Multiple sequence alignment - TraesCS2A01G405800

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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 TraesCS2A01G405800 chr2A 100.000 3047 0 0 1 3047 661586833 661583787 0.000000e+00 5627
1 TraesCS2A01G405800 chr2D 92.109 2674 126 36 359 2971 517265364 517262715 0.000000e+00 3690
2 TraesCS2A01G405800 chr2B 90.152 2691 163 43 397 3040 609202902 609200267 0.000000e+00 3408
3 TraesCS2A01G405800 chr2B 87.931 232 26 1 84 315 577601254 577601483 3.870000e-69 272
4 TraesCS2A01G405800 chr6A 76.838 1088 189 52 1002 2047 469109968 469111034 3.430000e-154 555
5 TraesCS2A01G405800 chr6D 76.147 1090 193 51 1002 2047 329884802 329885868 7.540000e-141 510
6 TraesCS2A01G405800 chr6D 90.756 119 11 0 1 119 82561126 82561244 3.140000e-35 159
7 TraesCS2A01G405800 chr6B 75.811 1017 185 47 1069 2047 490565815 490564822 2.770000e-125 459
8 TraesCS2A01G405800 chr6B 89.655 232 19 3 84 315 695448671 695448897 1.070000e-74 291
9 TraesCS2A01G405800 chr6B 87.500 232 26 1 84 315 601599028 601599256 6.480000e-67 265
10 TraesCS2A01G405800 chr3B 91.416 233 17 3 84 316 12453600 12453371 1.760000e-82 316
11 TraesCS2A01G405800 chr3B 89.627 241 23 1 84 324 602788808 602789046 3.820000e-79 305
12 TraesCS2A01G405800 chr7A 88.976 254 23 3 86 339 36559024 36559272 2.950000e-80 309
13 TraesCS2A01G405800 chr7A 90.517 232 20 2 84 315 108234815 108234586 3.820000e-79 305
14 TraesCS2A01G405800 chr5B 90.517 232 21 1 84 315 531156768 531156998 3.820000e-79 305
15 TraesCS2A01G405800 chr4A 87.983 233 25 2 84 316 541886399 541886628 3.870000e-69 272
16 TraesCS2A01G405800 chr4D 76.159 302 38 22 1219 1494 485163793 485164086 8.870000e-26 128
17 TraesCS2A01G405800 chr4B 75.084 297 46 18 1221 1494 618347484 618347775 2.480000e-21 113
18 TraesCS2A01G405800 chr5A 74.247 299 47 20 1220 1494 666204341 666204633 6.950000e-17 99


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 TraesCS2A01G405800 chr2A 661583787 661586833 3046 True 5627 5627 100.000 1 3047 1 chr2A.!!$R1 3046
1 TraesCS2A01G405800 chr2D 517262715 517265364 2649 True 3690 3690 92.109 359 2971 1 chr2D.!!$R1 2612
2 TraesCS2A01G405800 chr2B 609200267 609202902 2635 True 3408 3408 90.152 397 3040 1 chr2B.!!$R1 2643
3 TraesCS2A01G405800 chr6A 469109968 469111034 1066 False 555 555 76.838 1002 2047 1 chr6A.!!$F1 1045
4 TraesCS2A01G405800 chr6D 329884802 329885868 1066 False 510 510 76.147 1002 2047 1 chr6D.!!$F2 1045
5 TraesCS2A01G405800 chr6B 490564822 490565815 993 True 459 459 75.811 1069 2047 1 chr6B.!!$R1 978

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
69 70 0.039256 CTGCAACGTGGGTGGATTTG 60.039 55.0 0.00 0.00 0.00 2.32 F
239 240 0.179084 GGATCCAATCGAACGGCTGA 60.179 55.0 6.95 0.00 0.00 4.26 F
286 287 0.247301 GCGATCGGCTGAAACTTTCG 60.247 55.0 18.30 10.44 39.11 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 1892 0.594540 CGTCGTCGTTGGTGGTGTTA 60.595 55.000 0.00 0.00 0.0 2.41 R
1829 1894 2.278989 CGTCGTCGTTGGTGGTGT 60.279 61.111 0.00 0.00 0.0 4.16 R
2227 2311 2.742372 CTGTCAAGAACCGGGCCG 60.742 66.667 21.46 21.46 0.0 6.13 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 3.599704 GCATCAATGGCGAGGGGC 61.600 66.667 0.00 0.00 42.51 5.80
18 19 3.282157 CATCAATGGCGAGGGGCG 61.282 66.667 0.00 0.00 44.92 6.13
19 20 4.569180 ATCAATGGCGAGGGGCGG 62.569 66.667 0.00 0.00 44.92 6.13
41 42 4.796231 CGAGCTACAACCGCCGCT 62.796 66.667 0.00 0.00 35.03 5.52
42 43 3.188786 GAGCTACAACCGCCGCTG 61.189 66.667 0.00 0.00 31.96 5.18
43 44 3.934391 GAGCTACAACCGCCGCTGT 62.934 63.158 0.00 0.00 31.96 4.40
44 45 3.488090 GCTACAACCGCCGCTGTC 61.488 66.667 0.00 0.00 0.00 3.51
45 46 2.048597 CTACAACCGCCGCTGTCA 60.049 61.111 0.00 0.00 0.00 3.58
46 47 1.666553 CTACAACCGCCGCTGTCAA 60.667 57.895 0.00 0.00 0.00 3.18
47 48 1.626654 CTACAACCGCCGCTGTCAAG 61.627 60.000 0.00 0.00 0.00 3.02
48 49 2.089887 TACAACCGCCGCTGTCAAGA 62.090 55.000 0.00 0.00 0.00 3.02
49 50 2.357517 AACCGCCGCTGTCAAGAG 60.358 61.111 0.00 0.00 0.00 2.85
51 52 4.749310 CCGCCGCTGTCAAGAGCT 62.749 66.667 0.00 0.00 36.77 4.09
52 53 3.485431 CGCCGCTGTCAAGAGCTG 61.485 66.667 0.00 0.00 36.77 4.24
53 54 3.797546 GCCGCTGTCAAGAGCTGC 61.798 66.667 0.00 0.11 41.18 5.25
54 55 2.357881 CCGCTGTCAAGAGCTGCA 60.358 61.111 1.02 0.00 36.77 4.41
55 56 1.962822 CCGCTGTCAAGAGCTGCAA 60.963 57.895 1.02 0.00 36.77 4.08
56 57 1.206072 CGCTGTCAAGAGCTGCAAC 59.794 57.895 1.02 0.00 36.77 4.17
57 58 1.206072 GCTGTCAAGAGCTGCAACG 59.794 57.895 1.02 0.00 35.95 4.10
58 59 1.502163 GCTGTCAAGAGCTGCAACGT 61.502 55.000 1.02 0.00 35.95 3.99
59 60 0.234106 CTGTCAAGAGCTGCAACGTG 59.766 55.000 1.02 4.52 0.00 4.49
60 61 1.159713 TGTCAAGAGCTGCAACGTGG 61.160 55.000 1.02 0.00 0.00 4.94
61 62 1.597854 TCAAGAGCTGCAACGTGGG 60.598 57.895 1.02 0.00 0.00 4.61
62 63 1.893808 CAAGAGCTGCAACGTGGGT 60.894 57.895 1.02 0.00 0.00 4.51
63 64 1.893808 AAGAGCTGCAACGTGGGTG 60.894 57.895 1.02 0.00 0.00 4.61
64 65 3.357079 GAGCTGCAACGTGGGTGG 61.357 66.667 1.02 0.00 0.00 4.61
65 66 3.825160 GAGCTGCAACGTGGGTGGA 62.825 63.158 1.02 0.00 0.00 4.02
66 67 2.672996 GCTGCAACGTGGGTGGAT 60.673 61.111 0.00 0.00 0.00 3.41
67 68 2.268076 GCTGCAACGTGGGTGGATT 61.268 57.895 0.00 0.00 0.00 3.01
68 69 1.805428 GCTGCAACGTGGGTGGATTT 61.805 55.000 0.00 0.00 0.00 2.17
69 70 0.039256 CTGCAACGTGGGTGGATTTG 60.039 55.000 0.00 0.00 0.00 2.32
70 71 0.753479 TGCAACGTGGGTGGATTTGT 60.753 50.000 0.00 0.00 0.00 2.83
71 72 0.387565 GCAACGTGGGTGGATTTGTT 59.612 50.000 0.00 0.00 0.00 2.83
72 73 1.867698 GCAACGTGGGTGGATTTGTTG 60.868 52.381 0.00 0.00 39.61 3.33
73 74 0.387565 AACGTGGGTGGATTTGTTGC 59.612 50.000 0.00 0.00 0.00 4.17
74 75 0.753479 ACGTGGGTGGATTTGTTGCA 60.753 50.000 0.00 0.00 0.00 4.08
75 76 0.602562 CGTGGGTGGATTTGTTGCAT 59.397 50.000 0.00 0.00 0.00 3.96
76 77 1.669502 CGTGGGTGGATTTGTTGCATG 60.670 52.381 0.00 0.00 0.00 4.06
77 78 0.975135 TGGGTGGATTTGTTGCATGG 59.025 50.000 0.00 0.00 0.00 3.66
78 79 0.391528 GGGTGGATTTGTTGCATGGC 60.392 55.000 0.00 0.00 0.00 4.40
79 80 0.737019 GGTGGATTTGTTGCATGGCG 60.737 55.000 0.00 0.00 0.00 5.69
80 81 0.243365 GTGGATTTGTTGCATGGCGA 59.757 50.000 0.00 0.00 0.00 5.54
81 82 0.243365 TGGATTTGTTGCATGGCGAC 59.757 50.000 1.62 1.62 42.77 5.19
95 96 4.813526 CGACAGGCGACGAGGACG 62.814 72.222 0.00 0.00 44.57 4.79
96 97 4.477975 GACAGGCGACGAGGACGG 62.478 72.222 0.00 0.00 44.46 4.79
128 129 4.436998 GACCGACGGCCACCAGAG 62.437 72.222 15.39 0.00 0.00 3.35
129 130 4.988716 ACCGACGGCCACCAGAGA 62.989 66.667 15.39 0.00 0.00 3.10
130 131 4.135153 CCGACGGCCACCAGAGAG 62.135 72.222 2.24 0.00 0.00 3.20
131 132 4.135153 CGACGGCCACCAGAGAGG 62.135 72.222 2.24 0.00 45.67 3.69
132 133 2.680352 GACGGCCACCAGAGAGGA 60.680 66.667 2.24 0.00 41.22 3.71
133 134 2.997897 ACGGCCACCAGAGAGGAC 60.998 66.667 2.24 0.00 41.22 3.85
134 135 2.997315 CGGCCACCAGAGAGGACA 60.997 66.667 2.24 0.00 41.22 4.02
135 136 2.985456 GGCCACCAGAGAGGACAG 59.015 66.667 0.00 0.00 41.22 3.51
136 137 2.664081 GGCCACCAGAGAGGACAGG 61.664 68.421 0.00 0.00 41.22 4.00
137 138 1.610673 GCCACCAGAGAGGACAGGA 60.611 63.158 0.00 0.00 41.22 3.86
138 139 1.612395 GCCACCAGAGAGGACAGGAG 61.612 65.000 0.00 0.00 41.22 3.69
139 140 0.252012 CCACCAGAGAGGACAGGAGT 60.252 60.000 0.00 0.00 41.22 3.85
140 141 1.181786 CACCAGAGAGGACAGGAGTC 58.818 60.000 0.00 0.00 44.21 3.36
141 142 0.322997 ACCAGAGAGGACAGGAGTCG 60.323 60.000 0.00 0.00 45.92 4.18
142 143 1.662438 CCAGAGAGGACAGGAGTCGC 61.662 65.000 0.00 0.00 45.92 5.19
143 144 1.747367 AGAGAGGACAGGAGTCGCG 60.747 63.158 0.00 0.00 45.92 5.87
144 145 2.752238 AGAGGACAGGAGTCGCGG 60.752 66.667 6.13 0.00 45.92 6.46
145 146 4.500116 GAGGACAGGAGTCGCGGC 62.500 72.222 0.21 0.21 45.92 6.53
167 168 4.452733 CGCTCCCCCGAACAGGAC 62.453 72.222 0.00 0.00 45.00 3.85
168 169 3.003763 GCTCCCCCGAACAGGACT 61.004 66.667 0.00 0.00 45.00 3.85
169 170 2.982130 CTCCCCCGAACAGGACTG 59.018 66.667 0.00 0.00 45.00 3.51
170 171 3.316573 CTCCCCCGAACAGGACTGC 62.317 68.421 0.00 0.00 45.00 4.40
171 172 4.410400 CCCCCGAACAGGACTGCC 62.410 72.222 0.00 0.00 45.00 4.85
172 173 4.410400 CCCCGAACAGGACTGCCC 62.410 72.222 0.00 0.00 45.00 5.36
173 174 4.760047 CCCGAACAGGACTGCCCG 62.760 72.222 0.00 3.40 45.00 6.13
174 175 3.691342 CCGAACAGGACTGCCCGA 61.691 66.667 13.14 0.00 45.00 5.14
175 176 2.125912 CGAACAGGACTGCCCGAG 60.126 66.667 7.80 0.00 40.87 4.63
176 177 2.266055 GAACAGGACTGCCCGAGG 59.734 66.667 0.00 0.00 40.87 4.63
177 178 2.203788 AACAGGACTGCCCGAGGA 60.204 61.111 0.00 0.00 40.87 3.71
178 179 1.827399 GAACAGGACTGCCCGAGGAA 61.827 60.000 0.00 0.00 40.87 3.36
179 180 1.831652 AACAGGACTGCCCGAGGAAG 61.832 60.000 0.00 0.00 40.87 3.46
180 181 1.984570 CAGGACTGCCCGAGGAAGA 60.985 63.158 5.03 0.00 40.87 2.87
181 182 1.229209 AGGACTGCCCGAGGAAGAA 60.229 57.895 5.03 0.00 40.87 2.52
182 183 1.219393 GGACTGCCCGAGGAAGAAG 59.781 63.158 5.03 0.00 0.00 2.85
183 184 1.258445 GGACTGCCCGAGGAAGAAGA 61.258 60.000 5.03 0.00 0.00 2.87
184 185 0.608640 GACTGCCCGAGGAAGAAGAA 59.391 55.000 5.03 0.00 0.00 2.52
185 186 1.002087 GACTGCCCGAGGAAGAAGAAA 59.998 52.381 5.03 0.00 0.00 2.52
186 187 1.002544 ACTGCCCGAGGAAGAAGAAAG 59.997 52.381 5.03 0.00 0.00 2.62
187 188 1.276421 CTGCCCGAGGAAGAAGAAAGA 59.724 52.381 0.00 0.00 0.00 2.52
188 189 1.276421 TGCCCGAGGAAGAAGAAAGAG 59.724 52.381 0.00 0.00 0.00 2.85
189 190 1.550976 GCCCGAGGAAGAAGAAAGAGA 59.449 52.381 0.00 0.00 0.00 3.10
190 191 2.418060 GCCCGAGGAAGAAGAAAGAGAG 60.418 54.545 0.00 0.00 0.00 3.20
191 192 2.418060 CCCGAGGAAGAAGAAAGAGAGC 60.418 54.545 0.00 0.00 0.00 4.09
192 193 2.495669 CCGAGGAAGAAGAAAGAGAGCT 59.504 50.000 0.00 0.00 0.00 4.09
193 194 3.510719 CGAGGAAGAAGAAAGAGAGCTG 58.489 50.000 0.00 0.00 0.00 4.24
194 195 3.675775 CGAGGAAGAAGAAAGAGAGCTGG 60.676 52.174 0.00 0.00 0.00 4.85
195 196 2.027285 AGGAAGAAGAAAGAGAGCTGGC 60.027 50.000 0.00 0.00 0.00 4.85
196 197 1.999024 GAAGAAGAAAGAGAGCTGGCG 59.001 52.381 0.00 0.00 0.00 5.69
197 198 1.261480 AGAAGAAAGAGAGCTGGCGA 58.739 50.000 0.00 0.00 0.00 5.54
198 199 1.830477 AGAAGAAAGAGAGCTGGCGAT 59.170 47.619 0.00 0.00 0.00 4.58
199 200 1.932511 GAAGAAAGAGAGCTGGCGATG 59.067 52.381 0.00 0.00 0.00 3.84
200 201 1.189752 AGAAAGAGAGCTGGCGATGA 58.810 50.000 0.00 0.00 0.00 2.92
201 202 1.761784 AGAAAGAGAGCTGGCGATGAT 59.238 47.619 0.00 0.00 0.00 2.45
202 203 2.170187 AGAAAGAGAGCTGGCGATGATT 59.830 45.455 0.00 0.00 0.00 2.57
203 204 2.237393 AAGAGAGCTGGCGATGATTC 57.763 50.000 0.00 0.00 0.00 2.52
204 205 1.117994 AGAGAGCTGGCGATGATTCA 58.882 50.000 0.00 0.00 0.00 2.57
205 206 1.693062 AGAGAGCTGGCGATGATTCAT 59.307 47.619 0.00 0.00 0.00 2.57
206 207 2.104451 AGAGAGCTGGCGATGATTCATT 59.896 45.455 0.00 0.00 0.00 2.57
207 208 2.877168 GAGAGCTGGCGATGATTCATTT 59.123 45.455 0.00 0.00 0.00 2.32
208 209 3.285484 AGAGCTGGCGATGATTCATTTT 58.715 40.909 0.00 0.00 0.00 1.82
209 210 3.698040 AGAGCTGGCGATGATTCATTTTT 59.302 39.130 0.00 0.00 0.00 1.94
232 233 4.862902 TTTTTGCTTGGATCCAATCGAA 57.137 36.364 27.20 24.23 35.20 3.71
233 234 3.848272 TTTGCTTGGATCCAATCGAAC 57.152 42.857 27.20 14.43 35.20 3.95
234 235 1.368641 TGCTTGGATCCAATCGAACG 58.631 50.000 27.20 15.31 35.20 3.95
235 236 0.657840 GCTTGGATCCAATCGAACGG 59.342 55.000 27.20 14.60 35.20 4.44
236 237 0.657840 CTTGGATCCAATCGAACGGC 59.342 55.000 27.20 0.00 35.20 5.68
237 238 0.251916 TTGGATCCAATCGAACGGCT 59.748 50.000 23.63 0.00 0.00 5.52
238 239 0.461870 TGGATCCAATCGAACGGCTG 60.462 55.000 13.46 0.00 0.00 4.85
239 240 0.179084 GGATCCAATCGAACGGCTGA 60.179 55.000 6.95 0.00 0.00 4.26
240 241 1.212616 GATCCAATCGAACGGCTGAG 58.787 55.000 0.00 0.00 0.00 3.35
241 242 0.811616 ATCCAATCGAACGGCTGAGC 60.812 55.000 0.00 0.00 0.00 4.26
242 243 2.697425 CAATCGAACGGCTGAGCG 59.303 61.111 0.00 2.06 0.00 5.03
243 244 3.188786 AATCGAACGGCTGAGCGC 61.189 61.111 0.00 0.00 38.13 5.92
244 245 3.932580 AATCGAACGGCTGAGCGCA 62.933 57.895 11.47 0.00 41.67 6.09
247 248 3.121030 GAACGGCTGAGCGCACAT 61.121 61.111 11.47 0.00 41.67 3.21
248 249 3.372676 GAACGGCTGAGCGCACATG 62.373 63.158 11.47 5.22 41.67 3.21
252 253 3.515286 GCTGAGCGCACATGGCAT 61.515 61.111 11.47 0.00 45.17 4.40
253 254 2.713770 CTGAGCGCACATGGCATC 59.286 61.111 11.47 0.00 45.17 3.91
254 255 3.164390 CTGAGCGCACATGGCATCG 62.164 63.158 11.47 0.00 45.17 3.84
255 256 3.945434 GAGCGCACATGGCATCGG 61.945 66.667 11.47 0.00 45.17 4.18
261 262 4.424711 ACATGGCATCGGGCGGTT 62.425 61.111 0.00 0.00 46.16 4.44
262 263 3.891400 CATGGCATCGGGCGGTTG 61.891 66.667 0.00 0.00 46.16 3.77
280 281 2.813474 CGGTGCGATCGGCTGAAA 60.813 61.111 18.30 0.00 44.05 2.69
281 282 2.785258 GGTGCGATCGGCTGAAAC 59.215 61.111 18.30 3.60 44.05 2.78
282 283 1.741770 GGTGCGATCGGCTGAAACT 60.742 57.895 18.30 0.00 44.05 2.66
283 284 1.298859 GGTGCGATCGGCTGAAACTT 61.299 55.000 18.30 0.00 44.05 2.66
284 285 0.517316 GTGCGATCGGCTGAAACTTT 59.483 50.000 18.30 0.00 44.05 2.66
285 286 0.796312 TGCGATCGGCTGAAACTTTC 59.204 50.000 18.30 0.00 44.05 2.62
286 287 0.247301 GCGATCGGCTGAAACTTTCG 60.247 55.000 18.30 10.44 39.11 3.46
287 288 0.370273 CGATCGGCTGAAACTTTCGG 59.630 55.000 7.38 6.03 39.10 4.30
293 294 1.207593 CTGAAACTTTCGGCCAGCG 59.792 57.895 2.24 0.00 0.00 5.18
294 295 2.126850 GAAACTTTCGGCCAGCGC 60.127 61.111 2.24 0.00 0.00 5.92
295 296 2.903547 GAAACTTTCGGCCAGCGCA 61.904 57.895 11.47 0.00 36.38 6.09
296 297 3.194272 AAACTTTCGGCCAGCGCAC 62.194 57.895 11.47 0.00 36.38 5.34
344 345 8.798975 AATAAAGAGATATCACTTCTACCCCA 57.201 34.615 14.69 0.00 0.00 4.96
345 346 8.798975 ATAAAGAGATATCACTTCTACCCCAA 57.201 34.615 14.69 0.00 0.00 4.12
346 347 6.739331 AAGAGATATCACTTCTACCCCAAG 57.261 41.667 9.35 0.00 0.00 3.61
347 348 4.591072 AGAGATATCACTTCTACCCCAAGC 59.409 45.833 5.32 0.00 0.00 4.01
348 349 3.322254 AGATATCACTTCTACCCCAAGCG 59.678 47.826 5.32 0.00 0.00 4.68
349 350 1.276622 ATCACTTCTACCCCAAGCGT 58.723 50.000 0.00 0.00 0.00 5.07
350 351 0.606604 TCACTTCTACCCCAAGCGTC 59.393 55.000 0.00 0.00 0.00 5.19
351 352 0.391263 CACTTCTACCCCAAGCGTCC 60.391 60.000 0.00 0.00 0.00 4.79
352 353 1.221021 CTTCTACCCCAAGCGTCCC 59.779 63.158 0.00 0.00 0.00 4.46
353 354 1.536907 TTCTACCCCAAGCGTCCCA 60.537 57.895 0.00 0.00 0.00 4.37
354 355 1.550130 TTCTACCCCAAGCGTCCCAG 61.550 60.000 0.00 0.00 0.00 4.45
355 356 3.006728 TACCCCAAGCGTCCCAGG 61.007 66.667 0.00 0.00 0.00 4.45
356 357 3.857521 TACCCCAAGCGTCCCAGGT 62.858 63.158 0.00 0.00 0.00 4.00
357 358 4.410400 CCCCAAGCGTCCCAGGTC 62.410 72.222 0.00 0.00 0.00 3.85
385 386 7.698836 AAACATCAAGAACCAAAAAGAATCG 57.301 32.000 0.00 0.00 0.00 3.34
386 387 6.633500 ACATCAAGAACCAAAAAGAATCGA 57.367 33.333 0.00 0.00 0.00 3.59
387 388 6.438763 ACATCAAGAACCAAAAAGAATCGAC 58.561 36.000 0.00 0.00 0.00 4.20
388 389 5.090652 TCAAGAACCAAAAAGAATCGACG 57.909 39.130 0.00 0.00 0.00 5.12
390 391 5.065474 TCAAGAACCAAAAAGAATCGACGTT 59.935 36.000 0.00 0.00 0.00 3.99
391 392 4.844267 AGAACCAAAAAGAATCGACGTTG 58.156 39.130 0.00 0.00 0.00 4.10
394 395 4.844267 ACCAAAAAGAATCGACGTTGAAG 58.156 39.130 10.11 0.00 0.00 3.02
395 396 4.219033 CCAAAAAGAATCGACGTTGAAGG 58.781 43.478 10.11 0.00 0.00 3.46
407 408 4.143094 CGACGTTGAAGGAAAAGGATTCTC 60.143 45.833 0.00 0.00 0.00 2.87
480 481 1.948104 CACCGTACCACATACATGGG 58.052 55.000 0.00 0.00 44.81 4.00
508 509 4.851179 GCCCCCACCGAATCGACC 62.851 72.222 3.36 0.00 0.00 4.79
557 558 2.746277 AAACGGACGAGCCATGCC 60.746 61.111 0.00 0.00 35.94 4.40
565 566 2.956987 GAGCCATGCCACACACAC 59.043 61.111 0.00 0.00 0.00 3.82
635 639 1.870167 GCGTTTTGCCGGAAATCCAAA 60.870 47.619 5.05 2.24 37.76 3.28
679 683 4.757355 CATTGCCCCAGCCCCGAA 62.757 66.667 0.00 0.00 38.69 4.30
680 684 4.447342 ATTGCCCCAGCCCCGAAG 62.447 66.667 0.00 0.00 38.69 3.79
750 774 3.276091 CAAGCCCAACGCACGACA 61.276 61.111 0.00 0.00 41.38 4.35
751 775 3.276846 AAGCCCAACGCACGACAC 61.277 61.111 0.00 0.00 41.38 3.67
755 779 4.042060 CCAACGCACGACACGACG 62.042 66.667 0.00 0.00 36.48 5.12
758 782 4.969604 ACGCACGACACGACGTCC 62.970 66.667 10.58 0.00 44.76 4.79
760 784 4.634133 GCACGACACGACGTCCCA 62.634 66.667 10.58 0.00 44.76 4.37
761 785 2.026445 CACGACACGACGTCCCAA 59.974 61.111 10.58 0.00 44.76 4.12
762 786 1.589461 CACGACACGACGTCCCAAA 60.589 57.895 10.58 0.00 44.76 3.28
768 792 1.068585 ACGACGTCCCAAACTGACC 59.931 57.895 10.58 0.00 0.00 4.02
805 829 4.087892 CCCCAGAGTCCACCTGCG 62.088 72.222 0.00 0.00 0.00 5.18
1653 1691 3.068691 TCCTCCCTCTCCAACGCG 61.069 66.667 3.53 3.53 0.00 6.01
1748 1786 1.712081 CATCAGACGCGCCAAGAAG 59.288 57.895 5.73 0.00 0.00 2.85
1829 1894 1.078285 GGTCGGCCGGGAAACATAA 60.078 57.895 27.83 0.00 0.00 1.90
1832 1897 0.674269 TCGGCCGGGAAACATAACAC 60.674 55.000 27.83 0.00 0.00 3.32
1867 1932 3.667282 CGTCCACCTCGTCCACGT 61.667 66.667 0.00 0.00 40.80 4.49
2049 2123 1.558756 CTCAGCCCAACCTTCTGATCT 59.441 52.381 0.00 0.00 36.41 2.75
2052 2126 0.537188 GCCCAACCTTCTGATCTCGA 59.463 55.000 0.00 0.00 0.00 4.04
2054 2128 2.615493 GCCCAACCTTCTGATCTCGAAA 60.615 50.000 0.00 0.00 0.00 3.46
2056 2130 3.003480 CCAACCTTCTGATCTCGAAACC 58.997 50.000 0.00 0.00 0.00 3.27
2117 2200 8.368668 GCTTGGACAGGATTTGTATATAGTACT 58.631 37.037 0.00 0.00 41.05 2.73
2118 2201 9.915629 CTTGGACAGGATTTGTATATAGTACTC 57.084 37.037 0.00 0.00 41.05 2.59
2119 2202 9.656323 TTGGACAGGATTTGTATATAGTACTCT 57.344 33.333 0.00 0.00 41.05 3.24
2227 2311 0.374758 TCGCGCAATCTGCATTTCTC 59.625 50.000 8.75 0.00 45.36 2.87
2285 2379 0.024619 GACGCCGCGTATTCTTGTTC 59.975 55.000 20.22 0.00 41.37 3.18
2287 2381 1.719709 GCCGCGTATTCTTGTTCCC 59.280 57.895 4.92 0.00 0.00 3.97
2294 2388 2.159572 CGTATTCTTGTTCCCGGCAAAG 60.160 50.000 0.00 0.00 0.00 2.77
2307 2401 1.508088 GCAAAGATCCACGCCCTTG 59.492 57.895 0.00 0.00 0.00 3.61
2333 2427 2.304761 TGCCCGGTGAACTTTCTAGATT 59.695 45.455 0.00 0.00 0.00 2.40
2361 2455 4.142403 GGAAATTTTGGCTCATGTGATCGA 60.142 41.667 0.00 0.00 0.00 3.59
2362 2456 4.361451 AATTTTGGCTCATGTGATCGAC 57.639 40.909 0.00 0.00 0.00 4.20
2375 2469 2.802816 GTGATCGACCACAGAATATGCC 59.197 50.000 4.61 0.00 37.04 4.40
2376 2470 2.433970 TGATCGACCACAGAATATGCCA 59.566 45.455 0.00 0.00 0.00 4.92
2377 2471 3.118445 TGATCGACCACAGAATATGCCAA 60.118 43.478 0.00 0.00 0.00 4.52
2379 2473 2.499693 TCGACCACAGAATATGCCAAGA 59.500 45.455 0.00 0.00 0.00 3.02
2380 2474 3.055458 TCGACCACAGAATATGCCAAGAA 60.055 43.478 0.00 0.00 0.00 2.52
2381 2475 3.689161 CGACCACAGAATATGCCAAGAAA 59.311 43.478 0.00 0.00 0.00 2.52
2382 2476 4.155826 CGACCACAGAATATGCCAAGAAAA 59.844 41.667 0.00 0.00 0.00 2.29
2383 2477 5.335583 CGACCACAGAATATGCCAAGAAAAA 60.336 40.000 0.00 0.00 0.00 1.94
2436 2534 1.439679 CCAGCTTAGGTGAACCGAAC 58.560 55.000 13.44 0.00 42.08 3.95
2437 2535 1.068474 CAGCTTAGGTGAACCGAACG 58.932 55.000 5.36 0.00 42.08 3.95
2438 2536 0.963962 AGCTTAGGTGAACCGAACGA 59.036 50.000 0.00 0.00 42.08 3.85
2439 2537 1.342174 AGCTTAGGTGAACCGAACGAA 59.658 47.619 0.00 0.00 42.08 3.85
2524 2625 2.359975 AAGGAAAAGCGAGGCGGG 60.360 61.111 0.00 0.00 0.00 6.13
2539 2640 2.811317 GGGAACGTCAGCAGAGCG 60.811 66.667 0.00 0.00 0.00 5.03
2575 2678 0.233848 GTTAACCGAACCACACGCAG 59.766 55.000 0.00 0.00 31.20 5.18
2579 2682 3.403057 CGAACCACACGCAGGTCG 61.403 66.667 0.00 0.00 38.76 4.79
2608 2711 2.279517 GGCGAGCACGTATGGGAG 60.280 66.667 5.23 0.00 41.98 4.30
2619 2722 2.490148 TATGGGAGCTCGCACGAGG 61.490 63.158 32.94 3.99 41.67 4.63
2698 2802 2.359230 AGGCTTGACTTGAGCGGC 60.359 61.111 0.00 0.00 41.03 6.53
2816 2925 0.650476 CATAATGCGTTCGCGTTCGG 60.650 55.000 24.21 15.31 43.62 4.30
2823 2932 1.702299 GTTCGCGTTCGGTGATGAG 59.298 57.895 5.77 0.00 34.56 2.90
2896 3007 2.044946 AAGCCGCCCCTCATTCAC 60.045 61.111 0.00 0.00 0.00 3.18
2908 3019 3.370953 CCCTCATTCACAAAGACCTAGGG 60.371 52.174 14.81 0.00 34.17 3.53
2909 3020 3.264450 CCTCATTCACAAAGACCTAGGGT 59.736 47.826 14.81 0.00 39.44 4.34
2936 3048 4.269363 GTCAGCTTGGCAAAAATATCATGC 59.731 41.667 0.00 0.00 39.33 4.06
2972 3096 2.439701 TACACCCGAGCTCCTCCG 60.440 66.667 8.47 0.00 0.00 4.63
2986 3110 0.313987 CCTCCGCTATATGTCGTGCA 59.686 55.000 0.00 0.00 0.00 4.57
3011 3135 2.771089 GCATGGTATGTGATCGGTCAT 58.229 47.619 0.00 0.00 36.60 3.06
3025 3149 3.431856 TCGGTCATAAAATCGTGACTCG 58.568 45.455 5.60 7.46 43.23 4.18
3026 3150 2.534349 CGGTCATAAAATCGTGACTCGG 59.466 50.000 5.60 0.00 43.23 4.63
3027 3151 2.284417 GGTCATAAAATCGTGACTCGGC 59.716 50.000 5.60 0.00 43.23 5.54
3029 3153 2.093921 TCATAAAATCGTGACTCGGCCA 60.094 45.455 2.24 0.00 40.32 5.36
3040 3164 1.216710 CTCGGCCAGACTCCTCAAC 59.783 63.158 2.24 0.00 0.00 3.18
3041 3165 2.232298 CTCGGCCAGACTCCTCAACC 62.232 65.000 2.24 0.00 0.00 3.77
3042 3166 2.671682 GGCCAGACTCCTCAACCC 59.328 66.667 0.00 0.00 0.00 4.11
3043 3167 2.266055 GCCAGACTCCTCAACCCG 59.734 66.667 0.00 0.00 0.00 5.28
3044 3168 2.982130 CCAGACTCCTCAACCCGG 59.018 66.667 0.00 0.00 0.00 5.73
3045 3169 2.266055 CAGACTCCTCAACCCGGC 59.734 66.667 0.00 0.00 0.00 6.13
3046 3170 3.003763 AGACTCCTCAACCCGGCC 61.004 66.667 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.599704 GCCCCTCGCCATTGATGC 61.600 66.667 0.00 0.00 0.00 3.91
1 2 3.282157 CGCCCCTCGCCATTGATG 61.282 66.667 0.00 0.00 0.00 3.07
24 25 4.796231 AGCGGCGGTTGTAGCTCG 62.796 66.667 5.44 0.00 34.48 5.03
25 26 3.188786 CAGCGGCGGTTGTAGCTC 61.189 66.667 9.73 0.00 37.94 4.09
26 27 3.934391 GACAGCGGCGGTTGTAGCT 62.934 63.158 9.73 0.00 37.76 3.32
27 28 3.488090 GACAGCGGCGGTTGTAGC 61.488 66.667 9.73 0.00 37.76 3.58
28 29 1.626654 CTTGACAGCGGCGGTTGTAG 61.627 60.000 9.73 5.33 37.76 2.74
29 30 1.666553 CTTGACAGCGGCGGTTGTA 60.667 57.895 9.73 0.00 37.76 2.41
30 31 2.972505 CTTGACAGCGGCGGTTGT 60.973 61.111 9.73 13.47 40.58 3.32
31 32 2.664851 TCTTGACAGCGGCGGTTG 60.665 61.111 9.73 7.96 0.00 3.77
32 33 2.357517 CTCTTGACAGCGGCGGTT 60.358 61.111 9.73 0.40 0.00 4.44
34 35 4.749310 AGCTCTTGACAGCGGCGG 62.749 66.667 9.78 0.00 44.82 6.13
35 36 3.485431 CAGCTCTTGACAGCGGCG 61.485 66.667 0.51 0.51 44.82 6.46
37 38 1.962822 TTGCAGCTCTTGACAGCGG 60.963 57.895 0.00 0.00 44.82 5.52
38 39 1.206072 GTTGCAGCTCTTGACAGCG 59.794 57.895 0.00 0.00 44.82 5.18
39 40 1.206072 CGTTGCAGCTCTTGACAGC 59.794 57.895 0.00 0.00 39.99 4.40
40 41 0.234106 CACGTTGCAGCTCTTGACAG 59.766 55.000 0.00 0.00 0.00 3.51
41 42 1.159713 CCACGTTGCAGCTCTTGACA 61.160 55.000 0.00 0.00 0.00 3.58
42 43 1.571460 CCACGTTGCAGCTCTTGAC 59.429 57.895 0.00 0.00 0.00 3.18
43 44 1.597854 CCCACGTTGCAGCTCTTGA 60.598 57.895 0.00 0.00 0.00 3.02
44 45 1.893808 ACCCACGTTGCAGCTCTTG 60.894 57.895 0.00 0.00 0.00 3.02
45 46 1.893808 CACCCACGTTGCAGCTCTT 60.894 57.895 0.00 0.00 0.00 2.85
46 47 2.281070 CACCCACGTTGCAGCTCT 60.281 61.111 0.00 0.00 0.00 4.09
47 48 3.357079 CCACCCACGTTGCAGCTC 61.357 66.667 0.00 0.00 0.00 4.09
48 49 2.697147 AATCCACCCACGTTGCAGCT 62.697 55.000 0.00 0.00 0.00 4.24
49 50 1.805428 AAATCCACCCACGTTGCAGC 61.805 55.000 0.00 0.00 0.00 5.25
50 51 0.039256 CAAATCCACCCACGTTGCAG 60.039 55.000 0.00 0.00 0.00 4.41
51 52 0.753479 ACAAATCCACCCACGTTGCA 60.753 50.000 0.00 0.00 0.00 4.08
52 53 0.387565 AACAAATCCACCCACGTTGC 59.612 50.000 0.00 0.00 0.00 4.17
53 54 1.867698 GCAACAAATCCACCCACGTTG 60.868 52.381 0.00 0.00 37.41 4.10
54 55 0.387565 GCAACAAATCCACCCACGTT 59.612 50.000 0.00 0.00 0.00 3.99
55 56 0.753479 TGCAACAAATCCACCCACGT 60.753 50.000 0.00 0.00 0.00 4.49
56 57 0.602562 ATGCAACAAATCCACCCACG 59.397 50.000 0.00 0.00 0.00 4.94
57 58 1.338011 CCATGCAACAAATCCACCCAC 60.338 52.381 0.00 0.00 0.00 4.61
58 59 0.975135 CCATGCAACAAATCCACCCA 59.025 50.000 0.00 0.00 0.00 4.51
59 60 0.391528 GCCATGCAACAAATCCACCC 60.392 55.000 0.00 0.00 0.00 4.61
60 61 0.737019 CGCCATGCAACAAATCCACC 60.737 55.000 0.00 0.00 0.00 4.61
61 62 0.243365 TCGCCATGCAACAAATCCAC 59.757 50.000 0.00 0.00 0.00 4.02
62 63 0.243365 GTCGCCATGCAACAAATCCA 59.757 50.000 0.00 0.00 0.00 3.41
63 64 0.243365 TGTCGCCATGCAACAAATCC 59.757 50.000 0.00 0.00 0.00 3.01
64 65 1.621107 CTGTCGCCATGCAACAAATC 58.379 50.000 0.00 0.00 0.00 2.17
65 66 0.244450 CCTGTCGCCATGCAACAAAT 59.756 50.000 0.00 0.00 0.00 2.32
66 67 1.659233 CCTGTCGCCATGCAACAAA 59.341 52.632 0.00 0.00 0.00 2.83
67 68 2.918345 GCCTGTCGCCATGCAACAA 61.918 57.895 0.00 0.00 33.00 2.83
68 69 3.364441 GCCTGTCGCCATGCAACA 61.364 61.111 0.00 0.00 33.00 3.33
69 70 4.465512 CGCCTGTCGCCATGCAAC 62.466 66.667 0.00 0.00 32.36 4.17
70 71 4.695993 TCGCCTGTCGCCATGCAA 62.696 61.111 0.00 0.00 38.27 4.08
73 74 4.794439 TCGTCGCCTGTCGCCATG 62.794 66.667 0.00 0.00 38.27 3.66
74 75 4.498520 CTCGTCGCCTGTCGCCAT 62.499 66.667 0.00 0.00 38.27 4.40
78 79 4.813526 CGTCCTCGTCGCCTGTCG 62.814 72.222 0.00 0.00 40.15 4.35
79 80 4.477975 CCGTCCTCGTCGCCTGTC 62.478 72.222 0.00 0.00 35.01 3.51
111 112 4.436998 CTCTGGTGGCCGTCGGTC 62.437 72.222 9.51 9.51 0.00 4.79
112 113 4.988716 TCTCTGGTGGCCGTCGGT 62.989 66.667 13.94 0.00 0.00 4.69
113 114 4.135153 CTCTCTGGTGGCCGTCGG 62.135 72.222 6.99 6.99 0.00 4.79
114 115 4.135153 CCTCTCTGGTGGCCGTCG 62.135 72.222 0.00 0.00 0.00 5.12
115 116 2.680352 TCCTCTCTGGTGGCCGTC 60.680 66.667 0.00 0.00 37.07 4.79
116 117 2.997897 GTCCTCTCTGGTGGCCGT 60.998 66.667 0.00 0.00 37.07 5.68
117 118 2.997315 TGTCCTCTCTGGTGGCCG 60.997 66.667 0.00 0.00 37.07 6.13
118 119 2.664081 CCTGTCCTCTCTGGTGGCC 61.664 68.421 0.00 0.00 37.07 5.36
119 120 1.610673 TCCTGTCCTCTCTGGTGGC 60.611 63.158 0.00 0.00 37.07 5.01
120 121 0.252012 ACTCCTGTCCTCTCTGGTGG 60.252 60.000 0.00 0.00 37.07 4.61
121 122 1.181786 GACTCCTGTCCTCTCTGGTG 58.818 60.000 0.00 0.00 37.24 4.17
122 123 0.322997 CGACTCCTGTCCTCTCTGGT 60.323 60.000 0.00 0.00 39.94 4.00
123 124 1.662438 GCGACTCCTGTCCTCTCTGG 61.662 65.000 0.00 0.00 39.94 3.86
124 125 1.806568 GCGACTCCTGTCCTCTCTG 59.193 63.158 0.00 0.00 39.94 3.35
125 126 1.747367 CGCGACTCCTGTCCTCTCT 60.747 63.158 0.00 0.00 39.94 3.10
126 127 2.766400 CCGCGACTCCTGTCCTCTC 61.766 68.421 8.23 0.00 39.94 3.20
127 128 2.752238 CCGCGACTCCTGTCCTCT 60.752 66.667 8.23 0.00 39.94 3.69
128 129 4.500116 GCCGCGACTCCTGTCCTC 62.500 72.222 8.23 0.00 39.94 3.71
150 151 4.452733 GTCCTGTTCGGGGGAGCG 62.453 72.222 0.00 0.00 31.66 5.03
151 152 3.003763 AGTCCTGTTCGGGGGAGC 61.004 66.667 0.00 0.00 31.66 4.70
152 153 2.982130 CAGTCCTGTTCGGGGGAG 59.018 66.667 0.00 0.00 31.66 4.30
153 154 3.319198 GCAGTCCTGTTCGGGGGA 61.319 66.667 0.00 0.00 0.00 4.81
154 155 4.410400 GGCAGTCCTGTTCGGGGG 62.410 72.222 0.00 0.00 0.00 5.40
155 156 4.410400 GGGCAGTCCTGTTCGGGG 62.410 72.222 0.00 0.00 0.00 5.73
156 157 4.760047 CGGGCAGTCCTGTTCGGG 62.760 72.222 0.00 0.00 33.91 5.14
157 158 3.649277 CTCGGGCAGTCCTGTTCGG 62.649 68.421 9.98 2.92 39.81 4.30
158 159 2.125912 CTCGGGCAGTCCTGTTCG 60.126 66.667 0.00 1.37 39.81 3.95
159 160 1.827399 TTCCTCGGGCAGTCCTGTTC 61.827 60.000 0.00 0.00 39.81 3.18
160 161 1.831652 CTTCCTCGGGCAGTCCTGTT 61.832 60.000 0.00 0.00 39.81 3.16
161 162 2.203788 TTCCTCGGGCAGTCCTGT 60.204 61.111 0.00 0.00 39.81 4.00
162 163 1.544825 TTCTTCCTCGGGCAGTCCTG 61.545 60.000 0.00 0.00 40.23 3.86
163 164 1.229209 TTCTTCCTCGGGCAGTCCT 60.229 57.895 0.00 0.00 0.00 3.85
164 165 1.219393 CTTCTTCCTCGGGCAGTCC 59.781 63.158 0.00 0.00 0.00 3.85
165 166 0.608640 TTCTTCTTCCTCGGGCAGTC 59.391 55.000 0.00 0.00 0.00 3.51
166 167 1.002544 CTTTCTTCTTCCTCGGGCAGT 59.997 52.381 0.00 0.00 0.00 4.40
167 168 1.276421 TCTTTCTTCTTCCTCGGGCAG 59.724 52.381 0.00 0.00 0.00 4.85
168 169 1.276421 CTCTTTCTTCTTCCTCGGGCA 59.724 52.381 0.00 0.00 0.00 5.36
169 170 1.550976 TCTCTTTCTTCTTCCTCGGGC 59.449 52.381 0.00 0.00 0.00 6.13
170 171 2.418060 GCTCTCTTTCTTCTTCCTCGGG 60.418 54.545 0.00 0.00 0.00 5.14
171 172 2.495669 AGCTCTCTTTCTTCTTCCTCGG 59.504 50.000 0.00 0.00 0.00 4.63
172 173 3.510719 CAGCTCTCTTTCTTCTTCCTCG 58.489 50.000 0.00 0.00 0.00 4.63
173 174 3.860641 CCAGCTCTCTTTCTTCTTCCTC 58.139 50.000 0.00 0.00 0.00 3.71
174 175 2.027285 GCCAGCTCTCTTTCTTCTTCCT 60.027 50.000 0.00 0.00 0.00 3.36
175 176 2.355197 GCCAGCTCTCTTTCTTCTTCC 58.645 52.381 0.00 0.00 0.00 3.46
176 177 1.999024 CGCCAGCTCTCTTTCTTCTTC 59.001 52.381 0.00 0.00 0.00 2.87
177 178 1.620819 TCGCCAGCTCTCTTTCTTCTT 59.379 47.619 0.00 0.00 0.00 2.52
178 179 1.261480 TCGCCAGCTCTCTTTCTTCT 58.739 50.000 0.00 0.00 0.00 2.85
179 180 1.932511 CATCGCCAGCTCTCTTTCTTC 59.067 52.381 0.00 0.00 0.00 2.87
180 181 1.552337 TCATCGCCAGCTCTCTTTCTT 59.448 47.619 0.00 0.00 0.00 2.52
181 182 1.189752 TCATCGCCAGCTCTCTTTCT 58.810 50.000 0.00 0.00 0.00 2.52
182 183 2.237393 ATCATCGCCAGCTCTCTTTC 57.763 50.000 0.00 0.00 0.00 2.62
183 184 2.093288 TGAATCATCGCCAGCTCTCTTT 60.093 45.455 0.00 0.00 0.00 2.52
184 185 1.483827 TGAATCATCGCCAGCTCTCTT 59.516 47.619 0.00 0.00 0.00 2.85
185 186 1.117994 TGAATCATCGCCAGCTCTCT 58.882 50.000 0.00 0.00 0.00 3.10
186 187 2.166821 ATGAATCATCGCCAGCTCTC 57.833 50.000 0.00 0.00 0.00 3.20
187 188 2.634815 AATGAATCATCGCCAGCTCT 57.365 45.000 0.00 0.00 0.00 4.09
188 189 3.705043 AAAATGAATCATCGCCAGCTC 57.295 42.857 0.00 0.00 0.00 4.09
211 212 4.555262 GTTCGATTGGATCCAAGCAAAAA 58.445 39.130 35.01 24.38 41.81 1.94
212 213 3.365868 CGTTCGATTGGATCCAAGCAAAA 60.366 43.478 35.01 26.48 41.81 2.44
213 214 2.161410 CGTTCGATTGGATCCAAGCAAA 59.839 45.455 35.01 25.03 41.81 3.68
214 215 1.737236 CGTTCGATTGGATCCAAGCAA 59.263 47.619 35.01 25.82 41.81 3.91
215 216 1.368641 CGTTCGATTGGATCCAAGCA 58.631 50.000 35.01 22.36 41.81 3.91
216 217 0.657840 CCGTTCGATTGGATCCAAGC 59.342 55.000 29.06 29.06 39.47 4.01
217 218 0.657840 GCCGTTCGATTGGATCCAAG 59.342 55.000 29.98 18.63 39.47 3.61
218 219 0.251916 AGCCGTTCGATTGGATCCAA 59.748 50.000 28.92 28.92 40.47 3.53
219 220 0.461870 CAGCCGTTCGATTGGATCCA 60.462 55.000 11.44 11.44 0.00 3.41
220 221 0.179084 TCAGCCGTTCGATTGGATCC 60.179 55.000 4.20 4.20 0.00 3.36
221 222 1.212616 CTCAGCCGTTCGATTGGATC 58.787 55.000 7.58 0.00 0.00 3.36
222 223 0.811616 GCTCAGCCGTTCGATTGGAT 60.812 55.000 7.58 0.00 0.00 3.41
223 224 1.447838 GCTCAGCCGTTCGATTGGA 60.448 57.895 7.58 0.00 0.00 3.53
224 225 2.802667 CGCTCAGCCGTTCGATTGG 61.803 63.158 0.00 0.00 0.00 3.16
225 226 2.697425 CGCTCAGCCGTTCGATTG 59.303 61.111 0.00 0.00 0.00 2.67
226 227 3.188786 GCGCTCAGCCGTTCGATT 61.189 61.111 0.00 0.00 40.81 3.34
235 236 3.465296 GATGCCATGTGCGCTCAGC 62.465 63.158 17.93 16.08 45.60 4.26
236 237 2.713770 GATGCCATGTGCGCTCAG 59.286 61.111 17.93 6.34 45.60 3.35
237 238 3.197092 CGATGCCATGTGCGCTCA 61.197 61.111 15.29 15.29 45.60 4.26
238 239 3.945434 CCGATGCCATGTGCGCTC 61.945 66.667 9.73 5.51 45.60 5.03
244 245 4.424711 AACCGCCCGATGCCATGT 62.425 61.111 0.00 0.00 36.24 3.21
245 246 3.891400 CAACCGCCCGATGCCATG 61.891 66.667 0.00 0.00 36.24 3.66
263 264 2.813474 TTTCAGCCGATCGCACCG 60.813 61.111 10.32 0.00 41.38 4.94
264 265 1.298859 AAGTTTCAGCCGATCGCACC 61.299 55.000 10.32 0.00 41.38 5.01
265 266 0.517316 AAAGTTTCAGCCGATCGCAC 59.483 50.000 10.32 3.69 41.38 5.34
266 267 0.796312 GAAAGTTTCAGCCGATCGCA 59.204 50.000 10.32 0.00 41.38 5.10
267 268 0.247301 CGAAAGTTTCAGCCGATCGC 60.247 55.000 15.67 5.46 37.98 4.58
268 269 0.370273 CCGAAAGTTTCAGCCGATCG 59.630 55.000 15.67 8.51 0.00 3.69
269 270 0.097150 GCCGAAAGTTTCAGCCGATC 59.903 55.000 15.67 0.00 0.00 3.69
270 271 1.305930 GGCCGAAAGTTTCAGCCGAT 61.306 55.000 23.57 0.00 42.81 4.18
271 272 1.964373 GGCCGAAAGTTTCAGCCGA 60.964 57.895 23.57 0.00 42.81 5.54
272 273 2.561373 GGCCGAAAGTTTCAGCCG 59.439 61.111 23.57 7.20 42.81 5.52
274 275 1.081175 GCTGGCCGAAAGTTTCAGC 60.081 57.895 14.30 14.30 42.89 4.26
275 276 1.207593 CGCTGGCCGAAAGTTTCAG 59.792 57.895 15.67 5.46 40.02 3.02
276 277 2.903547 GCGCTGGCCGAAAGTTTCA 61.904 57.895 15.67 0.00 40.02 2.69
277 278 2.126850 GCGCTGGCCGAAAGTTTC 60.127 61.111 0.00 5.47 40.02 2.78
278 279 2.904866 TGCGCTGGCCGAAAGTTT 60.905 55.556 9.73 0.00 40.02 2.66
279 280 3.660111 GTGCGCTGGCCGAAAGTT 61.660 61.111 9.73 0.00 40.02 2.66
318 319 9.225682 TGGGGTAGAAGTGATATCTCTTTATTT 57.774 33.333 18.46 9.47 30.75 1.40
319 320 8.798975 TGGGGTAGAAGTGATATCTCTTTATT 57.201 34.615 18.46 11.36 30.75 1.40
320 321 8.798975 TTGGGGTAGAAGTGATATCTCTTTAT 57.201 34.615 18.46 13.57 30.75 1.40
321 322 7.202011 GCTTGGGGTAGAAGTGATATCTCTTTA 60.202 40.741 18.46 11.27 30.75 1.85
322 323 6.408662 GCTTGGGGTAGAAGTGATATCTCTTT 60.409 42.308 18.46 12.03 30.75 2.52
323 324 5.071115 GCTTGGGGTAGAAGTGATATCTCTT 59.929 44.000 17.68 17.68 32.98 2.85
324 325 4.591072 GCTTGGGGTAGAAGTGATATCTCT 59.409 45.833 3.98 2.61 0.00 3.10
325 326 4.559704 CGCTTGGGGTAGAAGTGATATCTC 60.560 50.000 3.98 0.00 33.55 2.75
326 327 3.322254 CGCTTGGGGTAGAAGTGATATCT 59.678 47.826 3.98 0.00 33.55 1.98
327 328 3.069729 ACGCTTGGGGTAGAAGTGATATC 59.930 47.826 0.00 0.00 35.36 1.63
328 329 3.039011 ACGCTTGGGGTAGAAGTGATAT 58.961 45.455 0.00 0.00 35.36 1.63
329 330 2.429610 GACGCTTGGGGTAGAAGTGATA 59.570 50.000 0.00 0.00 35.36 2.15
330 331 1.207329 GACGCTTGGGGTAGAAGTGAT 59.793 52.381 0.00 0.00 35.36 3.06
331 332 0.606604 GACGCTTGGGGTAGAAGTGA 59.393 55.000 0.00 0.00 35.36 3.41
332 333 0.391263 GGACGCTTGGGGTAGAAGTG 60.391 60.000 0.00 0.00 37.05 3.16
333 334 1.551019 GGGACGCTTGGGGTAGAAGT 61.551 60.000 0.00 0.00 0.00 3.01
334 335 1.221021 GGGACGCTTGGGGTAGAAG 59.779 63.158 0.00 0.00 0.00 2.85
335 336 1.536907 TGGGACGCTTGGGGTAGAA 60.537 57.895 0.00 0.00 0.00 2.10
336 337 1.987855 CTGGGACGCTTGGGGTAGA 60.988 63.158 0.00 0.00 0.00 2.59
337 338 2.584608 CTGGGACGCTTGGGGTAG 59.415 66.667 0.00 0.00 0.00 3.18
338 339 3.006728 CCTGGGACGCTTGGGGTA 61.007 66.667 0.00 0.00 0.00 3.69
340 341 4.410400 GACCTGGGACGCTTGGGG 62.410 72.222 0.00 0.00 0.00 4.96
341 342 2.690653 TTTGACCTGGGACGCTTGGG 62.691 60.000 0.00 2.41 0.00 4.12
342 343 0.821711 TTTTGACCTGGGACGCTTGG 60.822 55.000 0.00 0.00 0.00 3.61
343 344 1.028905 TTTTTGACCTGGGACGCTTG 58.971 50.000 0.00 0.00 0.00 4.01
344 345 3.505835 TTTTTGACCTGGGACGCTT 57.494 47.368 0.00 0.00 0.00 4.68
370 371 4.839796 TCAACGTCGATTCTTTTTGGTTC 58.160 39.130 0.00 0.00 0.00 3.62
374 375 5.090652 TCCTTCAACGTCGATTCTTTTTG 57.909 39.130 0.00 0.00 0.00 2.44
375 376 5.744666 TTCCTTCAACGTCGATTCTTTTT 57.255 34.783 0.00 0.00 0.00 1.94
380 381 3.744426 TCCTTTTCCTTCAACGTCGATTC 59.256 43.478 0.00 0.00 0.00 2.52
381 382 3.735591 TCCTTTTCCTTCAACGTCGATT 58.264 40.909 0.00 0.00 0.00 3.34
382 383 3.396260 TCCTTTTCCTTCAACGTCGAT 57.604 42.857 0.00 0.00 0.00 3.59
383 384 2.894763 TCCTTTTCCTTCAACGTCGA 57.105 45.000 0.00 0.00 0.00 4.20
384 385 3.746492 AGAATCCTTTTCCTTCAACGTCG 59.254 43.478 0.00 0.00 0.00 5.12
385 386 4.143094 CGAGAATCCTTTTCCTTCAACGTC 60.143 45.833 0.00 0.00 0.00 4.34
386 387 3.746492 CGAGAATCCTTTTCCTTCAACGT 59.254 43.478 0.00 0.00 0.00 3.99
387 388 3.424962 GCGAGAATCCTTTTCCTTCAACG 60.425 47.826 0.00 0.00 0.00 4.10
388 389 3.424962 CGCGAGAATCCTTTTCCTTCAAC 60.425 47.826 0.00 0.00 0.00 3.18
390 391 2.346803 CGCGAGAATCCTTTTCCTTCA 58.653 47.619 0.00 0.00 0.00 3.02
391 392 1.062733 GCGCGAGAATCCTTTTCCTTC 59.937 52.381 12.10 0.00 0.00 3.46
394 395 0.744771 AGGCGCGAGAATCCTTTTCC 60.745 55.000 12.10 0.00 0.00 3.13
395 396 0.653114 GAGGCGCGAGAATCCTTTTC 59.347 55.000 12.10 0.00 0.00 2.29
557 558 2.280797 CACGGAGGGGTGTGTGTG 60.281 66.667 0.00 0.00 33.24 3.82
565 566 2.755469 CATTTGGCCACGGAGGGG 60.755 66.667 3.88 0.00 38.09 4.79
635 639 4.157120 GTGCGGGCTACGGTGGAT 62.157 66.667 0.00 0.00 44.51 3.41
663 667 4.447342 CTTCGGGGCTGGGGCAAT 62.447 66.667 0.00 0.00 40.87 3.56
677 681 3.356640 CGTCGCCGTTACGTCTTC 58.643 61.111 3.52 0.00 35.66 2.87
716 740 1.462731 TTGTGCCACATTGACTGCCC 61.463 55.000 0.00 0.00 0.00 5.36
750 774 1.068585 GGTCAGTTTGGGACGTCGT 59.931 57.895 9.92 0.00 36.12 4.34
751 775 2.019951 CGGTCAGTTTGGGACGTCG 61.020 63.158 9.92 0.00 36.12 5.12
752 776 0.666577 CTCGGTCAGTTTGGGACGTC 60.667 60.000 7.13 7.13 36.12 4.34
753 777 1.366366 CTCGGTCAGTTTGGGACGT 59.634 57.895 0.00 0.00 36.12 4.34
755 779 1.671379 GGCTCGGTCAGTTTGGGAC 60.671 63.158 0.00 0.00 34.52 4.46
756 780 2.747686 GGCTCGGTCAGTTTGGGA 59.252 61.111 0.00 0.00 0.00 4.37
758 782 3.423154 GCGGCTCGGTCAGTTTGG 61.423 66.667 0.00 0.00 0.00 3.28
759 783 3.777925 CGCGGCTCGGTCAGTTTG 61.778 66.667 0.00 0.00 33.78 2.93
760 784 3.916392 CTCGCGGCTCGGTCAGTTT 62.916 63.158 6.13 0.00 39.05 2.66
761 785 4.421479 CTCGCGGCTCGGTCAGTT 62.421 66.667 6.13 0.00 39.05 3.16
1827 1892 0.594540 CGTCGTCGTTGGTGGTGTTA 60.595 55.000 0.00 0.00 0.00 2.41
1829 1894 2.278989 CGTCGTCGTTGGTGGTGT 60.279 61.111 0.00 0.00 0.00 4.16
1832 1897 3.095278 CGTCGTCGTCGTTGGTGG 61.095 66.667 3.67 0.00 38.33 4.61
2049 2123 4.511082 ACGTTTCCTAAATTTCGGTTTCGA 59.489 37.500 19.32 0.00 44.44 3.71
2052 2126 6.237888 GCAAAACGTTTCCTAAATTTCGGTTT 60.238 34.615 15.01 6.75 38.42 3.27
2054 2128 4.741185 GCAAAACGTTTCCTAAATTTCGGT 59.259 37.500 15.01 0.00 0.00 4.69
2056 2130 6.197468 TGAAGCAAAACGTTTCCTAAATTTCG 59.803 34.615 15.01 0.00 34.12 3.46
2117 2200 6.000219 GGGACAATATACCACGAGTAGTAGA 59.000 44.000 0.00 0.00 33.42 2.59
2118 2201 5.182760 GGGGACAATATACCACGAGTAGTAG 59.817 48.000 0.00 0.00 33.42 2.57
2119 2202 5.072741 GGGGACAATATACCACGAGTAGTA 58.927 45.833 0.00 0.00 33.42 1.82
2120 2203 3.893813 GGGGACAATATACCACGAGTAGT 59.106 47.826 0.00 0.00 33.42 2.73
2126 2209 3.599412 CGGGGGACAATATACCACG 57.401 57.895 0.00 0.00 45.52 4.94
2227 2311 2.742372 CTGTCAAGAACCGGGCCG 60.742 66.667 21.46 21.46 0.00 6.13
2285 2379 3.508840 GCGTGGATCTTTGCCGGG 61.509 66.667 2.18 0.00 0.00 5.73
2351 2445 4.084171 GCATATTCTGTGGTCGATCACATG 60.084 45.833 30.45 24.63 45.26 3.21
2381 2475 7.357303 GTCACACAATCGTATACCAACTTTTT 58.643 34.615 0.00 0.00 0.00 1.94
2382 2476 6.072893 GGTCACACAATCGTATACCAACTTTT 60.073 38.462 0.00 0.00 0.00 2.27
2383 2477 5.410439 GGTCACACAATCGTATACCAACTTT 59.590 40.000 0.00 0.00 0.00 2.66
2384 2478 4.933400 GGTCACACAATCGTATACCAACTT 59.067 41.667 0.00 0.00 0.00 2.66
2386 2480 3.619929 GGGTCACACAATCGTATACCAAC 59.380 47.826 0.00 0.00 0.00 3.77
2387 2481 3.369681 GGGGTCACACAATCGTATACCAA 60.370 47.826 0.00 0.00 0.00 3.67
2388 2482 2.168936 GGGGTCACACAATCGTATACCA 59.831 50.000 0.00 0.00 0.00 3.25
2389 2483 2.168936 TGGGGTCACACAATCGTATACC 59.831 50.000 0.00 0.00 0.00 2.73
2390 2484 3.530265 TGGGGTCACACAATCGTATAC 57.470 47.619 0.00 0.00 0.00 1.47
2391 2485 4.020039 ACTTTGGGGTCACACAATCGTATA 60.020 41.667 0.00 0.00 0.00 1.47
2393 2487 2.105134 ACTTTGGGGTCACACAATCGTA 59.895 45.455 0.00 0.00 0.00 3.43
2395 2489 1.535462 GACTTTGGGGTCACACAATCG 59.465 52.381 0.00 0.00 36.35 3.34
2436 2534 1.090052 GGATCCCTTCTTGCGGTTCG 61.090 60.000 0.00 0.00 0.00 3.95
2437 2535 0.748367 GGGATCCCTTCTTGCGGTTC 60.748 60.000 24.69 0.00 0.00 3.62
2438 2536 1.208165 AGGGATCCCTTCTTGCGGTT 61.208 55.000 28.96 1.06 45.70 4.44
2439 2537 1.616628 AGGGATCCCTTCTTGCGGT 60.617 57.895 28.96 1.92 45.70 5.68
2524 2625 1.071567 GTACCGCTCTGCTGACGTTC 61.072 60.000 12.06 0.00 0.00 3.95
2535 2636 2.391879 CGGTTATTAGCAGTACCGCTC 58.608 52.381 6.92 0.00 45.75 5.03
2539 2640 4.811024 GGTTAACCGGTTATTAGCAGTACC 59.189 45.833 27.03 22.72 0.00 3.34
2556 2657 0.233848 CTGCGTGTGGTTCGGTTAAC 59.766 55.000 0.00 0.00 37.36 2.01
2608 2711 4.742201 TGGCTTCCTCGTGCGAGC 62.742 66.667 15.32 5.65 40.69 5.03
2682 2786 3.793144 CGCCGCTCAAGTCAAGCC 61.793 66.667 0.00 0.00 36.36 4.35
2816 2925 1.804372 GCACCGACTCATCCTCATCAC 60.804 57.143 0.00 0.00 0.00 3.06
2823 2932 2.509336 CACCGCACCGACTCATCC 60.509 66.667 0.00 0.00 0.00 3.51
2896 3007 0.391263 GACGGCACCCTAGGTCTTTG 60.391 60.000 8.29 0.33 31.02 2.77
2972 3096 1.409412 CGGTCTGCACGACATATAGC 58.591 55.000 15.22 0.00 44.68 2.97
2986 3110 1.269778 CGATCACATACCATGCGGTCT 60.270 52.381 0.00 0.00 44.71 3.85
2990 3114 1.139989 GACCGATCACATACCATGCG 58.860 55.000 0.00 0.00 0.00 4.73
2992 3116 6.859420 TTTTATGACCGATCACATACCATG 57.141 37.500 0.00 0.00 37.79 3.66
2993 3117 6.368791 CGATTTTATGACCGATCACATACCAT 59.631 38.462 0.00 0.00 37.79 3.55
2995 3119 5.694910 ACGATTTTATGACCGATCACATACC 59.305 40.000 0.00 0.00 37.79 2.73
2996 3120 6.419710 TCACGATTTTATGACCGATCACATAC 59.580 38.462 0.00 0.00 37.79 2.39
2997 3121 6.419710 GTCACGATTTTATGACCGATCACATA 59.580 38.462 0.00 0.00 39.49 2.29
2998 3122 5.234329 GTCACGATTTTATGACCGATCACAT 59.766 40.000 0.00 0.00 39.49 3.21
2999 3123 4.565166 GTCACGATTTTATGACCGATCACA 59.435 41.667 0.00 0.00 39.49 3.58
3006 3130 2.284417 GCCGAGTCACGATTTTATGACC 59.716 50.000 0.00 0.00 45.28 4.02
3011 3135 1.546923 TCTGGCCGAGTCACGATTTTA 59.453 47.619 0.00 0.00 45.77 1.52
3025 3149 2.671682 GGGTTGAGGAGTCTGGCC 59.328 66.667 0.00 0.00 0.00 5.36
3026 3150 2.266055 CGGGTTGAGGAGTCTGGC 59.734 66.667 0.00 0.00 0.00 4.85
3027 3151 2.982130 CCGGGTTGAGGAGTCTGG 59.018 66.667 0.00 0.00 0.00 3.86
3029 3153 3.003763 GGCCGGGTTGAGGAGTCT 61.004 66.667 2.18 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.