Multiple sequence alignment - TraesCS3B01G085400

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 TraesCS3B01G085400 chr3B 100.000 3413 0 0 1 3413 53953515 53950103 0.000000e+00 6303.0
1 TraesCS3B01G085400 chr3B 92.570 1992 97 13 1449 3413 54304923 54302956 0.000000e+00 2811.0
2 TraesCS3B01G085400 chr3B 78.609 1697 279 54 1491 3158 54500369 54502010 0.000000e+00 1046.0
3 TraesCS3B01G085400 chr3B 94.880 625 28 3 2789 3413 54068965 54069585 0.000000e+00 974.0
4 TraesCS3B01G085400 chr3B 94.720 625 31 2 2789 3413 54145160 54145782 0.000000e+00 970.0
5 TraesCS3B01G085400 chr3B 95.150 433 9 4 431 860 54308382 54307959 0.000000e+00 673.0
6 TraesCS3B01G085400 chr3B 89.544 373 25 7 1108 1475 54305227 54304864 8.630000e-126 460.0
7 TraesCS3B01G085400 chr3B 96.337 273 10 0 1 273 53957444 53957716 1.870000e-122 449.0
8 TraesCS3B01G085400 chr3B 96.443 253 8 1 863 1115 54307737 54307486 1.890000e-112 416.0
9 TraesCS3B01G085400 chr3B 93.427 213 14 0 2789 3001 53996091 53996303 1.980000e-82 316.0
10 TraesCS3B01G085400 chr3B 85.614 285 28 8 1 273 187556045 187555762 1.550000e-73 287.0
11 TraesCS3B01G085400 chr3B 96.226 53 2 0 1427 1479 53952059 53952007 1.690000e-13 87.9
12 TraesCS3B01G085400 chr3B 96.226 53 2 0 1457 1509 53952089 53952037 1.690000e-13 87.9
13 TraesCS3B01G085400 chr3D 95.538 2017 58 6 1427 3413 31776918 31774904 0.000000e+00 3197.0
14 TraesCS3B01G085400 chr3D 78.235 1700 285 53 1486 3158 31846645 31848286 0.000000e+00 1011.0
15 TraesCS3B01G085400 chr3D 92.037 653 13 10 863 1509 31777485 31776866 0.000000e+00 881.0
16 TraesCS3B01G085400 chr3D 90.167 600 23 14 273 860 31778290 31777715 0.000000e+00 749.0
17 TraesCS3B01G085400 chr3D 87.500 232 23 3 48 273 352929952 352929721 2.610000e-66 263.0
18 TraesCS3B01G085400 chr3D 96.226 53 2 0 1457 1509 31776948 31776896 1.690000e-13 87.9
19 TraesCS3B01G085400 chr6A 97.802 273 6 0 1 273 559264699 559264427 3.990000e-129 472.0
20 TraesCS3B01G085400 chr6A 97.436 273 7 0 1 273 559268619 559268891 1.850000e-127 466.0
21 TraesCS3B01G085400 chr1B 97.048 271 7 1 3 273 457534261 457533992 4.010000e-124 455.0
22 TraesCS3B01G085400 chr1B 93.361 241 16 0 2 242 457538445 457538685 1.160000e-94 357.0
23 TraesCS3B01G085400 chr1B 88.350 103 3 6 361 463 482177144 482177051 7.740000e-22 115.0
24 TraesCS3B01G085400 chr1D 82.874 508 55 17 361 858 360280556 360280071 8.750000e-116 427.0
25 TraesCS3B01G085400 chr2D 93.548 186 12 0 91 276 601037390 601037205 9.330000e-71 278.0
26 TraesCS3B01G085400 chr6D 92.896 183 13 0 91 273 400558050 400557868 2.020000e-67 267.0
27 TraesCS3B01G085400 chr6D 92.896 183 13 0 91 273 400565990 400566172 2.020000e-67 267.0
28 TraesCS3B01G085400 chr7D 84.146 246 27 7 25 258 290912330 290912575 9.530000e-56 228.0
29 TraesCS3B01G085400 chr4B 82.308 260 35 5 25 273 574694227 574693968 7.420000e-52 215.0
30 TraesCS3B01G085400 chr1A 81.786 280 27 10 7 273 566493128 566492860 2.670000e-51 213.0


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 TraesCS3B01G085400 chr3B 53950103 53953515 3412 True 2159.600 6303 97.48400 1 3413 3 chr3B.!!$R2 3412
1 TraesCS3B01G085400 chr3B 54302956 54308382 5426 True 1090.000 2811 93.42675 431 3413 4 chr3B.!!$R3 2982
2 TraesCS3B01G085400 chr3B 54500369 54502010 1641 False 1046.000 1046 78.60900 1491 3158 1 chr3B.!!$F5 1667
3 TraesCS3B01G085400 chr3B 54068965 54069585 620 False 974.000 974 94.88000 2789 3413 1 chr3B.!!$F3 624
4 TraesCS3B01G085400 chr3B 54145160 54145782 622 False 970.000 970 94.72000 2789 3413 1 chr3B.!!$F4 624
5 TraesCS3B01G085400 chr3D 31774904 31778290 3386 True 1228.725 3197 93.49200 273 3413 4 chr3D.!!$R2 3140
6 TraesCS3B01G085400 chr3D 31846645 31848286 1641 False 1011.000 1011 78.23500 1486 3158 1 chr3D.!!$F1 1672

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
183 184 0.249280 CCTTTTGCAACGGTTCACCC 60.249 55.000 0.0 0.0 0.00 4.61 F
185 186 0.970937 TTTTGCAACGGTTCACCCCA 60.971 50.000 0.0 0.0 0.00 4.96 F
187 188 0.970937 TTGCAACGGTTCACCCCAAA 60.971 50.000 0.0 0.0 0.00 3.28 F
338 339 1.071385 CGAGCCCAGATAGCTTCCATT 59.929 52.381 0.0 0.0 41.75 3.16 F
341 342 1.143684 GCCCAGATAGCTTCCATTCCA 59.856 52.381 0.0 0.0 0.00 3.53 F
1962 4529 1.191535 CCGGTGTTGGAGGTGATCTA 58.808 55.000 0.0 0.0 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1408 3939 0.456312 CAGCACGGAGGTAAGACGAC 60.456 60.0 0.00 0.0 0.0 4.34 R
1498 4062 0.616395 TGCATAGTGGTTCCCTCCGA 60.616 55.0 0.00 0.0 0.0 4.55 R
1517 4081 1.029681 GTTGGGGAAAAACACTCGCT 58.970 50.0 0.00 0.0 0.0 4.93 R
2133 4700 1.413767 CTTCACGCGGGAGACATTCG 61.414 60.0 12.53 0.0 0.0 3.34 R
2213 4783 5.104318 ACCTTGTCAATCTTATCTCCTTCCC 60.104 44.0 0.00 0.0 0.0 3.97 R
3225 5830 0.529378 GTTTGCTTCCTGATGCCCTG 59.471 55.0 2.98 0.0 0.0 4.45 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
52 53 3.799755 CACCAGCCGCGCCTAAAC 61.800 66.667 0.00 0.00 0.00 2.01
53 54 4.323477 ACCAGCCGCGCCTAAACA 62.323 61.111 0.00 0.00 0.00 2.83
54 55 3.499737 CCAGCCGCGCCTAAACAG 61.500 66.667 0.00 0.00 0.00 3.16
55 56 2.742372 CAGCCGCGCCTAAACAGT 60.742 61.111 0.00 0.00 0.00 3.55
56 57 2.742372 AGCCGCGCCTAAACAGTG 60.742 61.111 0.00 0.00 0.00 3.66
57 58 4.460873 GCCGCGCCTAAACAGTGC 62.461 66.667 0.00 0.00 37.39 4.40
62 63 3.574780 GCCTAAACAGTGCGACCC 58.425 61.111 0.00 0.00 0.00 4.46
63 64 1.302192 GCCTAAACAGTGCGACCCA 60.302 57.895 0.00 0.00 0.00 4.51
64 65 1.298859 GCCTAAACAGTGCGACCCAG 61.299 60.000 0.00 0.00 0.00 4.45
65 66 1.298859 CCTAAACAGTGCGACCCAGC 61.299 60.000 0.00 0.00 37.71 4.85
66 67 0.320771 CTAAACAGTGCGACCCAGCT 60.321 55.000 0.00 0.00 38.13 4.24
67 68 0.320421 TAAACAGTGCGACCCAGCTC 60.320 55.000 0.00 0.00 38.13 4.09
68 69 3.865929 AACAGTGCGACCCAGCTCG 62.866 63.158 0.00 0.00 38.13 5.03
69 70 4.363990 CAGTGCGACCCAGCTCGT 62.364 66.667 0.00 0.00 35.99 4.18
70 71 4.057428 AGTGCGACCCAGCTCGTC 62.057 66.667 1.02 1.02 35.99 4.20
74 75 4.180946 CGACCCAGCTCGTCCGAG 62.181 72.222 12.19 12.19 44.56 4.63
75 76 3.063084 GACCCAGCTCGTCCGAGT 61.063 66.667 17.11 2.82 43.70 4.18
76 77 3.053849 GACCCAGCTCGTCCGAGTC 62.054 68.421 17.11 10.02 43.70 3.36
77 78 3.062466 CCCAGCTCGTCCGAGTCA 61.062 66.667 17.11 0.00 43.70 3.41
78 79 2.487428 CCAGCTCGTCCGAGTCAG 59.513 66.667 17.11 8.03 43.70 3.51
79 80 2.202544 CAGCTCGTCCGAGTCAGC 60.203 66.667 17.11 4.74 43.70 4.26
80 81 3.805307 AGCTCGTCCGAGTCAGCG 61.805 66.667 17.11 0.00 43.70 5.18
129 130 4.280019 GGGCCCAACCGGTCAGTT 62.280 66.667 19.95 0.00 38.37 3.16
130 131 2.203437 GGCCCAACCGGTCAGTTT 60.203 61.111 8.04 0.00 35.67 2.66
131 132 2.561037 GGCCCAACCGGTCAGTTTG 61.561 63.158 8.04 0.78 35.67 2.93
132 133 3.039134 CCCAACCGGTCAGTTTGC 58.961 61.111 8.04 0.00 0.00 3.68
133 134 2.561037 CCCAACCGGTCAGTTTGCC 61.561 63.158 8.04 0.00 0.00 4.52
134 135 1.528309 CCAACCGGTCAGTTTGCCT 60.528 57.895 8.04 0.00 0.00 4.75
135 136 1.654220 CAACCGGTCAGTTTGCCTG 59.346 57.895 8.04 0.00 42.97 4.85
136 137 1.101049 CAACCGGTCAGTTTGCCTGT 61.101 55.000 8.04 0.00 42.19 4.00
137 138 0.818040 AACCGGTCAGTTTGCCTGTC 60.818 55.000 8.04 0.00 42.19 3.51
138 139 1.227823 CCGGTCAGTTTGCCTGTCA 60.228 57.895 0.00 0.00 42.19 3.58
139 140 0.817634 CCGGTCAGTTTGCCTGTCAA 60.818 55.000 0.00 0.00 42.19 3.18
140 141 1.238439 CGGTCAGTTTGCCTGTCAAT 58.762 50.000 0.00 0.00 42.19 2.57
141 142 2.422597 CGGTCAGTTTGCCTGTCAATA 58.577 47.619 0.00 0.00 42.19 1.90
142 143 2.159627 CGGTCAGTTTGCCTGTCAATAC 59.840 50.000 0.00 0.00 42.19 1.89
143 144 2.159627 GGTCAGTTTGCCTGTCAATACG 59.840 50.000 0.00 0.00 42.19 3.06
144 145 2.806244 GTCAGTTTGCCTGTCAATACGT 59.194 45.455 0.00 0.00 42.19 3.57
145 146 3.991773 GTCAGTTTGCCTGTCAATACGTA 59.008 43.478 0.00 0.00 42.19 3.57
146 147 4.630069 GTCAGTTTGCCTGTCAATACGTAT 59.370 41.667 1.14 1.14 42.19 3.06
147 148 5.808540 GTCAGTTTGCCTGTCAATACGTATA 59.191 40.000 8.83 0.00 42.19 1.47
148 149 6.311935 GTCAGTTTGCCTGTCAATACGTATAA 59.688 38.462 8.83 0.00 42.19 0.98
149 150 6.874664 TCAGTTTGCCTGTCAATACGTATAAA 59.125 34.615 8.83 0.24 42.19 1.40
150 151 6.959311 CAGTTTGCCTGTCAATACGTATAAAC 59.041 38.462 8.83 12.30 36.37 2.01
151 152 6.651643 AGTTTGCCTGTCAATACGTATAAACA 59.348 34.615 20.17 18.78 34.12 2.83
152 153 7.173562 AGTTTGCCTGTCAATACGTATAAACAA 59.826 33.333 20.17 11.67 34.12 2.83
153 154 6.411630 TGCCTGTCAATACGTATAAACAAC 57.588 37.500 18.26 14.83 0.00 3.32
154 155 5.932883 TGCCTGTCAATACGTATAAACAACA 59.067 36.000 18.26 16.44 0.00 3.33
155 156 6.128499 TGCCTGTCAATACGTATAAACAACAC 60.128 38.462 18.26 12.94 0.00 3.32
156 157 6.091713 GCCTGTCAATACGTATAAACAACACT 59.908 38.462 18.26 0.00 0.00 3.55
157 158 7.360607 GCCTGTCAATACGTATAAACAACACTT 60.361 37.037 18.26 0.00 0.00 3.16
158 159 8.500773 CCTGTCAATACGTATAAACAACACTTT 58.499 33.333 18.26 0.00 0.00 2.66
159 160 9.872757 CTGTCAATACGTATAAACAACACTTTT 57.127 29.630 18.26 0.00 0.00 2.27
166 167 8.667076 ACGTATAAACAACACTTTTAGTTCCT 57.333 30.769 0.00 0.00 0.00 3.36
167 168 9.112725 ACGTATAAACAACACTTTTAGTTCCTT 57.887 29.630 0.00 0.00 0.00 3.36
168 169 9.940166 CGTATAAACAACACTTTTAGTTCCTTT 57.060 29.630 0.00 0.00 0.00 3.11
171 172 6.961359 AACAACACTTTTAGTTCCTTTTGC 57.039 33.333 0.00 0.00 0.00 3.68
172 173 6.031751 ACAACACTTTTAGTTCCTTTTGCA 57.968 33.333 0.00 0.00 0.00 4.08
173 174 6.459923 ACAACACTTTTAGTTCCTTTTGCAA 58.540 32.000 0.00 0.00 0.00 4.08
174 175 6.367695 ACAACACTTTTAGTTCCTTTTGCAAC 59.632 34.615 0.00 0.00 0.00 4.17
175 176 5.099575 ACACTTTTAGTTCCTTTTGCAACG 58.900 37.500 0.00 0.00 0.00 4.10
176 177 4.502645 CACTTTTAGTTCCTTTTGCAACGG 59.497 41.667 0.00 2.70 0.00 4.44
177 178 4.158949 ACTTTTAGTTCCTTTTGCAACGGT 59.841 37.500 0.00 0.00 0.00 4.83
178 179 4.722361 TTTAGTTCCTTTTGCAACGGTT 57.278 36.364 0.00 0.00 0.00 4.44
179 180 2.863401 AGTTCCTTTTGCAACGGTTC 57.137 45.000 0.00 1.44 0.00 3.62
180 181 2.096248 AGTTCCTTTTGCAACGGTTCA 58.904 42.857 0.00 0.00 0.00 3.18
181 182 2.159296 AGTTCCTTTTGCAACGGTTCAC 60.159 45.455 0.00 2.66 0.00 3.18
182 183 0.741915 TCCTTTTGCAACGGTTCACC 59.258 50.000 0.00 0.00 0.00 4.02
183 184 0.249280 CCTTTTGCAACGGTTCACCC 60.249 55.000 0.00 0.00 0.00 4.61
184 185 0.249280 CTTTTGCAACGGTTCACCCC 60.249 55.000 0.00 0.00 0.00 4.95
185 186 0.970937 TTTTGCAACGGTTCACCCCA 60.971 50.000 0.00 0.00 0.00 4.96
186 187 0.970937 TTTGCAACGGTTCACCCCAA 60.971 50.000 0.00 0.00 0.00 4.12
187 188 0.970937 TTGCAACGGTTCACCCCAAA 60.971 50.000 0.00 0.00 0.00 3.28
188 189 1.362355 GCAACGGTTCACCCCAAAG 59.638 57.895 0.00 0.00 0.00 2.77
189 190 1.388837 GCAACGGTTCACCCCAAAGT 61.389 55.000 0.00 0.00 0.00 2.66
190 191 1.107945 CAACGGTTCACCCCAAAGTT 58.892 50.000 0.00 0.00 0.00 2.66
191 192 1.107945 AACGGTTCACCCCAAAGTTG 58.892 50.000 0.00 0.00 0.00 3.16
203 204 2.557317 CCAAAGTTGGTACTGACACGT 58.443 47.619 1.63 0.00 43.43 4.49
204 205 3.719924 CCAAAGTTGGTACTGACACGTA 58.280 45.455 1.63 0.00 43.43 3.57
205 206 4.121317 CCAAAGTTGGTACTGACACGTAA 58.879 43.478 1.63 0.00 43.43 3.18
206 207 4.571580 CCAAAGTTGGTACTGACACGTAAA 59.428 41.667 1.63 0.00 43.43 2.01
207 208 5.064962 CCAAAGTTGGTACTGACACGTAAAA 59.935 40.000 1.63 0.00 43.43 1.52
208 209 6.403418 CCAAAGTTGGTACTGACACGTAAAAA 60.403 38.462 1.63 0.00 43.43 1.94
209 210 6.930667 AAGTTGGTACTGACACGTAAAAAT 57.069 33.333 0.00 0.00 34.01 1.82
210 211 6.930667 AGTTGGTACTGACACGTAAAAATT 57.069 33.333 0.00 0.00 31.99 1.82
211 212 8.436046 AAGTTGGTACTGACACGTAAAAATTA 57.564 30.769 0.00 0.00 34.01 1.40
212 213 7.854534 AGTTGGTACTGACACGTAAAAATTAC 58.145 34.615 0.00 0.00 31.99 1.89
213 214 6.783892 TGGTACTGACACGTAAAAATTACC 57.216 37.500 0.00 0.00 0.00 2.85
214 215 6.286758 TGGTACTGACACGTAAAAATTACCA 58.713 36.000 9.05 9.05 35.26 3.25
215 216 6.765036 TGGTACTGACACGTAAAAATTACCAA 59.235 34.615 10.19 0.00 34.82 3.67
216 217 7.444792 TGGTACTGACACGTAAAAATTACCAAT 59.555 33.333 10.19 0.00 34.82 3.16
217 218 7.959109 GGTACTGACACGTAAAAATTACCAATC 59.041 37.037 0.00 0.00 0.00 2.67
218 219 7.739498 ACTGACACGTAAAAATTACCAATCT 57.261 32.000 0.00 0.00 0.00 2.40
219 220 8.161699 ACTGACACGTAAAAATTACCAATCTT 57.838 30.769 0.00 0.00 0.00 2.40
220 221 8.073768 ACTGACACGTAAAAATTACCAATCTTG 58.926 33.333 0.00 0.00 0.00 3.02
235 236 6.461110 CCAATCTTGGTATCAATCTGCTTT 57.539 37.500 0.55 0.00 43.43 3.51
236 237 6.501781 CCAATCTTGGTATCAATCTGCTTTC 58.498 40.000 0.55 0.00 43.43 2.62
237 238 6.095860 CCAATCTTGGTATCAATCTGCTTTCA 59.904 38.462 0.55 0.00 43.43 2.69
238 239 7.363181 CCAATCTTGGTATCAATCTGCTTTCAA 60.363 37.037 0.55 0.00 43.43 2.69
239 240 7.893124 ATCTTGGTATCAATCTGCTTTCAAT 57.107 32.000 0.00 0.00 31.75 2.57
240 241 7.092137 TCTTGGTATCAATCTGCTTTCAATG 57.908 36.000 0.00 0.00 31.75 2.82
241 242 5.252969 TGGTATCAATCTGCTTTCAATGC 57.747 39.130 0.00 0.00 0.00 3.56
242 243 4.098349 TGGTATCAATCTGCTTTCAATGCC 59.902 41.667 0.00 0.00 0.00 4.40
243 244 4.340381 GGTATCAATCTGCTTTCAATGCCT 59.660 41.667 0.00 0.00 0.00 4.75
244 245 4.650754 ATCAATCTGCTTTCAATGCCTC 57.349 40.909 0.00 0.00 0.00 4.70
245 246 3.423749 TCAATCTGCTTTCAATGCCTCA 58.576 40.909 0.00 0.00 0.00 3.86
246 247 3.827876 TCAATCTGCTTTCAATGCCTCAA 59.172 39.130 0.00 0.00 0.00 3.02
247 248 4.464951 TCAATCTGCTTTCAATGCCTCAAT 59.535 37.500 0.00 0.00 0.00 2.57
248 249 5.046878 TCAATCTGCTTTCAATGCCTCAATT 60.047 36.000 0.00 0.00 0.00 2.32
249 250 4.182693 TCTGCTTTCAATGCCTCAATTG 57.817 40.909 0.00 0.00 38.63 2.32
250 251 3.575256 TCTGCTTTCAATGCCTCAATTGT 59.425 39.130 5.13 0.00 38.46 2.71
251 252 3.655486 TGCTTTCAATGCCTCAATTGTG 58.345 40.909 5.13 2.61 38.46 3.33
252 253 2.997986 GCTTTCAATGCCTCAATTGTGG 59.002 45.455 20.01 20.01 38.46 4.17
253 254 3.555586 GCTTTCAATGCCTCAATTGTGGT 60.556 43.478 23.73 6.19 38.46 4.16
254 255 4.321899 GCTTTCAATGCCTCAATTGTGGTA 60.322 41.667 23.73 20.91 38.46 3.25
255 256 4.782019 TTCAATGCCTCAATTGTGGTAC 57.218 40.909 23.73 11.54 38.46 3.34
256 257 4.032960 TCAATGCCTCAATTGTGGTACT 57.967 40.909 23.73 10.19 38.46 2.73
257 258 4.406456 TCAATGCCTCAATTGTGGTACTT 58.594 39.130 23.73 14.18 38.46 2.24
258 259 4.458989 TCAATGCCTCAATTGTGGTACTTC 59.541 41.667 23.73 10.31 38.46 3.01
259 260 3.788227 TGCCTCAATTGTGGTACTTCT 57.212 42.857 23.73 0.00 0.00 2.85
260 261 4.901197 TGCCTCAATTGTGGTACTTCTA 57.099 40.909 23.73 4.00 0.00 2.10
261 262 5.435686 TGCCTCAATTGTGGTACTTCTAT 57.564 39.130 23.73 0.00 0.00 1.98
262 263 5.185454 TGCCTCAATTGTGGTACTTCTATG 58.815 41.667 23.73 0.00 0.00 2.23
263 264 4.035675 GCCTCAATTGTGGTACTTCTATGC 59.964 45.833 23.73 5.60 0.00 3.14
264 265 5.185454 CCTCAATTGTGGTACTTCTATGCA 58.815 41.667 16.81 0.00 0.00 3.96
265 266 5.647658 CCTCAATTGTGGTACTTCTATGCAA 59.352 40.000 16.81 0.00 0.00 4.08
266 267 6.319658 CCTCAATTGTGGTACTTCTATGCAAT 59.680 38.462 16.81 0.00 0.00 3.56
267 268 7.148018 CCTCAATTGTGGTACTTCTATGCAATT 60.148 37.037 16.81 0.00 36.06 2.32
268 269 8.121305 TCAATTGTGGTACTTCTATGCAATTT 57.879 30.769 5.13 0.00 34.23 1.82
269 270 9.237187 TCAATTGTGGTACTTCTATGCAATTTA 57.763 29.630 5.13 0.00 34.23 1.40
270 271 9.289303 CAATTGTGGTACTTCTATGCAATTTAC 57.711 33.333 0.00 0.00 34.23 2.01
271 272 8.807948 ATTGTGGTACTTCTATGCAATTTACT 57.192 30.769 0.00 0.00 0.00 2.24
277 278 7.438459 GGTACTTCTATGCAATTTACTCATCGT 59.562 37.037 0.00 0.00 0.00 3.73
286 287 5.333645 GCAATTTACTCATCGTAGCAGGATG 60.334 44.000 10.62 10.62 40.70 3.51
317 318 5.598416 TGTGGATCACAAGAATAGACGAT 57.402 39.130 0.00 0.00 41.69 3.73
338 339 1.071385 CGAGCCCAGATAGCTTCCATT 59.929 52.381 0.00 0.00 41.75 3.16
339 340 2.777094 GAGCCCAGATAGCTTCCATTC 58.223 52.381 0.00 0.00 41.75 2.67
341 342 1.143684 GCCCAGATAGCTTCCATTCCA 59.856 52.381 0.00 0.00 0.00 3.53
342 343 2.224967 GCCCAGATAGCTTCCATTCCAT 60.225 50.000 0.00 0.00 0.00 3.41
346 347 3.058432 CAGATAGCTTCCATTCCATTGCG 60.058 47.826 0.00 0.00 0.00 4.85
347 348 2.708216 TAGCTTCCATTCCATTGCGA 57.292 45.000 0.00 0.00 0.00 5.10
348 349 2.062971 AGCTTCCATTCCATTGCGAT 57.937 45.000 0.00 0.00 0.00 4.58
351 352 2.542411 GCTTCCATTCCATTGCGATCAC 60.542 50.000 0.00 0.00 0.00 3.06
353 354 2.720915 TCCATTCCATTGCGATCACAA 58.279 42.857 0.00 0.00 0.00 3.33
355 356 2.684374 CCATTCCATTGCGATCACAAGA 59.316 45.455 2.20 0.00 31.96 3.02
356 357 3.129113 CCATTCCATTGCGATCACAAGAA 59.871 43.478 2.20 2.04 31.96 2.52
358 359 5.345702 CATTCCATTGCGATCACAAGAATT 58.654 37.500 2.20 0.00 31.96 2.17
406 417 7.147915 ACCCGCATCAACATTTATTTTGATAGT 60.148 33.333 4.33 0.00 39.86 2.12
407 418 7.706179 CCCGCATCAACATTTATTTTGATAGTT 59.294 33.333 4.33 0.00 39.86 2.24
408 419 8.745837 CCGCATCAACATTTATTTTGATAGTTC 58.254 33.333 4.33 0.00 39.86 3.01
409 420 8.745837 CGCATCAACATTTATTTTGATAGTTCC 58.254 33.333 4.33 0.00 39.86 3.62
410 421 9.807649 GCATCAACATTTATTTTGATAGTTCCT 57.192 29.630 4.33 0.00 39.86 3.36
551 562 7.722949 ATGTGTTGATAATGGACTTTGGATT 57.277 32.000 0.00 0.00 0.00 3.01
794 808 2.223947 CCATGCCGCACACATACTAGTA 60.224 50.000 4.77 4.77 0.00 1.82
795 809 2.863401 TGCCGCACACATACTAGTAG 57.137 50.000 8.85 3.62 0.00 2.57
796 810 2.097036 TGCCGCACACATACTAGTAGT 58.903 47.619 8.85 8.14 0.00 2.73
998 1255 2.969238 CTGCGCCGACCCATCATC 60.969 66.667 4.18 0.00 0.00 2.92
1246 3771 1.400494 CCAAAGGAAAATACGGCTCCG 59.600 52.381 6.79 6.79 46.03 4.63
1962 4529 1.191535 CCGGTGTTGGAGGTGATCTA 58.808 55.000 0.00 0.00 0.00 1.98
2022 4589 2.359975 GGCCCACTTGAACCTCGG 60.360 66.667 0.00 0.00 0.00 4.63
2088 4655 6.006275 AGTGGTGATATAAACTGCTTCCAT 57.994 37.500 0.00 0.00 0.00 3.41
2133 4700 1.904287 TGTGGCATTACAACACCTCC 58.096 50.000 0.00 0.00 34.33 4.30
2213 4783 6.765036 AGTATTGTGCACTATTTGATCTCTGG 59.235 38.462 18.73 0.00 0.00 3.86
2248 4818 4.281688 AGATTGACAAGGTTTCCATGGTTG 59.718 41.667 12.58 10.94 0.00 3.77
2273 4843 6.564873 GCGTTGGATATGATTACTCAGAAAGC 60.565 42.308 0.00 0.00 34.12 3.51
2981 5582 3.935828 GGTCCTATGAGTTGCTGAAGTTC 59.064 47.826 0.00 0.00 0.00 3.01
3025 5626 2.939103 ACTTGCTGTGTCAGTCTTGTTC 59.061 45.455 0.00 0.00 33.43 3.18
3174 5776 5.824624 TCTTGAATGGCCATCTCAGTTATTC 59.175 40.000 21.08 10.85 0.00 1.75
3212 5814 1.811778 TGCTCAATGCCTCTATCCCT 58.188 50.000 0.00 0.00 42.00 4.20
3225 5830 5.703130 GCCTCTATCCCTGTTATCATTGAAC 59.297 44.000 0.00 0.00 0.00 3.18
3278 5883 2.430921 GACAGTCCTCACGCCACG 60.431 66.667 0.00 0.00 0.00 4.94
3360 5971 3.932710 TGCTTTTCTCGGTGTATGTGATC 59.067 43.478 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.878519 CTCCGTCTCCGTCTCGCC 61.879 72.222 0.00 0.00 0.00 5.54
2 3 2.818714 TCTCCGTCTCCGTCTCGC 60.819 66.667 0.00 0.00 0.00 5.03
3 4 2.800581 CGTCTCCGTCTCCGTCTCG 61.801 68.421 0.00 0.00 0.00 4.04
4 5 2.462782 CCGTCTCCGTCTCCGTCTC 61.463 68.421 0.00 0.00 0.00 3.36
5 6 2.436292 CCGTCTCCGTCTCCGTCT 60.436 66.667 0.00 0.00 0.00 4.18
6 7 2.435586 TCCGTCTCCGTCTCCGTC 60.436 66.667 0.00 0.00 0.00 4.79
7 8 2.436292 CTCCGTCTCCGTCTCCGT 60.436 66.667 0.00 0.00 0.00 4.69
8 9 3.203412 CCTCCGTCTCCGTCTCCG 61.203 72.222 0.00 0.00 0.00 4.63
9 10 3.519930 GCCTCCGTCTCCGTCTCC 61.520 72.222 0.00 0.00 0.00 3.71
10 11 2.438795 AGCCTCCGTCTCCGTCTC 60.439 66.667 0.00 0.00 0.00 3.36
11 12 2.438795 GAGCCTCCGTCTCCGTCT 60.439 66.667 0.00 0.00 0.00 4.18
12 13 3.878519 CGAGCCTCCGTCTCCGTC 61.879 72.222 0.00 0.00 0.00 4.79
35 36 3.799755 GTTTAGGCGCGGCTGGTG 61.800 66.667 41.34 0.00 0.00 4.17
36 37 4.323477 TGTTTAGGCGCGGCTGGT 62.323 61.111 41.34 21.39 0.00 4.00
37 38 3.499737 CTGTTTAGGCGCGGCTGG 61.500 66.667 41.34 22.31 0.00 4.85
38 39 2.742372 ACTGTTTAGGCGCGGCTG 60.742 61.111 41.34 27.53 0.00 4.85
39 40 2.742372 CACTGTTTAGGCGCGGCT 60.742 61.111 37.69 37.69 0.00 5.52
40 41 4.460873 GCACTGTTTAGGCGCGGC 62.461 66.667 27.06 27.06 0.00 6.53
41 42 4.147322 CGCACTGTTTAGGCGCGG 62.147 66.667 8.83 0.00 44.49 6.46
45 46 1.298859 CTGGGTCGCACTGTTTAGGC 61.299 60.000 0.00 0.00 0.00 3.93
46 47 1.298859 GCTGGGTCGCACTGTTTAGG 61.299 60.000 0.00 0.00 0.00 2.69
47 48 0.320771 AGCTGGGTCGCACTGTTTAG 60.321 55.000 0.00 0.00 0.00 1.85
48 49 0.320421 GAGCTGGGTCGCACTGTTTA 60.320 55.000 0.00 0.00 0.00 2.01
49 50 1.598130 GAGCTGGGTCGCACTGTTT 60.598 57.895 0.00 0.00 0.00 2.83
50 51 2.031163 GAGCTGGGTCGCACTGTT 59.969 61.111 0.00 0.00 0.00 3.16
51 52 4.363990 CGAGCTGGGTCGCACTGT 62.364 66.667 9.16 0.00 32.22 3.55
52 53 4.363990 ACGAGCTGGGTCGCACTG 62.364 66.667 19.70 0.00 44.06 3.66
53 54 4.057428 GACGAGCTGGGTCGCACT 62.057 66.667 19.70 3.16 44.06 4.40
57 58 4.180946 CTCGGACGAGCTGGGTCG 62.181 72.222 18.48 18.48 45.76 4.79
58 59 3.053849 GACTCGGACGAGCTGGGTC 62.054 68.421 20.46 8.25 45.64 4.46
59 60 3.063084 GACTCGGACGAGCTGGGT 61.063 66.667 20.46 2.51 45.54 4.51
60 61 3.057547 CTGACTCGGACGAGCTGGG 62.058 68.421 20.46 6.03 45.54 4.45
61 62 2.487428 CTGACTCGGACGAGCTGG 59.513 66.667 20.46 7.64 45.54 4.85
62 63 2.202544 GCTGACTCGGACGAGCTG 60.203 66.667 20.46 16.50 45.54 4.24
63 64 3.805307 CGCTGACTCGGACGAGCT 61.805 66.667 20.46 8.77 45.54 4.09
112 113 3.802852 AAACTGACCGGTTGGGCCC 62.803 63.158 17.59 17.59 46.01 5.80
113 114 2.203437 AAACTGACCGGTTGGGCC 60.203 61.111 9.42 0.00 46.01 5.80
115 116 2.561037 GGCAAACTGACCGGTTGGG 61.561 63.158 9.42 4.56 40.75 4.12
116 117 1.528309 AGGCAAACTGACCGGTTGG 60.528 57.895 9.42 7.44 42.84 3.77
117 118 4.157607 AGGCAAACTGACCGGTTG 57.842 55.556 9.42 7.88 0.00 3.77
126 127 6.651643 TGTTTATACGTATTGACAGGCAAACT 59.348 34.615 14.33 0.00 40.48 2.66
127 128 6.833839 TGTTTATACGTATTGACAGGCAAAC 58.166 36.000 14.33 14.65 40.48 2.93
128 129 7.041303 TGTTGTTTATACGTATTGACAGGCAAA 60.041 33.333 14.33 2.70 40.48 3.68
129 130 6.427242 TGTTGTTTATACGTATTGACAGGCAA 59.573 34.615 14.33 0.00 41.53 4.52
130 131 5.932883 TGTTGTTTATACGTATTGACAGGCA 59.067 36.000 14.33 15.91 0.00 4.75
131 132 6.091713 AGTGTTGTTTATACGTATTGACAGGC 59.908 38.462 14.33 14.01 0.00 4.85
132 133 7.591006 AGTGTTGTTTATACGTATTGACAGG 57.409 36.000 14.33 0.00 0.00 4.00
133 134 9.872757 AAAAGTGTTGTTTATACGTATTGACAG 57.127 29.630 14.33 0.00 0.00 3.51
140 141 9.762933 AGGAACTAAAAGTGTTGTTTATACGTA 57.237 29.630 0.00 0.00 36.02 3.57
141 142 8.667076 AGGAACTAAAAGTGTTGTTTATACGT 57.333 30.769 0.00 0.00 36.02 3.57
142 143 9.940166 AAAGGAACTAAAAGTGTTGTTTATACG 57.060 29.630 0.00 0.00 38.49 3.06
145 146 9.093970 GCAAAAGGAACTAAAAGTGTTGTTTAT 57.906 29.630 0.00 0.00 38.49 1.40
146 147 8.088981 TGCAAAAGGAACTAAAAGTGTTGTTTA 58.911 29.630 0.00 0.00 38.49 2.01
147 148 6.931840 TGCAAAAGGAACTAAAAGTGTTGTTT 59.068 30.769 0.00 0.00 38.49 2.83
148 149 6.459923 TGCAAAAGGAACTAAAAGTGTTGTT 58.540 32.000 0.00 0.00 38.49 2.83
149 150 6.031751 TGCAAAAGGAACTAAAAGTGTTGT 57.968 33.333 0.00 0.00 38.49 3.32
150 151 6.453659 CGTTGCAAAAGGAACTAAAAGTGTTG 60.454 38.462 0.00 0.00 38.49 3.33
151 152 5.575218 CGTTGCAAAAGGAACTAAAAGTGTT 59.425 36.000 0.00 0.00 38.49 3.32
152 153 5.099575 CGTTGCAAAAGGAACTAAAAGTGT 58.900 37.500 0.00 0.00 38.49 3.55
153 154 5.620098 CGTTGCAAAAGGAACTAAAAGTG 57.380 39.130 0.00 0.00 38.49 3.16
165 166 0.249280 GGGGTGAACCGTTGCAAAAG 60.249 55.000 0.00 0.00 41.60 2.27
166 167 0.970937 TGGGGTGAACCGTTGCAAAA 60.971 50.000 0.00 0.00 41.60 2.44
167 168 0.970937 TTGGGGTGAACCGTTGCAAA 60.971 50.000 0.00 0.00 41.60 3.68
168 169 0.970937 TTTGGGGTGAACCGTTGCAA 60.971 50.000 0.00 0.00 41.60 4.08
169 170 1.379977 TTTGGGGTGAACCGTTGCA 60.380 52.632 0.00 0.00 41.60 4.08
170 171 1.362355 CTTTGGGGTGAACCGTTGC 59.638 57.895 0.00 0.00 41.60 4.17
171 172 1.107945 AACTTTGGGGTGAACCGTTG 58.892 50.000 0.00 0.00 41.60 4.10
172 173 1.107945 CAACTTTGGGGTGAACCGTT 58.892 50.000 0.00 0.00 41.60 4.44
173 174 0.753848 CCAACTTTGGGGTGAACCGT 60.754 55.000 0.00 0.00 44.70 4.83
174 175 2.037871 CCAACTTTGGGGTGAACCG 58.962 57.895 0.00 0.00 44.70 4.44
184 185 5.721876 TTTACGTGTCAGTACCAACTTTG 57.278 39.130 0.00 0.00 31.97 2.77
185 186 6.740411 TTTTTACGTGTCAGTACCAACTTT 57.260 33.333 0.00 0.00 31.97 2.66
186 187 6.930667 ATTTTTACGTGTCAGTACCAACTT 57.069 33.333 0.00 0.00 31.97 2.66
187 188 6.930667 AATTTTTACGTGTCAGTACCAACT 57.069 33.333 0.00 0.00 35.91 3.16
188 189 7.071414 GGTAATTTTTACGTGTCAGTACCAAC 58.929 38.462 0.00 0.00 0.00 3.77
189 190 6.765036 TGGTAATTTTTACGTGTCAGTACCAA 59.235 34.615 12.78 2.05 36.44 3.67
190 191 6.286758 TGGTAATTTTTACGTGTCAGTACCA 58.713 36.000 11.71 11.71 36.89 3.25
191 192 6.783892 TGGTAATTTTTACGTGTCAGTACC 57.216 37.500 0.00 3.56 0.00 3.34
192 193 8.715088 AGATTGGTAATTTTTACGTGTCAGTAC 58.285 33.333 0.00 0.00 0.00 2.73
193 194 8.836268 AGATTGGTAATTTTTACGTGTCAGTA 57.164 30.769 0.00 0.00 0.00 2.74
194 195 7.739498 AGATTGGTAATTTTTACGTGTCAGT 57.261 32.000 0.00 0.00 0.00 3.41
195 196 7.537306 CCAAGATTGGTAATTTTTACGTGTCAG 59.463 37.037 0.00 0.00 43.43 3.51
196 197 7.364200 CCAAGATTGGTAATTTTTACGTGTCA 58.636 34.615 0.00 0.00 43.43 3.58
197 198 7.790861 CCAAGATTGGTAATTTTTACGTGTC 57.209 36.000 0.00 0.00 43.43 3.67
213 214 7.092137 TGAAAGCAGATTGATACCAAGATTG 57.908 36.000 0.00 0.00 35.48 2.67
214 215 7.707624 TTGAAAGCAGATTGATACCAAGATT 57.292 32.000 0.00 0.00 35.48 2.40
215 216 7.683704 GCATTGAAAGCAGATTGATACCAAGAT 60.684 37.037 0.00 0.00 35.48 2.40
216 217 6.405065 GCATTGAAAGCAGATTGATACCAAGA 60.405 38.462 0.00 0.00 35.48 3.02
217 218 5.747197 GCATTGAAAGCAGATTGATACCAAG 59.253 40.000 0.00 0.00 35.48 3.61
218 219 5.394443 GGCATTGAAAGCAGATTGATACCAA 60.394 40.000 0.00 0.00 36.61 3.67
219 220 4.098349 GGCATTGAAAGCAGATTGATACCA 59.902 41.667 0.00 0.00 0.00 3.25
220 221 4.340381 AGGCATTGAAAGCAGATTGATACC 59.660 41.667 0.00 0.00 0.00 2.73
221 222 5.066893 TGAGGCATTGAAAGCAGATTGATAC 59.933 40.000 0.00 0.00 0.00 2.24
222 223 5.195185 TGAGGCATTGAAAGCAGATTGATA 58.805 37.500 0.00 0.00 0.00 2.15
223 224 4.021229 TGAGGCATTGAAAGCAGATTGAT 58.979 39.130 0.00 0.00 0.00 2.57
224 225 3.423749 TGAGGCATTGAAAGCAGATTGA 58.576 40.909 0.00 0.00 0.00 2.57
225 226 3.861276 TGAGGCATTGAAAGCAGATTG 57.139 42.857 0.00 0.00 0.00 2.67
226 227 5.175859 CAATTGAGGCATTGAAAGCAGATT 58.824 37.500 0.00 0.00 0.00 2.40
227 228 4.222145 ACAATTGAGGCATTGAAAGCAGAT 59.778 37.500 13.59 0.00 0.00 2.90
228 229 3.575256 ACAATTGAGGCATTGAAAGCAGA 59.425 39.130 13.59 0.00 0.00 4.26
229 230 3.678072 CACAATTGAGGCATTGAAAGCAG 59.322 43.478 13.59 0.00 0.00 4.24
230 231 3.555377 CCACAATTGAGGCATTGAAAGCA 60.555 43.478 13.59 0.00 0.00 3.91
231 232 2.997986 CCACAATTGAGGCATTGAAAGC 59.002 45.455 13.59 0.00 0.00 3.51
232 233 4.261578 ACCACAATTGAGGCATTGAAAG 57.738 40.909 20.41 0.00 0.00 2.62
233 234 4.832266 AGTACCACAATTGAGGCATTGAAA 59.168 37.500 20.41 0.00 0.00 2.69
234 235 4.406456 AGTACCACAATTGAGGCATTGAA 58.594 39.130 20.41 0.00 0.00 2.69
235 236 4.032960 AGTACCACAATTGAGGCATTGA 57.967 40.909 20.41 0.22 0.00 2.57
236 237 4.460382 AGAAGTACCACAATTGAGGCATTG 59.540 41.667 20.41 3.34 0.00 2.82
237 238 4.666512 AGAAGTACCACAATTGAGGCATT 58.333 39.130 20.41 12.82 0.00 3.56
238 239 4.307032 AGAAGTACCACAATTGAGGCAT 57.693 40.909 20.41 6.10 0.00 4.40
239 240 3.788227 AGAAGTACCACAATTGAGGCA 57.212 42.857 20.41 6.28 0.00 4.75
240 241 4.035675 GCATAGAAGTACCACAATTGAGGC 59.964 45.833 20.41 6.62 0.00 4.70
241 242 5.185454 TGCATAGAAGTACCACAATTGAGG 58.815 41.667 19.10 19.10 0.00 3.86
242 243 6.741992 TTGCATAGAAGTACCACAATTGAG 57.258 37.500 13.59 3.79 0.00 3.02
243 244 7.701539 AATTGCATAGAAGTACCACAATTGA 57.298 32.000 13.59 0.00 35.55 2.57
244 245 9.289303 GTAAATTGCATAGAAGTACCACAATTG 57.711 33.333 3.24 3.24 36.62 2.32
245 246 9.243105 AGTAAATTGCATAGAAGTACCACAATT 57.757 29.630 0.00 0.00 37.73 2.32
246 247 8.807948 AGTAAATTGCATAGAAGTACCACAAT 57.192 30.769 0.00 0.00 0.00 2.71
247 248 7.880713 TGAGTAAATTGCATAGAAGTACCACAA 59.119 33.333 0.00 0.00 0.00 3.33
248 249 7.390823 TGAGTAAATTGCATAGAAGTACCACA 58.609 34.615 0.00 0.00 0.00 4.17
249 250 7.843490 TGAGTAAATTGCATAGAAGTACCAC 57.157 36.000 0.00 0.00 0.00 4.16
250 251 7.438160 CGATGAGTAAATTGCATAGAAGTACCA 59.562 37.037 0.00 0.00 0.00 3.25
251 252 7.438459 ACGATGAGTAAATTGCATAGAAGTACC 59.562 37.037 0.00 0.00 0.00 3.34
252 253 8.354011 ACGATGAGTAAATTGCATAGAAGTAC 57.646 34.615 0.00 0.00 0.00 2.73
253 254 9.678941 CTACGATGAGTAAATTGCATAGAAGTA 57.321 33.333 0.00 0.00 34.45 2.24
254 255 7.169982 GCTACGATGAGTAAATTGCATAGAAGT 59.830 37.037 0.00 0.00 34.45 3.01
255 256 7.169813 TGCTACGATGAGTAAATTGCATAGAAG 59.830 37.037 0.00 0.00 34.45 2.85
256 257 6.983890 TGCTACGATGAGTAAATTGCATAGAA 59.016 34.615 0.00 0.00 34.45 2.10
257 258 6.512297 TGCTACGATGAGTAAATTGCATAGA 58.488 36.000 0.00 0.00 34.45 1.98
258 259 6.128715 CCTGCTACGATGAGTAAATTGCATAG 60.129 42.308 0.00 0.00 33.97 2.23
259 260 5.696270 CCTGCTACGATGAGTAAATTGCATA 59.304 40.000 0.00 0.00 33.97 3.14
260 261 4.512944 CCTGCTACGATGAGTAAATTGCAT 59.487 41.667 0.00 0.00 33.97 3.96
261 262 3.871006 CCTGCTACGATGAGTAAATTGCA 59.129 43.478 0.00 0.00 34.45 4.08
262 263 4.119862 TCCTGCTACGATGAGTAAATTGC 58.880 43.478 0.00 0.00 34.45 3.56
263 264 5.985530 TCATCCTGCTACGATGAGTAAATTG 59.014 40.000 6.79 0.00 40.88 2.32
264 265 6.161855 TCATCCTGCTACGATGAGTAAATT 57.838 37.500 6.79 0.00 40.88 1.82
265 266 5.791336 TCATCCTGCTACGATGAGTAAAT 57.209 39.130 6.79 0.00 40.88 1.40
266 267 5.592054 CTTCATCCTGCTACGATGAGTAAA 58.408 41.667 9.74 0.00 45.11 2.01
267 268 4.499865 GCTTCATCCTGCTACGATGAGTAA 60.500 45.833 9.74 0.00 45.11 2.24
268 269 3.004839 GCTTCATCCTGCTACGATGAGTA 59.995 47.826 9.74 0.00 45.11 2.59
269 270 2.223923 GCTTCATCCTGCTACGATGAGT 60.224 50.000 9.74 0.00 45.11 3.41
270 271 2.223900 TGCTTCATCCTGCTACGATGAG 60.224 50.000 9.74 6.97 45.11 2.90
271 272 1.756538 TGCTTCATCCTGCTACGATGA 59.243 47.619 6.79 6.79 43.35 2.92
277 278 3.181462 CCACATACTGCTTCATCCTGCTA 60.181 47.826 0.00 0.00 0.00 3.49
286 287 4.507710 TCTTGTGATCCACATACTGCTTC 58.492 43.478 0.27 0.00 44.16 3.86
314 315 0.600557 AAGCTATCTGGGCTCGATCG 59.399 55.000 9.36 9.36 39.30 3.69
315 316 1.067213 GGAAGCTATCTGGGCTCGATC 60.067 57.143 0.00 0.00 39.30 3.69
316 317 0.972883 GGAAGCTATCTGGGCTCGAT 59.027 55.000 0.00 0.00 39.30 3.59
317 318 0.397114 TGGAAGCTATCTGGGCTCGA 60.397 55.000 0.00 0.00 39.30 4.04
338 339 4.009002 TCAATTCTTGTGATCGCAATGGA 58.991 39.130 21.33 13.54 0.00 3.41
339 340 4.100529 GTCAATTCTTGTGATCGCAATGG 58.899 43.478 21.33 11.46 0.00 3.16
341 342 3.436704 ACGTCAATTCTTGTGATCGCAAT 59.563 39.130 21.33 4.99 0.00 3.56
342 343 2.805671 ACGTCAATTCTTGTGATCGCAA 59.194 40.909 20.01 20.01 0.00 4.85
346 347 5.784750 TCATGACGTCAATTCTTGTGATC 57.215 39.130 24.13 0.00 0.00 2.92
347 348 5.876460 TGATCATGACGTCAATTCTTGTGAT 59.124 36.000 24.13 22.90 0.00 3.06
348 349 5.237048 TGATCATGACGTCAATTCTTGTGA 58.763 37.500 24.13 19.22 0.00 3.58
351 352 5.969435 CCATTGATCATGACGTCAATTCTTG 59.031 40.000 24.13 15.82 41.70 3.02
353 354 5.430886 TCCATTGATCATGACGTCAATTCT 58.569 37.500 24.13 7.67 41.70 2.40
355 356 6.513806 TTTCCATTGATCATGACGTCAATT 57.486 33.333 24.13 10.19 41.70 2.32
356 357 6.704289 ATTTCCATTGATCATGACGTCAAT 57.296 33.333 24.13 12.75 43.75 2.57
358 359 5.527214 GGTATTTCCATTGATCATGACGTCA 59.473 40.000 22.48 22.48 34.31 4.35
359 360 5.049405 GGGTATTTCCATTGATCATGACGTC 60.049 44.000 9.11 9.11 38.11 4.34
551 562 9.755804 CAGATGAAGCTAATACATGAAAGAGTA 57.244 33.333 0.00 0.00 0.00 2.59
750 764 1.544691 GACTCCTCGAGGCACAGTTTA 59.455 52.381 27.39 5.79 37.69 2.01
860 874 7.875554 CGATCTCGATCTAATGATATAGAGGGA 59.124 40.741 5.47 0.00 43.02 4.20
861 875 7.875554 TCGATCTCGATCTAATGATATAGAGGG 59.124 40.741 0.00 0.00 44.22 4.30
892 1149 3.407698 TCACTGCGAGATAGGAGATCTC 58.592 50.000 14.75 14.75 40.73 2.75
893 1150 3.500448 TCACTGCGAGATAGGAGATCT 57.500 47.619 0.00 0.00 33.57 2.75
894 1151 5.008613 GGATATCACTGCGAGATAGGAGATC 59.991 48.000 4.83 0.00 32.00 2.75
895 1152 4.887071 GGATATCACTGCGAGATAGGAGAT 59.113 45.833 4.83 0.00 32.00 2.75
896 1153 4.265893 GGATATCACTGCGAGATAGGAGA 58.734 47.826 4.83 0.00 32.00 3.71
897 1154 3.380004 GGGATATCACTGCGAGATAGGAG 59.620 52.174 4.83 0.00 32.00 3.69
998 1255 4.511246 ATCCAGCCACGGCCATGG 62.511 66.667 15.21 15.21 43.17 3.66
1246 3771 3.518068 GGCCATAAGCACGGTGCC 61.518 66.667 28.14 12.38 46.52 5.01
1276 3807 1.478510 GACGAGCTGGAAGAGGATGAA 59.521 52.381 1.44 0.00 34.07 2.57
1408 3939 0.456312 CAGCACGGAGGTAAGACGAC 60.456 60.000 0.00 0.00 0.00 4.34
1409 3940 0.892358 ACAGCACGGAGGTAAGACGA 60.892 55.000 0.00 0.00 0.00 4.20
1410 3941 0.732880 CACAGCACGGAGGTAAGACG 60.733 60.000 0.00 0.00 0.00 4.18
1498 4062 0.616395 TGCATAGTGGTTCCCTCCGA 60.616 55.000 0.00 0.00 0.00 4.55
1517 4081 1.029681 GTTGGGGAAAAACACTCGCT 58.970 50.000 0.00 0.00 0.00 4.93
1663 4230 2.734591 GTCAGGAGCCGACACACA 59.265 61.111 6.62 0.00 33.43 3.72
1962 4529 4.804139 CGAACAACAGAAGTGTACTTGAGT 59.196 41.667 1.35 0.00 35.08 3.41
2022 4589 4.097437 TCAGTGACGATGGTATAACCTGTC 59.903 45.833 0.00 4.20 39.58 3.51
2088 4655 8.650143 ATTCAAAAGCTATCTTTACCCTTTCA 57.350 30.769 0.00 0.00 41.40 2.69
2133 4700 1.413767 CTTCACGCGGGAGACATTCG 61.414 60.000 12.53 0.00 0.00 3.34
2213 4783 5.104318 ACCTTGTCAATCTTATCTCCTTCCC 60.104 44.000 0.00 0.00 0.00 3.97
2248 4818 6.564873 GCTTTCTGAGTAATCATATCCAACGC 60.565 42.308 0.00 0.00 0.00 4.84
2496 5068 1.271379 TGAGGGCCTACTTCAAACTGC 60.271 52.381 5.73 0.00 0.00 4.40
2965 5566 5.106791 CGAAATCTGAACTTCAGCAACTCAT 60.107 40.000 13.24 0.00 43.95 2.90
2981 5582 7.030165 AGTAGATAGAACACACACGAAATCTG 58.970 38.462 0.00 0.00 0.00 2.90
3025 5626 3.305110 GTCCCATACAAGTTTGCAAACG 58.695 45.455 30.90 22.06 43.51 3.60
3212 5814 4.598022 TGATGCCCTGTTCAATGATAACA 58.402 39.130 0.00 0.00 35.61 2.41
3225 5830 0.529378 GTTTGCTTCCTGATGCCCTG 59.471 55.000 2.98 0.00 0.00 4.45
3278 5883 1.670811 CAATCCGACATAACAGTGGCC 59.329 52.381 0.00 0.00 0.00 5.36
3360 5971 2.271800 CTACTACAAAAGCAGAGCCCG 58.728 52.381 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.