC 58.083 37.500 0.00 0.00 0.00 4.11
1430 1766 6.818142 ACAAGAAAAGCCATGCAAATATAACC 59.182 34.615 0.00 0.00 0.00 2.85
1431 1767 7.832503 ACAAGAAAAGCCATGCAAATATAAC 57.167 32.000 0.00 0.00 0.00 1.89
1491 1827 6.448207 ACTAATCTTTCGTACTCTGGTACC 57.552 41.667 4.43 4.43 43.78 3.34
1493 1829 7.533426 GTGAACTAATCTTTCGTACTCTGGTA 58.467 38.462 0.00 0.00 0.00 3.25
1494 1830 6.388278 GTGAACTAATCTTTCGTACTCTGGT 58.612 40.000 0.00 0.00 0.00 4.00
1495 1831 5.512082 CGTGAACTAATCTTTCGTACTCTGG 59.488 44.000 0.00 0.00 0.00 3.86
1496 1832 6.084925 ACGTGAACTAATCTTTCGTACTCTG 58.915 40.000 0.00 0.00 32.40 3.35
1497 1833 6.251655 ACGTGAACTAATCTTTCGTACTCT 57.748 37.500 0.00 0.00 32.40 3.24
1498 1834 6.924629 AACGTGAACTAATCTTTCGTACTC 57.075 37.500 0.00 0.00 33.23 2.59
1499 1835 8.976986 AATAACGTGAACTAATCTTTCGTACT 57.023 30.769 0.00 0.00 33.23 2.73
1500 1836 8.316753 GGAATAACGTGAACTAATCTTTCGTAC 58.683 37.037 0.00 0.00 33.23 3.67
1501 1837 8.028354 TGGAATAACGTGAACTAATCTTTCGTA 58.972 33.333 0.00 0.00 33.23 3.43
1502 1838 6.869913 TGGAATAACGTGAACTAATCTTTCGT 59.130 34.615 0.00 0.00 34.26 3.85
1503 1839 7.063074 ACTGGAATAACGTGAACTAATCTTTCG 59.937 37.037 0.00 0.00 0.00 3.46
1504 1840 8.252964 ACTGGAATAACGTGAACTAATCTTTC 57.747 34.615 0.00 0.00 0.00 2.62
1505 1841 9.715121 TTACTGGAATAACGTGAACTAATCTTT 57.285 29.630 0.00 0.00 0.00 2.52
1506 1842 9.886132 ATTACTGGAATAACGTGAACTAATCTT 57.114 29.630 0.00 0.00 0.00 2.40
1507 1843 9.314321 CATTACTGGAATAACGTGAACTAATCT 57.686 33.333 0.00 0.00 0.00 2.40
1508 1844 9.095065 ACATTACTGGAATAACGTGAACTAATC 57.905 33.333 0.00 0.00 0.00 1.75
1510 1846 9.357652 GTACATTACTGGAATAACGTGAACTAA 57.642 33.333 0.00 0.00 0.00 2.24
1547 1883 2.303707 ATTGTTCACGTTAAACCGCG 57.696 45.000 0.00 0.00 0.00 6.46
1550 1886 4.036352 TCGCAAATTGTTCACGTTAAACC 58.964 39.130 7.83 0.00 0.00 3.27
1641 1978 2.393271 AAATCAGTCAAGGAGCCTCG 57.607 50.000 0.00 0.00 0.00 4.63
1672 2039 1.072505 GTGAGGCACCCCTTTTCGA 59.927 57.895 0.00 0.00 43.12 3.71
1673 2040 1.228124 TGTGAGGCACCCCTTTTCG 60.228 57.895 0.00 0.00 43.12 3.46
1674 2041 0.895559 CCTGTGAGGCACCCCTTTTC 60.896 60.000 0.00 0.00 43.12 2.29
1695 2066 2.362077 AGTCAAAGAATGGTTGTGTGCC 59.638 45.455 0.00 0.00 0.00 5.01
1737 2108 6.201044 GTGTGGTCTGATTGAAGTAATATCCG 59.799 42.308 0.00 0.00 0.00 4.18
1864 2241 3.904339 ACCACATCTGACTACCTCTGTTT 59.096 43.478 0.00 0.00 0.00 2.83
1875 2252 5.122396 GTCAGGAAAATGTACCACATCTGAC 59.878 44.000 16.50 16.50 43.24 3.51
1898 2276 7.934120 GTCCTATATTCATTTCCTGCTTACTGT 59.066 37.037 0.00 0.00 0.00 3.55
1900 2278 8.034313 TGTCCTATATTCATTTCCTGCTTACT 57.966 34.615 0.00 0.00 0.00 2.24
1901 2279 7.934120 ACTGTCCTATATTCATTTCCTGCTTAC 59.066 37.037 0.00 0.00 0.00 2.34
1922 2318 6.403866 AGAGACCATGATCAGAATACTGTC 57.596 41.667 0.09 0.37 43.81 3.51
1940 2336 1.004918 CCACGTCCACCCAAGAGAC 60.005 63.158 0.00 0.00 0.00 3.36
2009 2405 0.036105 TGCATGCAACCTCGAGTCAT 60.036 50.000 20.30 6.32 0.00 3.06
2039 2435 1.617322 ACGTAGTCTGCAGTTGAGGA 58.383 50.000 14.67 0.00 29.74 3.71
2079 2475 7.093201 ACCTAACGATTAATTGGACTGGACTTA 60.093 37.037 7.61 0.00 0.00 2.24
2128 2524 6.753107 AATGAAAAGGGGAAACATAGTACG 57.247 37.500 0.00 0.00 0.00 3.67
2129 2525 8.244113 CAGAAATGAAAAGGGGAAACATAGTAC 58.756 37.037 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.