Multiple sequence alignment - TraesCS6A01G147400

Loading Multiple Alignment...

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 TraesCS6A01G147400 chr6A 100.000 4261 0 0 1 4261 127567145 127571405 0.000000e+00 7869.0
1 TraesCS6A01G147400 chr6A 90.747 281 13 11 3 277 161148960 161148687 3.130000e-96 363.0
2 TraesCS6A01G147400 chr6A 91.209 273 13 10 1 269 528493071 528493336 1.130000e-95 361.0
3 TraesCS6A01G147400 chr6B 92.482 2953 154 33 1357 4261 191749888 191752820 0.000000e+00 4161.0
4 TraesCS6A01G147400 chr6B 89.773 616 56 7 269 878 523507827 523507213 0.000000e+00 782.0
5 TraesCS6A01G147400 chr6B 92.428 449 28 3 885 1330 191749445 191749890 1.670000e-178 636.0
6 TraesCS6A01G147400 chr6D 92.952 2568 111 25 1658 4182 105537326 105539866 0.000000e+00 3675.0
7 TraesCS6A01G147400 chr6D 89.229 817 38 12 877 1659 105536499 105537299 0.000000e+00 976.0
8 TraesCS6A01G147400 chr6D 97.872 47 1 0 4204 4250 105539861 105539907 9.820000e-12 82.4
9 TraesCS6A01G147400 chr7D 90.291 618 52 6 269 879 51420140 51419524 0.000000e+00 802.0
10 TraesCS6A01G147400 chr4A 89.661 619 59 5 269 882 273176871 273177489 0.000000e+00 784.0
11 TraesCS6A01G147400 chr4A 90.016 611 54 6 278 882 521286571 521287180 0.000000e+00 784.0
12 TraesCS6A01G147400 chr4A 95.506 267 11 1 1 266 472361391 472361657 3.940000e-115 425.0
13 TraesCS6A01G147400 chr2A 89.677 620 55 8 268 880 46835352 46835969 0.000000e+00 782.0
14 TraesCS6A01G147400 chr2A 91.209 273 18 6 1 269 498035966 498036236 2.420000e-97 366.0
15 TraesCS6A01G147400 chr1A 89.644 618 57 7 269 882 73811164 73810550 0.000000e+00 780.0
16 TraesCS6A01G147400 chr1A 89.068 622 61 7 272 890 218120955 218120338 0.000000e+00 765.0
17 TraesCS6A01G147400 chr5A 89.465 617 60 5 269 880 562974268 562973652 0.000000e+00 774.0
18 TraesCS6A01G147400 chr5A 95.985 274 9 2 1 272 473447478 473447205 1.090000e-120 444.0
19 TraesCS6A01G147400 chr5A 91.241 274 12 10 1 269 16428412 16428146 3.130000e-96 363.0
20 TraesCS6A01G147400 chr4D 89.355 620 57 8 269 881 329142336 329141719 0.000000e+00 771.0
21 TraesCS6A01G147400 chr7A 94.139 273 10 3 1 272 184613906 184613639 1.100000e-110 411.0
22 TraesCS6A01G147400 chr7A 91.606 274 11 10 1 269 260013679 260013413 6.730000e-98 368.0
23 TraesCS6A01G147400 chr5B 89.744 273 21 7 1 269 548199419 548199150 4.080000e-90 342.0


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 TraesCS6A01G147400 chr6A 127567145 127571405 4260 False 7869.0 7869 100.000 1 4261 1 chr6A.!!$F1 4260
1 TraesCS6A01G147400 chr6B 191749445 191752820 3375 False 2398.5 4161 92.455 885 4261 2 chr6B.!!$F1 3376
2 TraesCS6A01G147400 chr6B 523507213 523507827 614 True 782.0 782 89.773 269 878 1 chr6B.!!$R1 609
3 TraesCS6A01G147400 chr6D 105536499 105539907 3408 False 1577.8 3675 93.351 877 4250 3 chr6D.!!$F1 3373
4 TraesCS6A01G147400 chr7D 51419524 51420140 616 True 802.0 802 90.291 269 879 1 chr7D.!!$R1 610
5 TraesCS6A01G147400 chr4A 273176871 273177489 618 False 784.0 784 89.661 269 882 1 chr4A.!!$F1 613
6 TraesCS6A01G147400 chr4A 521286571 521287180 609 False 784.0 784 90.016 278 882 1 chr4A.!!$F3 604
7 TraesCS6A01G147400 chr2A 46835352 46835969 617 False 782.0 782 89.677 268 880 1 chr2A.!!$F1 612
8 TraesCS6A01G147400 chr1A 73810550 73811164 614 True 780.0 780 89.644 269 882 1 chr1A.!!$R1 613
9 TraesCS6A01G147400 chr1A 218120338 218120955 617 True 765.0 765 89.068 272 890 1 chr1A.!!$R2 618
10 TraesCS6A01G147400 chr5A 562973652 562974268 616 True 774.0 774 89.465 269 880 1 chr5A.!!$R3 611
11 TraesCS6A01G147400 chr4D 329141719 329142336 617 True 771.0 771 89.355 269 881 1 chr4D.!!$R1 612

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
229 230 0.108396 GGTTGTTGGCTTGGGCATTT 59.892 50.000 0.00 0.0 38.08 2.32 F
1232 1251 0.178944 TCTTGACTTCCCACCGAGGA 60.179 55.000 0.00 0.0 41.22 3.71 F
1454 1494 0.530288 GGCTAATTTGGCCTTGCGAA 59.470 50.000 15.91 0.0 45.57 4.70 F
2882 2975 1.078426 ACCGTTGCATACAGGCCTC 60.078 57.895 0.00 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 1507 0.247736 AGTGCTAGTGTGCTGCCTAC 59.752 55.000 0.00 0.00 0.0 3.18 R
2840 2933 1.337728 CCATAGACAACACACTCGGCA 60.338 52.381 0.00 0.00 0.0 5.69 R
3245 3338 1.413767 CGAATCAGTCAAGACGCCGG 61.414 60.000 0.00 0.00 36.2 6.13 R
4067 4202 1.600957 CGACTATTAAGACCCTCGCGA 59.399 52.381 9.26 9.26 0.0 5.87 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
17 18 3.727146 TCGCCGATCTTCGATCGA 58.273 55.556 23.29 15.15 43.74 3.59
18 19 2.244946 TCGCCGATCTTCGATCGAT 58.755 52.632 20.18 3.58 43.74 3.59
19 20 0.110192 TCGCCGATCTTCGATCGATG 60.110 55.000 20.18 20.94 43.74 3.84
20 21 1.067743 CGCCGATCTTCGATCGATGG 61.068 60.000 25.37 18.99 43.74 3.51
21 22 1.347817 GCCGATCTTCGATCGATGGC 61.348 60.000 25.37 23.31 43.74 4.40
22 23 0.734253 CCGATCTTCGATCGATGGCC 60.734 60.000 25.37 17.50 43.74 5.36
23 24 0.242286 CGATCTTCGATCGATGGCCT 59.758 55.000 25.37 13.77 43.74 5.19
24 25 1.336332 CGATCTTCGATCGATGGCCTT 60.336 52.381 25.37 11.89 43.74 4.35
25 26 2.333014 GATCTTCGATCGATGGCCTTC 58.667 52.381 25.37 6.40 0.00 3.46
26 27 0.389391 TCTTCGATCGATGGCCTTCC 59.611 55.000 25.37 0.00 0.00 3.46
27 28 0.941463 CTTCGATCGATGGCCTTCCG 60.941 60.000 20.18 10.56 34.14 4.30
28 29 2.971428 TTCGATCGATGGCCTTCCGC 62.971 60.000 20.18 2.16 34.14 5.54
29 30 2.423446 GATCGATGGCCTTCCGCT 59.577 61.111 12.77 0.82 37.74 5.52
30 31 1.227674 GATCGATGGCCTTCCGCTT 60.228 57.895 12.77 1.00 37.74 4.68
31 32 1.502163 GATCGATGGCCTTCCGCTTG 61.502 60.000 12.77 0.00 37.74 4.01
32 33 2.947938 ATCGATGGCCTTCCGCTTGG 62.948 60.000 12.77 0.00 37.74 3.61
76 77 3.669354 GGAGCCCGACTAGATGTTG 57.331 57.895 0.00 0.00 0.00 3.33
77 78 0.824759 GGAGCCCGACTAGATGTTGT 59.175 55.000 0.00 0.00 0.00 3.32
78 79 1.471676 GGAGCCCGACTAGATGTTGTG 60.472 57.143 0.00 0.00 0.00 3.33
79 80 1.204941 GAGCCCGACTAGATGTTGTGT 59.795 52.381 0.00 0.00 0.00 3.72
80 81 1.204941 AGCCCGACTAGATGTTGTGTC 59.795 52.381 0.00 0.00 0.00 3.67
81 82 1.067142 GCCCGACTAGATGTTGTGTCA 60.067 52.381 0.00 0.00 0.00 3.58
82 83 2.607187 CCCGACTAGATGTTGTGTCAC 58.393 52.381 0.00 0.00 0.00 3.67
83 84 2.231478 CCCGACTAGATGTTGTGTCACT 59.769 50.000 4.27 0.00 0.00 3.41
84 85 3.502920 CCGACTAGATGTTGTGTCACTC 58.497 50.000 4.27 0.00 0.00 3.51
85 86 3.502920 CGACTAGATGTTGTGTCACTCC 58.497 50.000 4.27 0.00 0.00 3.85
86 87 3.673594 CGACTAGATGTTGTGTCACTCCC 60.674 52.174 4.27 0.00 0.00 4.30
87 88 2.231478 ACTAGATGTTGTGTCACTCCCG 59.769 50.000 4.27 0.00 0.00 5.14
88 89 0.321671 AGATGTTGTGTCACTCCCGG 59.678 55.000 4.27 0.00 0.00 5.73
89 90 1.298859 GATGTTGTGTCACTCCCGGC 61.299 60.000 4.27 0.00 0.00 6.13
90 91 3.041940 GTTGTGTCACTCCCGGCG 61.042 66.667 0.00 0.00 0.00 6.46
91 92 4.980805 TTGTGTCACTCCCGGCGC 62.981 66.667 0.00 0.00 0.00 6.53
93 94 4.760047 GTGTCACTCCCGGCGCAT 62.760 66.667 10.83 0.00 0.00 4.73
94 95 4.758251 TGTCACTCCCGGCGCATG 62.758 66.667 10.83 0.00 0.00 4.06
95 96 4.760047 GTCACTCCCGGCGCATGT 62.760 66.667 10.83 0.00 0.00 3.21
96 97 4.758251 TCACTCCCGGCGCATGTG 62.758 66.667 10.83 9.63 0.00 3.21
105 106 4.341827 GCGCATGTGCCTTTTTGT 57.658 50.000 20.70 0.00 37.91 2.83
106 107 2.603915 GCGCATGTGCCTTTTTGTT 58.396 47.368 20.70 0.00 37.91 2.83
107 108 0.936600 GCGCATGTGCCTTTTTGTTT 59.063 45.000 20.70 0.00 37.91 2.83
108 109 1.330213 GCGCATGTGCCTTTTTGTTTT 59.670 42.857 20.70 0.00 37.91 2.43
109 110 2.223226 GCGCATGTGCCTTTTTGTTTTT 60.223 40.909 20.70 0.00 37.91 1.94
132 133 4.488790 CTTGTTGAGCTGTGCCCT 57.511 55.556 0.00 0.00 0.00 5.19
133 134 2.251600 CTTGTTGAGCTGTGCCCTC 58.748 57.895 0.00 0.00 0.00 4.30
134 135 0.535780 CTTGTTGAGCTGTGCCCTCA 60.536 55.000 0.00 0.00 37.54 3.86
135 136 0.535780 TTGTTGAGCTGTGCCCTCAG 60.536 55.000 0.00 0.00 40.16 3.35
146 147 3.102090 GCCCTCAGCATTAACCCTC 57.898 57.895 0.00 0.00 42.97 4.30
147 148 0.466372 GCCCTCAGCATTAACCCTCC 60.466 60.000 0.00 0.00 42.97 4.30
148 149 0.918983 CCCTCAGCATTAACCCTCCA 59.081 55.000 0.00 0.00 0.00 3.86
149 150 1.408822 CCCTCAGCATTAACCCTCCAC 60.409 57.143 0.00 0.00 0.00 4.02
150 151 1.561542 CCTCAGCATTAACCCTCCACT 59.438 52.381 0.00 0.00 0.00 4.00
151 152 2.771943 CCTCAGCATTAACCCTCCACTA 59.228 50.000 0.00 0.00 0.00 2.74
152 153 3.432326 CCTCAGCATTAACCCTCCACTAC 60.432 52.174 0.00 0.00 0.00 2.73
153 154 3.450904 TCAGCATTAACCCTCCACTACT 58.549 45.455 0.00 0.00 0.00 2.57
154 155 3.844211 TCAGCATTAACCCTCCACTACTT 59.156 43.478 0.00 0.00 0.00 2.24
155 156 5.027460 TCAGCATTAACCCTCCACTACTTA 58.973 41.667 0.00 0.00 0.00 2.24
156 157 5.665812 TCAGCATTAACCCTCCACTACTTAT 59.334 40.000 0.00 0.00 0.00 1.73
157 158 6.842280 TCAGCATTAACCCTCCACTACTTATA 59.158 38.462 0.00 0.00 0.00 0.98
158 159 7.512746 TCAGCATTAACCCTCCACTACTTATAT 59.487 37.037 0.00 0.00 0.00 0.86
159 160 7.604164 CAGCATTAACCCTCCACTACTTATATG 59.396 40.741 0.00 0.00 0.00 1.78
160 161 7.292591 AGCATTAACCCTCCACTACTTATATGT 59.707 37.037 0.00 0.00 0.00 2.29
161 162 7.603024 GCATTAACCCTCCACTACTTATATGTC 59.397 40.741 0.00 0.00 0.00 3.06
162 163 8.871125 CATTAACCCTCCACTACTTATATGTCT 58.129 37.037 0.00 0.00 0.00 3.41
163 164 6.732896 AACCCTCCACTACTTATATGTCTG 57.267 41.667 0.00 0.00 0.00 3.51
164 165 5.148502 ACCCTCCACTACTTATATGTCTGG 58.851 45.833 8.24 8.24 0.00 3.86
165 166 5.103215 ACCCTCCACTACTTATATGTCTGGA 60.103 44.000 13.44 13.44 0.00 3.86
166 167 6.019748 CCCTCCACTACTTATATGTCTGGAT 58.980 44.000 14.08 0.00 30.92 3.41
167 168 6.153680 CCCTCCACTACTTATATGTCTGGATC 59.846 46.154 14.08 0.00 30.92 3.36
168 169 6.951198 CCTCCACTACTTATATGTCTGGATCT 59.049 42.308 14.08 0.00 30.92 2.75
169 170 7.453126 CCTCCACTACTTATATGTCTGGATCTT 59.547 40.741 14.08 0.00 30.92 2.40
170 171 8.183104 TCCACTACTTATATGTCTGGATCTTG 57.817 38.462 11.39 0.00 0.00 3.02
171 172 6.870965 CCACTACTTATATGTCTGGATCTTGC 59.129 42.308 8.65 0.00 0.00 4.01
172 173 6.584184 CACTACTTATATGTCTGGATCTTGCG 59.416 42.308 0.00 0.00 0.00 4.85
173 174 5.537300 ACTTATATGTCTGGATCTTGCGT 57.463 39.130 0.00 0.00 0.00 5.24
174 175 5.292765 ACTTATATGTCTGGATCTTGCGTG 58.707 41.667 0.00 0.00 0.00 5.34
175 176 3.827008 ATATGTCTGGATCTTGCGTGT 57.173 42.857 0.00 0.00 0.00 4.49
176 177 1.730501 ATGTCTGGATCTTGCGTGTG 58.269 50.000 0.00 0.00 0.00 3.82
177 178 0.392706 TGTCTGGATCTTGCGTGTGT 59.607 50.000 0.00 0.00 0.00 3.72
178 179 0.792640 GTCTGGATCTTGCGTGTGTG 59.207 55.000 0.00 0.00 0.00 3.82
179 180 0.392706 TCTGGATCTTGCGTGTGTGT 59.607 50.000 0.00 0.00 0.00 3.72
180 181 0.514255 CTGGATCTTGCGTGTGTGTG 59.486 55.000 0.00 0.00 0.00 3.82
181 182 0.179059 TGGATCTTGCGTGTGTGTGT 60.179 50.000 0.00 0.00 0.00 3.72
182 183 0.235665 GGATCTTGCGTGTGTGTGTG 59.764 55.000 0.00 0.00 0.00 3.82
183 184 0.937304 GATCTTGCGTGTGTGTGTGT 59.063 50.000 0.00 0.00 0.00 3.72
184 185 0.657312 ATCTTGCGTGTGTGTGTGTG 59.343 50.000 0.00 0.00 0.00 3.82
185 186 0.672091 TCTTGCGTGTGTGTGTGTGT 60.672 50.000 0.00 0.00 0.00 3.72
186 187 0.521034 CTTGCGTGTGTGTGTGTGTG 60.521 55.000 0.00 0.00 0.00 3.82
187 188 1.231296 TTGCGTGTGTGTGTGTGTGT 61.231 50.000 0.00 0.00 0.00 3.72
188 189 1.225991 GCGTGTGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
189 190 1.906994 GCGTGTGTGTGTGTGTGTGT 61.907 55.000 0.00 0.00 0.00 3.72
190 191 0.515127 CGTGTGTGTGTGTGTGTGTT 59.485 50.000 0.00 0.00 0.00 3.32
191 192 1.069568 CGTGTGTGTGTGTGTGTGTTT 60.070 47.619 0.00 0.00 0.00 2.83
192 193 2.315011 GTGTGTGTGTGTGTGTGTTTG 58.685 47.619 0.00 0.00 0.00 2.93
193 194 1.950216 TGTGTGTGTGTGTGTGTTTGT 59.050 42.857 0.00 0.00 0.00 2.83
194 195 2.287248 TGTGTGTGTGTGTGTGTTTGTG 60.287 45.455 0.00 0.00 0.00 3.33
195 196 1.950216 TGTGTGTGTGTGTGTTTGTGT 59.050 42.857 0.00 0.00 0.00 3.72
196 197 2.287248 TGTGTGTGTGTGTGTTTGTGTG 60.287 45.455 0.00 0.00 0.00 3.82
197 198 1.335415 TGTGTGTGTGTGTTTGTGTGC 60.335 47.619 0.00 0.00 0.00 4.57
198 199 1.068610 GTGTGTGTGTGTTTGTGTGCT 60.069 47.619 0.00 0.00 0.00 4.40
199 200 1.611006 TGTGTGTGTGTTTGTGTGCTT 59.389 42.857 0.00 0.00 0.00 3.91
200 201 1.984990 GTGTGTGTGTTTGTGTGCTTG 59.015 47.619 0.00 0.00 0.00 4.01
201 202 1.882623 TGTGTGTGTTTGTGTGCTTGA 59.117 42.857 0.00 0.00 0.00 3.02
202 203 2.294512 TGTGTGTGTTTGTGTGCTTGAA 59.705 40.909 0.00 0.00 0.00 2.69
203 204 2.661195 GTGTGTGTTTGTGTGCTTGAAC 59.339 45.455 0.00 0.00 0.00 3.18
204 205 2.258755 GTGTGTTTGTGTGCTTGAACC 58.741 47.619 0.00 0.00 0.00 3.62
205 206 2.094752 GTGTGTTTGTGTGCTTGAACCT 60.095 45.455 0.00 0.00 0.00 3.50
206 207 2.560542 TGTGTTTGTGTGCTTGAACCTT 59.439 40.909 0.00 0.00 0.00 3.50
207 208 2.923020 GTGTTTGTGTGCTTGAACCTTG 59.077 45.455 0.00 0.00 0.00 3.61
208 209 2.560542 TGTTTGTGTGCTTGAACCTTGT 59.439 40.909 0.00 0.00 0.00 3.16
209 210 3.006323 TGTTTGTGTGCTTGAACCTTGTT 59.994 39.130 0.00 0.00 0.00 2.83
210 211 2.937469 TGTGTGCTTGAACCTTGTTG 57.063 45.000 0.00 0.00 0.00 3.33
211 212 1.476085 TGTGTGCTTGAACCTTGTTGG 59.524 47.619 0.00 0.00 42.93 3.77
222 223 1.938625 CCTTGTTGGTTGTTGGCTTG 58.061 50.000 0.00 0.00 0.00 4.01
223 224 1.473080 CCTTGTTGGTTGTTGGCTTGG 60.473 52.381 0.00 0.00 0.00 3.61
224 225 0.539051 TTGTTGGTTGTTGGCTTGGG 59.461 50.000 0.00 0.00 0.00 4.12
225 226 1.227527 GTTGGTTGTTGGCTTGGGC 60.228 57.895 0.00 0.00 37.82 5.36
226 227 1.687146 TTGGTTGTTGGCTTGGGCA 60.687 52.632 0.00 0.00 40.87 5.36
227 228 1.053264 TTGGTTGTTGGCTTGGGCAT 61.053 50.000 0.00 0.00 38.08 4.40
228 229 1.053264 TGGTTGTTGGCTTGGGCATT 61.053 50.000 0.00 0.00 38.08 3.56
229 230 0.108396 GGTTGTTGGCTTGGGCATTT 59.892 50.000 0.00 0.00 38.08 2.32
230 231 1.228533 GTTGTTGGCTTGGGCATTTG 58.771 50.000 0.00 0.00 38.08 2.32
231 232 0.534652 TTGTTGGCTTGGGCATTTGC 60.535 50.000 0.00 0.00 38.08 3.68
232 233 1.372307 GTTGGCTTGGGCATTTGCT 59.628 52.632 2.12 0.00 41.70 3.91
233 234 0.250424 GTTGGCTTGGGCATTTGCTT 60.250 50.000 2.12 0.00 41.70 3.91
234 235 0.473326 TTGGCTTGGGCATTTGCTTT 59.527 45.000 2.12 0.00 41.70 3.51
235 236 1.346062 TGGCTTGGGCATTTGCTTTA 58.654 45.000 2.12 0.00 41.70 1.85
236 237 1.907936 TGGCTTGGGCATTTGCTTTAT 59.092 42.857 2.12 0.00 41.70 1.40
237 238 3.102972 TGGCTTGGGCATTTGCTTTATA 58.897 40.909 2.12 0.00 41.70 0.98
238 239 3.517100 TGGCTTGGGCATTTGCTTTATAA 59.483 39.130 2.12 0.00 41.70 0.98
239 240 4.163839 TGGCTTGGGCATTTGCTTTATAAT 59.836 37.500 2.12 0.00 41.70 1.28
240 241 5.365025 TGGCTTGGGCATTTGCTTTATAATA 59.635 36.000 2.12 0.00 41.70 0.98
241 242 6.043012 TGGCTTGGGCATTTGCTTTATAATAT 59.957 34.615 2.12 0.00 41.70 1.28
242 243 7.234371 TGGCTTGGGCATTTGCTTTATAATATA 59.766 33.333 2.12 0.00 41.70 0.86
243 244 8.093927 GGCTTGGGCATTTGCTTTATAATATAA 58.906 33.333 2.12 0.00 41.70 0.98
244 245 9.487790 GCTTGGGCATTTGCTTTATAATATAAA 57.512 29.630 5.46 5.46 41.70 1.40
252 253 4.905269 GCTTTATAATATAAAGCGGGGCG 58.095 43.478 30.20 10.34 46.31 6.13
253 254 4.632688 GCTTTATAATATAAAGCGGGGCGA 59.367 41.667 30.20 0.05 46.31 5.54
254 255 5.122711 GCTTTATAATATAAAGCGGGGCGAA 59.877 40.000 30.20 0.00 46.31 4.70
255 256 6.348704 GCTTTATAATATAAAGCGGGGCGAAA 60.349 38.462 30.20 0.57 46.31 3.46
256 257 6.730960 TTATAATATAAAGCGGGGCGAAAG 57.269 37.500 0.00 0.00 0.00 2.62
435 441 9.743581 ATAAAACGGGGAATTAAGAAACTAGAA 57.256 29.630 0.00 0.00 0.00 2.10
440 446 7.668469 ACGGGGAATTAAGAAACTAGAATTGTT 59.332 33.333 0.00 0.00 0.00 2.83
534 541 8.450578 TTTCATGATCAAAGTACTGAAGTTGT 57.549 30.769 0.00 0.00 0.00 3.32
567 574 9.754382 CAAAATACTAAAATTGCCATGCTCTAT 57.246 29.630 0.00 0.00 0.00 1.98
610 617 5.800438 GGCAACTTTAGTTTAAGCACTATGC 59.200 40.000 5.98 0.00 38.95 3.14
812 827 9.783081 TGCTAATGTCATCTATTTACATGTGAT 57.217 29.630 9.11 5.21 34.20 3.06
866 882 2.557924 GTGAAGATGCCACATGTTTGGA 59.442 45.455 6.54 0.00 39.24 3.53
1180 1199 1.373748 TTCTTCGTTCGGGAAGCCG 60.374 57.895 0.00 0.00 42.48 5.52
1232 1251 0.178944 TCTTGACTTCCCACCGAGGA 60.179 55.000 0.00 0.00 41.22 3.71
1236 1255 0.976073 GACTTCCCACCGAGGATCCA 60.976 60.000 15.82 0.00 41.22 3.41
1237 1256 1.265454 ACTTCCCACCGAGGATCCAC 61.265 60.000 15.82 6.85 41.22 4.02
1243 1262 2.039418 CCACCGAGGATCCACAGATTA 58.961 52.381 15.82 0.00 41.22 1.75
1246 1265 3.133003 CACCGAGGATCCACAGATTAACT 59.867 47.826 15.82 0.00 30.90 2.24
1255 1274 6.092807 GGATCCACAGATTAACTCAGTTGTTC 59.907 42.308 6.95 0.00 30.90 3.18
1262 1281 2.135664 AACTCAGTTGTTCGGACGAG 57.864 50.000 0.00 0.00 0.00 4.18
1296 1315 1.071239 CGCGCGGATCAGTTTAGATTG 60.071 52.381 24.84 0.00 0.00 2.67
1301 1320 3.545703 CGGATCAGTTTAGATTGGGCTT 58.454 45.455 0.00 0.00 0.00 4.35
1304 1323 4.949856 GGATCAGTTTAGATTGGGCTTTCA 59.050 41.667 0.00 0.00 0.00 2.69
1314 1333 5.815581 AGATTGGGCTTTCATGTTACTGTA 58.184 37.500 0.00 0.00 0.00 2.74
1326 1345 2.969950 TGTTACTGTAGCAGGTTCAGGT 59.030 45.455 10.61 0.35 35.51 4.00
1340 1359 3.305608 GGTTCAGGTTTTTGATCTGGCTG 60.306 47.826 0.00 0.00 37.09 4.85
1367 1407 3.070018 CTCCATCCGCTTTGACCATATC 58.930 50.000 0.00 0.00 0.00 1.63
1380 1420 1.202533 ACCATATCGTAGTGCAGCCAC 60.203 52.381 0.00 0.00 42.39 5.01
1392 1432 2.036571 CAGCCACGATGAGCTTGCA 61.037 57.895 0.00 0.00 37.18 4.08
1435 1475 3.439857 TTCCAGGGGAAACTCTTCATG 57.560 47.619 0.00 0.00 38.96 3.07
1446 1486 4.725790 AACTCTTCATGGCTAATTTGGC 57.274 40.909 6.50 6.50 0.00 4.52
1454 1494 0.530288 GGCTAATTTGGCCTTGCGAA 59.470 50.000 15.91 0.00 45.57 4.70
1501 1547 3.077484 AGCACTTCAATACACAGCCAT 57.923 42.857 0.00 0.00 0.00 4.40
1502 1548 3.012518 AGCACTTCAATACACAGCCATC 58.987 45.455 0.00 0.00 0.00 3.51
1541 1589 5.245075 TGGAATTAACGGCCTTTTCTTTCAT 59.755 36.000 0.00 0.00 0.00 2.57
1542 1590 6.163476 GGAATTAACGGCCTTTTCTTTCATT 58.837 36.000 0.00 0.00 0.00 2.57
1543 1591 6.310467 GGAATTAACGGCCTTTTCTTTCATTC 59.690 38.462 0.00 0.12 0.00 2.67
1544 1592 5.776173 TTAACGGCCTTTTCTTTCATTCA 57.224 34.783 0.00 0.00 0.00 2.57
1545 1593 4.871933 AACGGCCTTTTCTTTCATTCAT 57.128 36.364 0.00 0.00 0.00 2.57
1546 1594 4.440839 ACGGCCTTTTCTTTCATTCATC 57.559 40.909 0.00 0.00 0.00 2.92
1547 1595 3.826157 ACGGCCTTTTCTTTCATTCATCA 59.174 39.130 0.00 0.00 0.00 3.07
1548 1596 4.168760 CGGCCTTTTCTTTCATTCATCAC 58.831 43.478 0.00 0.00 0.00 3.06
1549 1597 4.082571 CGGCCTTTTCTTTCATTCATCACT 60.083 41.667 0.00 0.00 0.00 3.41
1550 1598 5.565439 CGGCCTTTTCTTTCATTCATCACTT 60.565 40.000 0.00 0.00 0.00 3.16
1551 1599 5.636543 GGCCTTTTCTTTCATTCATCACTTG 59.363 40.000 0.00 0.00 0.00 3.16
1686 1773 2.213499 GCTTGTGTCATATTCCGAGGG 58.787 52.381 0.00 0.00 0.00 4.30
1716 1803 6.579865 TCTTGCTTATGTAGGGTTAGCTAAC 58.420 40.000 25.52 25.52 35.50 2.34
1721 1808 6.475596 TTATGTAGGGTTAGCTAACTGTCC 57.524 41.667 30.36 23.81 36.47 4.02
1744 1831 3.916989 AGATTACCTCCTGTTCCAAAGGT 59.083 43.478 0.00 0.00 44.24 3.50
1752 1839 3.699038 TCCTGTTCCAAAGGTCAAACAAG 59.301 43.478 0.00 0.00 36.14 3.16
1762 1849 3.555966 AGGTCAAACAAGGAACCTGAAG 58.444 45.455 0.00 0.00 0.00 3.02
1776 1863 1.341531 CCTGAAGTCTGACCAGTTCGT 59.658 52.381 3.76 0.00 0.00 3.85
1803 1890 5.961395 GCAGATAGCCAATTTGATTGTTG 57.039 39.130 0.00 0.00 38.59 3.33
1805 1892 6.278363 GCAGATAGCCAATTTGATTGTTGAT 58.722 36.000 0.00 0.00 38.59 2.57
2107 2198 3.326747 CTGTCTTTCCTACCAAAGGTCG 58.673 50.000 0.00 0.00 46.62 4.79
2258 2349 3.557228 TTTGCACCCTTTTGCTTCATT 57.443 38.095 0.00 0.00 43.41 2.57
2523 2616 5.181811 TGAGATCAGTGAAATGCGTTGATTT 59.818 36.000 0.00 0.00 0.00 2.17
2633 2726 4.448210 CCACCAATACGTGCTAAGGTTAT 58.552 43.478 0.00 0.00 32.10 1.89
2844 2937 4.854399 TCAAGTTTGAACAATAACTGCCG 58.146 39.130 0.00 0.00 34.95 5.69
2855 2948 1.860676 TAACTGCCGAGTGTGTTGTC 58.139 50.000 0.00 0.00 30.61 3.18
2860 2953 1.337728 TGCCGAGTGTGTTGTCTATGG 60.338 52.381 0.00 0.00 0.00 2.74
2882 2975 1.078426 ACCGTTGCATACAGGCCTC 60.078 57.895 0.00 0.00 0.00 4.70
2921 3014 3.084786 AGTGCTTTCCATGTTAAGCTCC 58.915 45.455 22.14 15.42 45.37 4.70
2961 3054 3.323403 GTGATAGCCTGATAGGAACTGCT 59.677 47.826 0.00 0.00 41.52 4.24
3023 3116 2.391616 TGCAGGACACTAATGCTCTG 57.608 50.000 0.00 0.00 40.62 3.35
3038 3131 6.893958 AATGCTCTGATGAACTTACTAACG 57.106 37.500 0.00 0.00 0.00 3.18
3047 3140 3.243501 TGAACTTACTAACGTTCACGGCT 60.244 43.478 2.82 0.00 43.10 5.52
3245 3338 7.206687 AGGATGTTGAAGTCGAATATCTTCTC 58.793 38.462 12.92 8.01 40.20 2.87
3353 3446 4.322567 AGAGGCTTTCTTGAATGTGAGAC 58.677 43.478 0.00 0.00 29.61 3.36
3354 3447 4.067896 GAGGCTTTCTTGAATGTGAGACA 58.932 43.478 0.00 0.00 0.00 3.41
3355 3448 4.660168 AGGCTTTCTTGAATGTGAGACAT 58.340 39.130 0.00 0.00 41.31 3.06
3356 3449 4.699257 AGGCTTTCTTGAATGTGAGACATC 59.301 41.667 0.00 0.00 37.97 3.06
3357 3450 4.456911 GGCTTTCTTGAATGTGAGACATCA 59.543 41.667 0.00 0.00 37.97 3.07
3461 3556 5.125097 GTGATTCCACAAGCATTCTGAATCT 59.875 40.000 14.96 0.00 42.72 2.40
3529 3632 1.419922 CGATGGTTTTCGCACCGAG 59.580 57.895 0.00 0.00 40.09 4.63
3581 3684 5.067273 CGATCTATCACCTCAGTAACCTCT 58.933 45.833 0.00 0.00 0.00 3.69
3588 3691 6.928348 TCACCTCAGTAACCTCTTTTGATA 57.072 37.500 0.00 0.00 0.00 2.15
3680 3790 4.064388 GCAAAGCATTGGGTACAAAATGT 58.936 39.130 16.61 5.75 40.55 2.71
3681 3791 4.152223 GCAAAGCATTGGGTACAAAATGTC 59.848 41.667 16.61 11.16 40.55 3.06
3759 3871 7.192913 TCCGTCATCAAATTATTTTCCATTCG 58.807 34.615 0.00 0.00 0.00 3.34
3760 3872 6.972328 CCGTCATCAAATTATTTTCCATTCGT 59.028 34.615 0.00 0.00 0.00 3.85
3764 3876 9.703892 TCATCAAATTATTTTCCATTCGTTTGT 57.296 25.926 0.00 0.00 0.00 2.83
3812 3924 4.036971 CACAGAGCTAGTATAAACCGAGCT 59.963 45.833 0.00 0.00 44.22 4.09
3865 3999 4.452825 TCAAACCAAATACGGTGTTCTGA 58.547 39.130 0.00 0.00 39.95 3.27
3981 4115 2.446435 ACCATCATGGGTGCAAGTTAC 58.554 47.619 9.04 0.00 43.37 2.50
4012 4146 0.107654 CTTCCTTGTAGGGGCCTTCG 60.108 60.000 0.84 0.00 35.59 3.79
4039 4173 2.915349 TGATTAGAGTAGAGGTCGCGT 58.085 47.619 5.77 0.00 0.00 6.01
4067 4202 3.131933 CAGAGCTTACTGCCTGACATAGT 59.868 47.826 0.00 0.00 44.23 2.12
4088 4223 1.332997 CGCGAGGGTCTTAATAGTCGT 59.667 52.381 0.00 0.00 0.00 4.34
4089 4224 2.728922 GCGAGGGTCTTAATAGTCGTG 58.271 52.381 0.00 0.00 0.00 4.35
4090 4225 2.357009 GCGAGGGTCTTAATAGTCGTGA 59.643 50.000 0.00 0.00 0.00 4.35
4091 4226 3.791455 GCGAGGGTCTTAATAGTCGTGAC 60.791 52.174 0.00 0.00 0.00 3.67
4161 4296 2.225727 GGTAAGTTCTTTGGCTTGGACG 59.774 50.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.067743 CCATCGATCGAAGATCGGCG 61.068 60.000 23.50 18.35 45.12 6.46
2 3 1.347817 GCCATCGATCGAAGATCGGC 61.348 60.000 23.50 22.40 45.12 5.54
6 7 1.001406 GGAAGGCCATCGATCGAAGAT 59.999 52.381 23.50 2.26 45.12 2.40
8 9 0.941463 CGGAAGGCCATCGATCGAAG 60.941 60.000 23.50 18.04 0.00 3.79
9 10 1.067416 CGGAAGGCCATCGATCGAA 59.933 57.895 23.50 5.77 0.00 3.71
10 11 2.728180 CGGAAGGCCATCGATCGA 59.272 61.111 21.86 21.86 0.00 3.59
11 12 2.978452 AAGCGGAAGGCCATCGATCG 62.978 60.000 9.36 9.36 45.17 3.69
12 13 1.227674 AAGCGGAAGGCCATCGATC 60.228 57.895 5.01 0.00 45.17 3.69
13 14 1.524621 CAAGCGGAAGGCCATCGAT 60.525 57.895 5.01 0.51 45.17 3.59
14 15 2.125147 CAAGCGGAAGGCCATCGA 60.125 61.111 5.01 0.00 45.17 3.59
15 16 3.204827 CCAAGCGGAAGGCCATCG 61.205 66.667 5.01 6.79 45.17 3.84
16 17 3.521796 GCCAAGCGGAAGGCCATC 61.522 66.667 5.01 0.92 45.18 3.51
58 59 0.824759 ACAACATCTAGTCGGGCTCC 59.175 55.000 0.00 0.00 0.00 4.70
59 60 1.204941 ACACAACATCTAGTCGGGCTC 59.795 52.381 0.00 0.00 0.00 4.70
60 61 1.204941 GACACAACATCTAGTCGGGCT 59.795 52.381 0.00 0.00 0.00 5.19
61 62 1.067142 TGACACAACATCTAGTCGGGC 60.067 52.381 0.00 0.00 33.83 6.13
62 63 2.231478 AGTGACACAACATCTAGTCGGG 59.769 50.000 8.59 0.00 33.83 5.14
63 64 3.502920 GAGTGACACAACATCTAGTCGG 58.497 50.000 8.59 0.00 33.83 4.79
64 65 3.502920 GGAGTGACACAACATCTAGTCG 58.497 50.000 8.59 0.00 33.83 4.18
65 66 3.673594 CGGGAGTGACACAACATCTAGTC 60.674 52.174 8.59 0.00 0.00 2.59
66 67 2.231478 CGGGAGTGACACAACATCTAGT 59.769 50.000 8.59 0.00 0.00 2.57
67 68 2.417379 CCGGGAGTGACACAACATCTAG 60.417 54.545 8.59 0.00 0.00 2.43
68 69 1.548719 CCGGGAGTGACACAACATCTA 59.451 52.381 8.59 0.00 0.00 1.98
69 70 0.321671 CCGGGAGTGACACAACATCT 59.678 55.000 8.59 0.00 0.00 2.90
70 71 1.298859 GCCGGGAGTGACACAACATC 61.299 60.000 8.59 0.00 0.00 3.06
71 72 1.302511 GCCGGGAGTGACACAACAT 60.303 57.895 8.59 0.00 0.00 2.71
72 73 2.110213 GCCGGGAGTGACACAACA 59.890 61.111 8.59 0.00 0.00 3.33
73 74 3.041940 CGCCGGGAGTGACACAAC 61.042 66.667 8.59 1.34 0.00 3.32
74 75 4.980805 GCGCCGGGAGTGACACAA 62.981 66.667 8.59 0.00 0.00 3.33
76 77 4.760047 ATGCGCCGGGAGTGACAC 62.760 66.667 4.18 0.00 0.00 3.67
77 78 4.758251 CATGCGCCGGGAGTGACA 62.758 66.667 4.18 0.00 0.00 3.58
78 79 4.760047 ACATGCGCCGGGAGTGAC 62.760 66.667 4.18 0.00 0.00 3.67
79 80 4.758251 CACATGCGCCGGGAGTGA 62.758 66.667 4.18 0.00 32.14 3.41
88 89 0.936600 AAACAAAAAGGCACATGCGC 59.063 45.000 0.00 0.00 43.26 6.09
89 90 3.672028 AAAAACAAAAAGGCACATGCG 57.328 38.095 0.00 0.00 43.26 4.73
115 116 0.535780 TGAGGGCACAGCTCAACAAG 60.536 55.000 0.00 0.00 0.00 3.16
116 117 0.535780 CTGAGGGCACAGCTCAACAA 60.536 55.000 0.00 0.00 0.00 2.83
117 118 1.071987 CTGAGGGCACAGCTCAACA 59.928 57.895 0.00 0.00 0.00 3.33
118 119 3.978272 CTGAGGGCACAGCTCAAC 58.022 61.111 0.00 0.00 0.00 3.18
128 129 0.466372 GGAGGGTTAATGCTGAGGGC 60.466 60.000 0.00 0.00 42.22 5.19
129 130 0.918983 TGGAGGGTTAATGCTGAGGG 59.081 55.000 0.00 0.00 0.00 4.30
130 131 1.561542 AGTGGAGGGTTAATGCTGAGG 59.438 52.381 0.00 0.00 0.00 3.86
131 132 3.452627 AGTAGTGGAGGGTTAATGCTGAG 59.547 47.826 0.00 0.00 0.00 3.35
132 133 3.450904 AGTAGTGGAGGGTTAATGCTGA 58.549 45.455 0.00 0.00 0.00 4.26
133 134 3.914426 AGTAGTGGAGGGTTAATGCTG 57.086 47.619 0.00 0.00 0.00 4.41
134 135 7.292591 ACATATAAGTAGTGGAGGGTTAATGCT 59.707 37.037 0.00 0.00 0.00 3.79
135 136 7.450903 ACATATAAGTAGTGGAGGGTTAATGC 58.549 38.462 0.00 0.00 0.00 3.56
136 137 8.871125 AGACATATAAGTAGTGGAGGGTTAATG 58.129 37.037 0.00 0.00 0.00 1.90
137 138 8.871125 CAGACATATAAGTAGTGGAGGGTTAAT 58.129 37.037 0.00 0.00 0.00 1.40
138 139 7.289317 CCAGACATATAAGTAGTGGAGGGTTAA 59.711 40.741 3.80 0.00 30.66 2.01
139 140 6.781014 CCAGACATATAAGTAGTGGAGGGTTA 59.219 42.308 3.80 0.00 30.66 2.85
140 141 5.602978 CCAGACATATAAGTAGTGGAGGGTT 59.397 44.000 3.80 0.00 30.66 4.11
141 142 5.103215 TCCAGACATATAAGTAGTGGAGGGT 60.103 44.000 7.33 0.00 32.53 4.34
142 143 5.394738 TCCAGACATATAAGTAGTGGAGGG 58.605 45.833 7.33 0.00 32.53 4.30
143 144 6.951198 AGATCCAGACATATAAGTAGTGGAGG 59.049 42.308 14.00 0.00 37.84 4.30
144 145 8.303156 CAAGATCCAGACATATAAGTAGTGGAG 58.697 40.741 14.00 1.92 37.84 3.86
145 146 7.255977 GCAAGATCCAGACATATAAGTAGTGGA 60.256 40.741 11.96 11.96 38.43 4.02
146 147 6.870965 GCAAGATCCAGACATATAAGTAGTGG 59.129 42.308 3.55 3.55 0.00 4.00
147 148 6.584184 CGCAAGATCCAGACATATAAGTAGTG 59.416 42.308 0.00 0.00 43.02 2.74
148 149 6.265649 ACGCAAGATCCAGACATATAAGTAGT 59.734 38.462 0.00 0.00 43.62 2.73
149 150 6.584184 CACGCAAGATCCAGACATATAAGTAG 59.416 42.308 0.00 0.00 43.62 2.57
150 151 6.040504 ACACGCAAGATCCAGACATATAAGTA 59.959 38.462 0.00 0.00 43.62 2.24
151 152 5.163405 ACACGCAAGATCCAGACATATAAGT 60.163 40.000 0.00 0.00 43.62 2.24
152 153 5.176406 CACACGCAAGATCCAGACATATAAG 59.824 44.000 0.00 0.00 43.62 1.73
153 154 5.049828 CACACGCAAGATCCAGACATATAA 58.950 41.667 0.00 0.00 43.62 0.98
154 155 4.099419 ACACACGCAAGATCCAGACATATA 59.901 41.667 0.00 0.00 43.62 0.86
155 156 3.118629 ACACACGCAAGATCCAGACATAT 60.119 43.478 0.00 0.00 43.62 1.78
156 157 2.233676 ACACACGCAAGATCCAGACATA 59.766 45.455 0.00 0.00 43.62 2.29
157 158 1.002430 ACACACGCAAGATCCAGACAT 59.998 47.619 0.00 0.00 43.62 3.06
158 159 0.392706 ACACACGCAAGATCCAGACA 59.607 50.000 0.00 0.00 43.62 3.41
159 160 0.792640 CACACACGCAAGATCCAGAC 59.207 55.000 0.00 0.00 43.62 3.51
160 161 0.392706 ACACACACGCAAGATCCAGA 59.607 50.000 0.00 0.00 43.62 3.86
161 162 0.514255 CACACACACGCAAGATCCAG 59.486 55.000 0.00 0.00 43.62 3.86
162 163 0.179059 ACACACACACGCAAGATCCA 60.179 50.000 0.00 0.00 43.62 3.41
163 164 0.235665 CACACACACACGCAAGATCC 59.764 55.000 0.00 0.00 43.62 3.36
164 165 0.937304 ACACACACACACGCAAGATC 59.063 50.000 0.00 0.00 43.62 2.75
165 166 0.657312 CACACACACACACGCAAGAT 59.343 50.000 0.00 0.00 43.62 2.40
166 167 0.672091 ACACACACACACACGCAAGA 60.672 50.000 0.00 0.00 43.62 3.02
168 169 1.231296 ACACACACACACACACGCAA 61.231 50.000 0.00 0.00 0.00 4.85
169 170 1.669437 ACACACACACACACACGCA 60.669 52.632 0.00 0.00 0.00 5.24
170 171 1.225991 CACACACACACACACACGC 60.226 57.895 0.00 0.00 0.00 5.34
171 172 0.515127 AACACACACACACACACACG 59.485 50.000 0.00 0.00 0.00 4.49
172 173 2.287308 ACAAACACACACACACACACAC 60.287 45.455 0.00 0.00 0.00 3.82
173 174 1.950216 ACAAACACACACACACACACA 59.050 42.857 0.00 0.00 0.00 3.72
174 175 2.287308 ACACAAACACACACACACACAC 60.287 45.455 0.00 0.00 0.00 3.82
175 176 1.950216 ACACAAACACACACACACACA 59.050 42.857 0.00 0.00 0.00 3.72
176 177 2.315011 CACACAAACACACACACACAC 58.685 47.619 0.00 0.00 0.00 3.82
177 178 1.335415 GCACACAAACACACACACACA 60.335 47.619 0.00 0.00 0.00 3.72
178 179 1.068610 AGCACACAAACACACACACAC 60.069 47.619 0.00 0.00 0.00 3.82
179 180 1.242989 AGCACACAAACACACACACA 58.757 45.000 0.00 0.00 0.00 3.72
180 181 1.984990 CAAGCACACAAACACACACAC 59.015 47.619 0.00 0.00 0.00 3.82
181 182 1.882623 TCAAGCACACAAACACACACA 59.117 42.857 0.00 0.00 0.00 3.72
182 183 2.627863 TCAAGCACACAAACACACAC 57.372 45.000 0.00 0.00 0.00 3.82
183 184 2.352225 GGTTCAAGCACACAAACACACA 60.352 45.455 0.00 0.00 0.00 3.72
184 185 2.094752 AGGTTCAAGCACACAAACACAC 60.095 45.455 0.00 0.00 0.00 3.82
185 186 2.166829 AGGTTCAAGCACACAAACACA 58.833 42.857 0.00 0.00 0.00 3.72
186 187 2.923020 CAAGGTTCAAGCACACAAACAC 59.077 45.455 0.00 0.00 0.00 3.32
187 188 2.560542 ACAAGGTTCAAGCACACAAACA 59.439 40.909 0.00 0.00 0.00 2.83
188 189 3.230743 ACAAGGTTCAAGCACACAAAC 57.769 42.857 0.00 0.00 0.00 2.93
189 190 3.583806 CAACAAGGTTCAAGCACACAAA 58.416 40.909 0.00 0.00 0.00 2.83
190 191 2.094286 CCAACAAGGTTCAAGCACACAA 60.094 45.455 0.00 0.00 0.00 3.33
191 192 1.476085 CCAACAAGGTTCAAGCACACA 59.524 47.619 0.00 0.00 0.00 3.72
192 193 2.208326 CCAACAAGGTTCAAGCACAC 57.792 50.000 0.00 0.00 0.00 3.82
203 204 1.473080 CCAAGCCAACAACCAACAAGG 60.473 52.381 0.00 0.00 45.67 3.61
204 205 1.473080 CCCAAGCCAACAACCAACAAG 60.473 52.381 0.00 0.00 0.00 3.16
205 206 0.539051 CCCAAGCCAACAACCAACAA 59.461 50.000 0.00 0.00 0.00 2.83
206 207 1.965754 GCCCAAGCCAACAACCAACA 61.966 55.000 0.00 0.00 0.00 3.33
207 208 1.227527 GCCCAAGCCAACAACCAAC 60.228 57.895 0.00 0.00 0.00 3.77
208 209 1.053264 ATGCCCAAGCCAACAACCAA 61.053 50.000 0.00 0.00 38.69 3.67
209 210 1.053264 AATGCCCAAGCCAACAACCA 61.053 50.000 0.00 0.00 38.69 3.67
210 211 0.108396 AAATGCCCAAGCCAACAACC 59.892 50.000 0.00 0.00 38.69 3.77
211 212 1.228533 CAAATGCCCAAGCCAACAAC 58.771 50.000 0.00 0.00 38.69 3.32
212 213 0.534652 GCAAATGCCCAAGCCAACAA 60.535 50.000 0.00 0.00 38.69 2.83
213 214 1.071128 GCAAATGCCCAAGCCAACA 59.929 52.632 0.00 0.00 38.69 3.33
214 215 0.250424 AAGCAAATGCCCAAGCCAAC 60.250 50.000 0.94 0.00 43.38 3.77
215 216 0.473326 AAAGCAAATGCCCAAGCCAA 59.527 45.000 0.94 0.00 43.38 4.52
216 217 1.346062 TAAAGCAAATGCCCAAGCCA 58.654 45.000 0.94 0.00 43.38 4.75
217 218 2.696989 ATAAAGCAAATGCCCAAGCC 57.303 45.000 0.94 0.00 43.38 4.35
218 219 9.487790 TTTATATTATAAAGCAAATGCCCAAGC 57.512 29.630 0.94 0.00 43.38 4.01
231 232 6.730960 TTCGCCCCGCTTTATATTATAAAG 57.269 37.500 23.28 23.28 37.53 1.85
232 233 6.348704 GCTTTCGCCCCGCTTTATATTATAAA 60.349 38.462 8.26 8.26 0.00 1.40
233 234 5.122711 GCTTTCGCCCCGCTTTATATTATAA 59.877 40.000 0.00 0.00 0.00 0.98
234 235 4.632688 GCTTTCGCCCCGCTTTATATTATA 59.367 41.667 0.00 0.00 0.00 0.98
235 236 3.439129 GCTTTCGCCCCGCTTTATATTAT 59.561 43.478 0.00 0.00 0.00 1.28
236 237 2.809696 GCTTTCGCCCCGCTTTATATTA 59.190 45.455 0.00 0.00 0.00 0.98
237 238 1.607148 GCTTTCGCCCCGCTTTATATT 59.393 47.619 0.00 0.00 0.00 1.28
238 239 1.235724 GCTTTCGCCCCGCTTTATAT 58.764 50.000 0.00 0.00 0.00 0.86
239 240 2.697819 GCTTTCGCCCCGCTTTATA 58.302 52.632 0.00 0.00 0.00 0.98
240 241 3.509659 GCTTTCGCCCCGCTTTAT 58.490 55.556 0.00 0.00 0.00 1.40
250 251 2.913777 ATACCGAAAAAGGCTTTCGC 57.086 45.000 13.76 7.41 46.89 4.70
450 456 7.920151 GTGCATGTATCATGGCAATTTTAGTTA 59.080 33.333 10.96 0.00 38.10 2.24
610 617 6.426633 TGTCATGATGTTTACACTGTACTTGG 59.573 38.462 0.00 0.00 0.00 3.61
703 714 6.597832 AATCCGTTTTCACCATTAAATCCA 57.402 33.333 0.00 0.00 0.00 3.41
782 797 9.445878 CATGTAAATAGATGACATTAGCAGGAT 57.554 33.333 0.00 0.00 31.44 3.24
833 848 4.238514 GGCATCTTCACATCGTCTATACC 58.761 47.826 0.00 0.00 0.00 2.73
836 851 3.132824 TGTGGCATCTTCACATCGTCTAT 59.867 43.478 0.00 0.00 39.83 1.98
838 853 1.276138 TGTGGCATCTTCACATCGTCT 59.724 47.619 0.00 0.00 39.83 4.18
882 898 4.025979 CGACGCTTATTTGACCATAGAACC 60.026 45.833 0.00 0.00 0.00 3.62
886 902 2.221055 GCCGACGCTTATTTGACCATAG 59.779 50.000 0.00 0.00 0.00 2.23
1180 1199 2.743928 CTTGGCGTGCAGGACCTC 60.744 66.667 10.29 0.00 0.00 3.85
1206 1225 2.505405 GTGGGAAGTCAAGAAGGAACC 58.495 52.381 0.00 0.00 0.00 3.62
1232 1251 5.639506 CGAACAACTGAGTTAATCTGTGGAT 59.360 40.000 0.00 0.00 39.76 3.41
1236 1255 4.989168 GTCCGAACAACTGAGTTAATCTGT 59.011 41.667 0.00 0.00 41.44 3.41
1237 1256 4.090066 CGTCCGAACAACTGAGTTAATCTG 59.910 45.833 0.00 0.00 0.00 2.90
1243 1262 1.269621 CCTCGTCCGAACAACTGAGTT 60.270 52.381 0.00 0.00 0.00 3.01
1246 1265 1.111116 ACCCTCGTCCGAACAACTGA 61.111 55.000 0.00 0.00 0.00 3.41
1296 1315 3.343617 TGCTACAGTAACATGAAAGCCC 58.656 45.455 0.00 0.00 34.20 5.19
1301 1320 5.222079 TGAACCTGCTACAGTAACATGAA 57.778 39.130 0.00 0.00 0.00 2.57
1304 1323 3.583086 ACCTGAACCTGCTACAGTAACAT 59.417 43.478 0.00 0.00 0.00 2.71
1314 1333 3.571401 CAGATCAAAAACCTGAACCTGCT 59.429 43.478 0.00 0.00 0.00 4.24
1326 1345 1.542915 GCAGAGCAGCCAGATCAAAAA 59.457 47.619 0.00 0.00 34.30 1.94
1340 1359 1.451028 AAAGCGGATGGAGCAGAGC 60.451 57.895 0.00 0.00 37.01 4.09
1380 1420 2.996444 TGCCTATGCAAGCTCATCG 58.004 52.632 8.04 0.00 46.66 3.84
1392 1432 1.133976 GCCAGAACTCCACATGCCTAT 60.134 52.381 0.00 0.00 0.00 2.57
1467 1507 0.247736 AGTGCTAGTGTGCTGCCTAC 59.752 55.000 0.00 0.00 0.00 3.18
1501 1547 9.394767 CGTTAATTCCATCATATTATCCATGGA 57.605 33.333 18.88 18.88 42.55 3.41
1502 1548 8.623903 CCGTTAATTCCATCATATTATCCATGG 58.376 37.037 4.97 4.97 37.70 3.66
1508 1554 8.650143 AAAGGCCGTTAATTCCATCATATTAT 57.350 30.769 0.54 0.00 0.00 1.28
1525 1573 3.826157 TGATGAATGAAAGAAAAGGCCGT 59.174 39.130 0.00 0.00 0.00 5.68
1541 1589 7.714813 TGACAAAGATGACTAACAAGTGATGAA 59.285 33.333 0.00 0.00 0.00 2.57
1542 1590 7.216494 TGACAAAGATGACTAACAAGTGATGA 58.784 34.615 0.00 0.00 0.00 2.92
1543 1591 7.425577 TGACAAAGATGACTAACAAGTGATG 57.574 36.000 0.00 0.00 0.00 3.07
1544 1592 7.879677 TGATGACAAAGATGACTAACAAGTGAT 59.120 33.333 0.00 0.00 0.00 3.06
1545 1593 7.216494 TGATGACAAAGATGACTAACAAGTGA 58.784 34.615 0.00 0.00 0.00 3.41
1546 1594 7.425577 TGATGACAAAGATGACTAACAAGTG 57.574 36.000 0.00 0.00 0.00 3.16
1547 1595 7.879677 TGATGATGACAAAGATGACTAACAAGT 59.120 33.333 0.00 0.00 0.00 3.16
1548 1596 8.260270 TGATGATGACAAAGATGACTAACAAG 57.740 34.615 0.00 0.00 0.00 3.16
1549 1597 7.879677 ACTGATGATGACAAAGATGACTAACAA 59.120 33.333 0.00 0.00 0.00 2.83
1550 1598 7.332678 CACTGATGATGACAAAGATGACTAACA 59.667 37.037 0.00 0.00 0.00 2.41
1551 1599 7.332926 ACACTGATGATGACAAAGATGACTAAC 59.667 37.037 0.00 0.00 0.00 2.34
1686 1773 6.759497 AACCCTACATAAGCAAGATTTGAC 57.241 37.500 0.00 0.00 0.00 3.18
1716 1803 3.118592 GGAACAGGAGGTAATCTGGACAG 60.119 52.174 0.00 0.00 35.47 3.51
1721 1808 4.265073 CCTTTGGAACAGGAGGTAATCTG 58.735 47.826 0.00 0.00 42.39 2.90
1744 1831 4.080582 TCAGACTTCAGGTTCCTTGTTTGA 60.081 41.667 0.00 0.00 0.00 2.69
1752 1839 1.694696 ACTGGTCAGACTTCAGGTTCC 59.305 52.381 10.55 0.00 33.19 3.62
1762 1849 2.094700 TGCTCATACGAACTGGTCAGAC 60.095 50.000 4.84 0.00 0.00 3.51
1776 1863 6.774170 ACAATCAAATTGGCTATCTGCTCATA 59.226 34.615 4.82 0.00 44.42 2.15
1801 1888 7.966246 AATAAAGCATCAACAAAGCAATCAA 57.034 28.000 0.00 0.00 0.00 2.57
1803 1890 8.693542 ACTAATAAAGCATCAACAAAGCAATC 57.306 30.769 0.00 0.00 0.00 2.67
1805 1892 7.656412 TGACTAATAAAGCATCAACAAAGCAA 58.344 30.769 0.00 0.00 0.00 3.91
1983 2073 3.550950 AGATCACGCATACAGATCTCG 57.449 47.619 0.00 0.00 43.63 4.04
2107 2198 1.474330 CCCAGTATTCACCTTTGGGC 58.526 55.000 0.00 0.00 41.79 5.36
2181 2272 4.277174 CCAGCGATAGTTAGTCATCACTCT 59.723 45.833 0.00 0.00 33.98 3.24
2258 2349 2.565046 TGCATCATTCACACAGACCA 57.435 45.000 0.00 0.00 0.00 4.02
2523 2616 5.187772 TCTTGAGAGAGCCTACAAGCAAATA 59.812 40.000 0.00 0.00 39.33 1.40
2633 2726 8.685838 AGTAAAGTGTAAGATGCCAACTAAAA 57.314 30.769 0.00 0.00 0.00 1.52
2704 2797 2.485657 GGGGAAGCAGAGTATAAGGTGC 60.486 54.545 0.00 0.00 36.10 5.01
2707 2800 4.503714 TTTGGGGAAGCAGAGTATAAGG 57.496 45.455 0.00 0.00 0.00 2.69
2840 2933 1.337728 CCATAGACAACACACTCGGCA 60.338 52.381 0.00 0.00 0.00 5.69
2844 2937 2.480419 GTGCACCATAGACAACACACTC 59.520 50.000 5.22 0.00 0.00 3.51
2877 2970 7.001073 ACTTCAATGAAATAGGAATAGAGGCC 58.999 38.462 0.00 0.00 0.00 5.19
2882 2975 9.727627 GAAAGCACTTCAATGAAATAGGAATAG 57.272 33.333 0.00 0.00 33.86 1.73
2961 3054 6.879458 GGAACTTAAAGGCTTGATTCAGACTA 59.121 38.462 0.00 0.00 28.91 2.59
3014 3107 7.544622 ACGTTAGTAAGTTCATCAGAGCATTA 58.455 34.615 0.00 0.00 0.00 1.90
3038 3131 3.363178 CTTTTCTTCAACAGCCGTGAAC 58.637 45.455 0.00 0.00 0.00 3.18
3047 3140 6.414732 TCTCTTCTTGACCTTTTCTTCAACA 58.585 36.000 0.00 0.00 0.00 3.33
3245 3338 1.413767 CGAATCAGTCAAGACGCCGG 61.414 60.000 0.00 0.00 36.20 6.13
3330 3423 4.759183 GTCTCACATTCAAGAAAGCCTCTT 59.241 41.667 0.00 0.00 45.80 2.85
3350 3443 8.522830 ACAAATTTTATGGATTTCGTGATGTCT 58.477 29.630 0.00 0.00 0.00 3.41
3351 3444 8.687824 ACAAATTTTATGGATTTCGTGATGTC 57.312 30.769 0.00 0.00 0.00 3.06
3353 3446 9.138062 TGAACAAATTTTATGGATTTCGTGATG 57.862 29.630 0.00 0.00 0.00 3.07
3354 3447 9.357652 CTGAACAAATTTTATGGATTTCGTGAT 57.642 29.630 0.00 0.00 0.00 3.06
3355 3448 8.572185 TCTGAACAAATTTTATGGATTTCGTGA 58.428 29.630 0.00 0.00 0.00 4.35
3356 3449 8.741101 TCTGAACAAATTTTATGGATTTCGTG 57.259 30.769 0.00 0.00 0.00 4.35
3357 3450 9.573133 GATCTGAACAAATTTTATGGATTTCGT 57.427 29.630 0.00 0.00 0.00 3.85
3358 3451 9.023967 GGATCTGAACAAATTTTATGGATTTCG 57.976 33.333 0.00 0.00 0.00 3.46
3461 3556 3.073678 CCAGATGGTCGAATTTCACACA 58.926 45.455 0.00 0.00 0.00 3.72
3529 3632 1.104630 TGGTTTTGGTCCGTTCCAAC 58.895 50.000 7.84 0.14 45.60 3.77
3581 3684 5.966503 CGGAACACGTTCAAAACTATCAAAA 59.033 36.000 11.77 0.00 41.20 2.44
3680 3790 9.784531 AAAGAGAAACAACATTATCAAGAGAGA 57.215 29.630 0.00 0.00 0.00 3.10
3759 3871 2.614983 TCTTACCAAAGCACGGACAAAC 59.385 45.455 0.00 0.00 32.36 2.93
3760 3872 2.920524 TCTTACCAAAGCACGGACAAA 58.079 42.857 0.00 0.00 32.36 2.83
3764 3876 4.138290 TCATTTTCTTACCAAAGCACGGA 58.862 39.130 0.00 0.00 32.36 4.69
3812 3924 9.823647 TTTGATTAACTAACCAGATTTTGCAAA 57.176 25.926 8.05 8.05 0.00 3.68
3865 3999 8.292448 CAGAAATGACACTAAGTAGCACAAAAT 58.708 33.333 0.00 0.00 0.00 1.82
3952 4086 4.080072 TGCACCCATGATGGTTATCACTTA 60.080 41.667 11.09 0.00 45.54 2.24
3981 4115 3.923017 ACAAGGAAGATGAAAAAGGCG 57.077 42.857 0.00 0.00 0.00 5.52
4012 4146 6.267070 CGACCTCTACTCTAATCAAAAGACC 58.733 44.000 0.00 0.00 0.00 3.85
4061 4196 2.048444 TAAGACCCTCGCGACTATGT 57.952 50.000 3.71 0.00 0.00 2.29
4067 4202 1.600957 CGACTATTAAGACCCTCGCGA 59.399 52.381 9.26 9.26 0.00 5.87
4088 4223 2.888414 TGACTATGACAACAGTCGGTCA 59.112 45.455 9.71 9.71 46.92 4.02
4089 4224 3.570926 TGACTATGACAACAGTCGGTC 57.429 47.619 13.11 0.00 43.38 4.79
4090 4225 3.650139 GTTGACTATGACAACAGTCGGT 58.350 45.455 13.11 0.00 43.38 4.69
4091 4226 2.661675 CGTTGACTATGACAACAGTCGG 59.338 50.000 13.11 4.79 45.09 4.79
4161 4296 3.119137 GGGCAACATGAACTAAATGTCCC 60.119 47.826 0.00 0.00 37.27 4.46


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

AutoCloner maintained by Alex Coulton.