Multiple sequence alignment - TraesCS7B01G101700

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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 TraesCS7B01G101700 chr7B 100.000 2264 0 0 1 2264 115960879 115963142 0.000000e+00 4181.0
1 TraesCS7B01G101700 chr7D 90.006 1651 92 39 229 1842 153971234 153972848 0.000000e+00 2067.0
2 TraesCS7B01G101700 chr7D 91.667 120 10 0 15 134 635666066 635665947 1.390000e-37 167.0
3 TraesCS7B01G101700 chr7D 90.000 120 12 0 15 134 636341779 636341898 3.010000e-34 156.0
4 TraesCS7B01G101700 chr7D 86.207 58 6 2 1833 1890 53731160 53731215 6.750000e-06 62.1
5 TraesCS7B01G101700 chr7A 89.620 395 15 10 901 1283 155951797 155952177 1.570000e-131 479.0
6 TraesCS7B01G101700 chr7A 88.252 349 33 6 1891 2237 155963561 155963903 5.820000e-111 411.0
7 TraesCS7B01G101700 chr7A 90.354 311 28 2 1529 1839 155963261 155963569 7.530000e-110 407.0
8 TraesCS7B01G101700 chr7A 87.205 297 25 9 229 514 155950894 155951188 2.170000e-85 326.0
9 TraesCS7B01G101700 chr7A 89.069 247 20 3 500 740 155951201 155951446 1.310000e-77 300.0
10 TraesCS7B01G101700 chr7A 87.907 215 11 12 1336 1544 155952583 155952788 2.910000e-59 239.0
11 TraesCS7B01G101700 chr7A 92.623 122 8 1 14 134 530862579 530862458 8.310000e-40 174.0
12 TraesCS7B01G101700 chr6D 82.547 212 29 8 1001 1208 400650894 400651101 1.790000e-41 180.0
13 TraesCS7B01G101700 chr6D 93.878 49 3 0 1842 1890 438445740 438445692 8.670000e-10 75.0
14 TraesCS7B01G101700 chr6D 86.441 59 7 1 1845 1902 436471640 436471698 1.880000e-06 63.9
15 TraesCS7B01G101700 chr6B 82.212 208 25 5 1001 1208 599693475 599693670 3.870000e-38 169.0
16 TraesCS7B01G101700 chr6A 82.212 208 25 5 1001 1208 546599205 546599400 3.870000e-38 169.0
17 TraesCS7B01G101700 chr6A 86.429 140 17 2 14 153 89897346 89897209 3.890000e-33 152.0
18 TraesCS7B01G101700 chr3B 94.545 110 5 1 13 121 791649201 791649310 3.870000e-38 169.0
19 TraesCS7B01G101700 chr3B 95.833 48 2 0 1843 1890 751943549 751943502 6.700000e-11 78.7
20 TraesCS7B01G101700 chr3B 93.878 49 3 0 1843 1891 782646547 782646595 8.670000e-10 75.0
21 TraesCS7B01G101700 chr3A 89.344 122 12 1 14 134 154028084 154027963 3.890000e-33 152.0
22 TraesCS7B01G101700 chr4B 85.827 127 15 3 10 134 653469104 653469229 5.070000e-27 132.0
23 TraesCS7B01G101700 chr4B 82.927 123 16 3 17 134 17032804 17032926 3.080000e-19 106.0
24 TraesCS7B01G101700 chr4B 97.436 39 1 0 1855 1893 673112417 673112379 1.450000e-07 67.6
25 TraesCS7B01G101700 chr1B 87.619 105 13 0 1104 1208 727951 728055 3.050000e-24 122.0
26 TraesCS7B01G101700 chr3D 90.566 53 2 2 1839 1890 53484613 53484663 1.450000e-07 67.6
27 TraesCS7B01G101700 chr2A 91.837 49 3 1 1844 1892 94325262 94325215 1.450000e-07 67.6
28 TraesCS7B01G101700 chr5D 83.824 68 5 4 1837 1903 45603474 45603536 2.430000e-05 60.2


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 TraesCS7B01G101700 chr7B 115960879 115963142 2263 False 4181 4181 100.00000 1 2264 1 chr7B.!!$F1 2263
1 TraesCS7B01G101700 chr7D 153971234 153972848 1614 False 2067 2067 90.00600 229 1842 1 chr7D.!!$F2 1613
2 TraesCS7B01G101700 chr7A 155963261 155963903 642 False 409 411 89.30300 1529 2237 2 chr7A.!!$F2 708
3 TraesCS7B01G101700 chr7A 155950894 155952788 1894 False 336 479 88.45025 229 1544 4 chr7A.!!$F1 1315

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
461 468 0.040425 CCGCACCGTCCTTGAAAAAG 60.04 55.0 0.0 0.0 0.0 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 2286 0.038343 CCGGGTGCACATTTTTCAGG 60.038 55.0 20.43 6.24 0.0 3.86 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
35 36 3.717842 AAAAACTAGCTGCACGGGA 57.282 47.368 1.02 0.00 0.00 5.14
36 37 1.235724 AAAAACTAGCTGCACGGGAC 58.764 50.000 1.02 0.00 0.00 4.46
37 38 0.396811 AAAACTAGCTGCACGGGACT 59.603 50.000 1.02 0.00 0.00 3.85
38 39 0.396811 AAACTAGCTGCACGGGACTT 59.603 50.000 1.02 0.00 0.00 3.01
39 40 0.320771 AACTAGCTGCACGGGACTTG 60.321 55.000 1.02 0.00 0.00 3.16
40 41 1.293498 CTAGCTGCACGGGACTTGT 59.707 57.895 1.02 0.00 0.00 3.16
41 42 0.737715 CTAGCTGCACGGGACTTGTC 60.738 60.000 1.02 0.00 0.00 3.18
42 43 2.486636 TAGCTGCACGGGACTTGTCG 62.487 60.000 1.02 0.00 0.00 4.35
43 44 3.414700 CTGCACGGGACTTGTCGC 61.415 66.667 7.62 7.62 0.00 5.19
44 45 4.980805 TGCACGGGACTTGTCGCC 62.981 66.667 11.33 5.51 0.00 5.54
45 46 4.980805 GCACGGGACTTGTCGCCA 62.981 66.667 11.33 0.00 0.00 5.69
46 47 2.738521 CACGGGACTTGTCGCCAG 60.739 66.667 11.33 2.62 0.00 4.85
47 48 3.231736 ACGGGACTTGTCGCCAGT 61.232 61.111 11.33 3.16 0.00 4.00
48 49 2.738521 CGGGACTTGTCGCCAGTG 60.739 66.667 11.33 0.00 0.00 3.66
49 50 3.050275 GGGACTTGTCGCCAGTGC 61.050 66.667 6.56 0.00 0.00 4.40
70 71 3.599046 GAGCGCTCGATCAAAATCAAT 57.401 42.857 23.61 0.00 31.76 2.57
71 72 3.539756 GAGCGCTCGATCAAAATCAATC 58.460 45.455 23.61 0.00 31.76 2.67
72 73 2.289002 AGCGCTCGATCAAAATCAATCC 59.711 45.455 2.64 0.00 31.76 3.01
73 74 2.896289 CGCTCGATCAAAATCAATCCG 58.104 47.619 0.00 0.00 31.76 4.18
74 75 2.539688 CGCTCGATCAAAATCAATCCGA 59.460 45.455 0.00 0.00 31.76 4.55
75 76 3.602491 CGCTCGATCAAAATCAATCCGAC 60.602 47.826 0.00 0.00 31.76 4.79
76 77 3.602491 GCTCGATCAAAATCAATCCGACG 60.602 47.826 0.00 0.00 31.76 5.12
77 78 2.863740 TCGATCAAAATCAATCCGACGG 59.136 45.455 7.84 7.84 31.76 4.79
78 79 2.599848 CGATCAAAATCAATCCGACGGC 60.600 50.000 9.66 0.00 31.76 5.68
79 80 2.107950 TCAAAATCAATCCGACGGCT 57.892 45.000 9.66 0.00 0.00 5.52
80 81 3.254470 TCAAAATCAATCCGACGGCTA 57.746 42.857 9.66 0.00 0.00 3.93
81 82 2.933906 TCAAAATCAATCCGACGGCTAC 59.066 45.455 9.66 0.00 0.00 3.58
82 83 7.509110 GATCAAAATCAATCCGACGGCTACG 62.509 48.000 9.66 0.00 37.73 3.51
83 84 0.874607 AATCAATCCGACGGCTACGC 60.875 55.000 9.66 0.00 46.04 4.42
84 85 2.011741 ATCAATCCGACGGCTACGCA 62.012 55.000 9.66 0.00 46.04 5.24
85 86 2.104331 AATCCGACGGCTACGCAG 59.896 61.111 9.66 0.00 46.04 5.18
86 87 3.426117 AATCCGACGGCTACGCAGG 62.426 63.158 9.66 0.00 46.04 4.85
88 89 3.511595 CCGACGGCTACGCAGGTA 61.512 66.667 0.00 0.00 46.04 3.08
99 100 4.617875 GCAGGTAGCGGATGTTGT 57.382 55.556 0.00 0.00 0.00 3.32
100 101 2.089854 GCAGGTAGCGGATGTTGTG 58.910 57.895 0.00 0.00 0.00 3.33
101 102 1.369091 GCAGGTAGCGGATGTTGTGG 61.369 60.000 0.00 0.00 0.00 4.17
102 103 0.744414 CAGGTAGCGGATGTTGTGGG 60.744 60.000 0.00 0.00 0.00 4.61
103 104 1.198759 AGGTAGCGGATGTTGTGGGT 61.199 55.000 0.00 0.00 0.00 4.51
104 105 1.024579 GGTAGCGGATGTTGTGGGTG 61.025 60.000 0.00 0.00 0.00 4.61
105 106 1.376683 TAGCGGATGTTGTGGGTGC 60.377 57.895 0.00 0.00 0.00 5.01
106 107 2.118233 TAGCGGATGTTGTGGGTGCA 62.118 55.000 0.00 0.00 0.00 4.57
107 108 2.342650 GCGGATGTTGTGGGTGCAT 61.343 57.895 0.00 0.00 0.00 3.96
108 109 1.802636 CGGATGTTGTGGGTGCATC 59.197 57.895 0.00 0.00 38.51 3.91
109 110 0.959867 CGGATGTTGTGGGTGCATCA 60.960 55.000 0.00 0.00 40.35 3.07
110 111 0.813184 GGATGTTGTGGGTGCATCAG 59.187 55.000 0.00 0.00 40.35 2.90
111 112 0.171903 GATGTTGTGGGTGCATCAGC 59.828 55.000 0.00 0.00 38.92 4.26
127 128 2.315925 CAGCCGGCTGAAGATTAGAA 57.684 50.000 46.72 0.00 46.30 2.10
128 129 2.843701 CAGCCGGCTGAAGATTAGAAT 58.156 47.619 46.72 10.82 46.30 2.40
129 130 3.209410 CAGCCGGCTGAAGATTAGAATT 58.791 45.455 46.72 10.30 46.30 2.17
130 131 3.629398 CAGCCGGCTGAAGATTAGAATTT 59.371 43.478 46.72 9.53 46.30 1.82
131 132 4.096984 CAGCCGGCTGAAGATTAGAATTTT 59.903 41.667 46.72 9.07 46.30 1.82
132 133 4.336713 AGCCGGCTGAAGATTAGAATTTTC 59.663 41.667 32.33 0.00 32.01 2.29
133 134 4.498177 GCCGGCTGAAGATTAGAATTTTCC 60.498 45.833 22.15 0.00 30.74 3.13
134 135 4.640201 CCGGCTGAAGATTAGAATTTTCCA 59.360 41.667 0.00 0.00 30.74 3.53
135 136 5.125417 CCGGCTGAAGATTAGAATTTTCCAA 59.875 40.000 0.00 0.00 30.74 3.53
136 137 6.350110 CCGGCTGAAGATTAGAATTTTCCAAA 60.350 38.462 0.00 0.00 30.74 3.28
137 138 7.090173 CGGCTGAAGATTAGAATTTTCCAAAA 58.910 34.615 3.78 0.00 30.74 2.44
138 139 7.062255 CGGCTGAAGATTAGAATTTTCCAAAAC 59.938 37.037 3.78 0.00 30.74 2.43
139 140 7.872483 GGCTGAAGATTAGAATTTTCCAAAACA 59.128 33.333 3.78 0.00 30.74 2.83
140 141 9.428097 GCTGAAGATTAGAATTTTCCAAAACAT 57.572 29.630 3.78 0.00 30.74 2.71
150 151 9.357652 AGAATTTTCCAAAACATAATGACGATG 57.642 29.630 0.00 0.00 0.00 3.84
151 152 9.352784 GAATTTTCCAAAACATAATGACGATGA 57.647 29.630 0.00 0.00 0.00 2.92
152 153 9.703892 AATTTTCCAAAACATAATGACGATGAA 57.296 25.926 0.00 0.00 0.00 2.57
153 154 9.874205 ATTTTCCAAAACATAATGACGATGAAT 57.126 25.926 0.00 0.00 0.00 2.57
154 155 8.909708 TTTCCAAAACATAATGACGATGAATC 57.090 30.769 0.00 0.00 0.00 2.52
155 156 7.026631 TCCAAAACATAATGACGATGAATCC 57.973 36.000 0.00 0.00 0.00 3.01
156 157 5.909054 CCAAAACATAATGACGATGAATCCG 59.091 40.000 0.00 0.00 0.00 4.18
157 158 6.238347 CCAAAACATAATGACGATGAATCCGA 60.238 38.462 0.00 0.00 0.00 4.55
158 159 5.907197 AACATAATGACGATGAATCCGAC 57.093 39.130 0.00 0.00 0.00 4.79
159 160 5.201713 ACATAATGACGATGAATCCGACT 57.798 39.130 0.00 0.00 0.00 4.18
160 161 6.327279 ACATAATGACGATGAATCCGACTA 57.673 37.500 0.00 0.00 0.00 2.59
161 162 6.745116 ACATAATGACGATGAATCCGACTAA 58.255 36.000 0.00 0.00 0.00 2.24
162 163 7.207383 ACATAATGACGATGAATCCGACTAAA 58.793 34.615 0.00 0.00 0.00 1.85
163 164 7.709182 ACATAATGACGATGAATCCGACTAAAA 59.291 33.333 0.00 0.00 0.00 1.52
164 165 5.968387 ATGACGATGAATCCGACTAAAAC 57.032 39.130 0.00 0.00 0.00 2.43
165 166 4.811908 TGACGATGAATCCGACTAAAACA 58.188 39.130 0.00 0.00 0.00 2.83
166 167 5.231702 TGACGATGAATCCGACTAAAACAA 58.768 37.500 0.00 0.00 0.00 2.83
167 168 5.872617 TGACGATGAATCCGACTAAAACAAT 59.127 36.000 0.00 0.00 0.00 2.71
168 169 6.106877 ACGATGAATCCGACTAAAACAATG 57.893 37.500 0.00 0.00 0.00 2.82
169 170 4.963953 CGATGAATCCGACTAAAACAATGC 59.036 41.667 0.00 0.00 0.00 3.56
170 171 4.335082 TGAATCCGACTAAAACAATGCG 57.665 40.909 0.00 0.00 0.00 4.73
171 172 3.749088 TGAATCCGACTAAAACAATGCGT 59.251 39.130 0.00 0.00 0.00 5.24
172 173 4.930405 TGAATCCGACTAAAACAATGCGTA 59.070 37.500 0.00 0.00 0.00 4.42
173 174 4.852609 ATCCGACTAAAACAATGCGTAC 57.147 40.909 0.00 0.00 0.00 3.67
174 175 3.916761 TCCGACTAAAACAATGCGTACT 58.083 40.909 0.00 0.00 0.00 2.73
175 176 4.309099 TCCGACTAAAACAATGCGTACTT 58.691 39.130 0.00 0.00 0.00 2.24
176 177 4.751098 TCCGACTAAAACAATGCGTACTTT 59.249 37.500 0.00 0.00 0.00 2.66
177 178 5.925397 TCCGACTAAAACAATGCGTACTTTA 59.075 36.000 0.00 0.00 0.00 1.85
178 179 6.089820 TCCGACTAAAACAATGCGTACTTTAG 59.910 38.462 10.54 10.54 35.43 1.85
179 180 6.089820 CCGACTAAAACAATGCGTACTTTAGA 59.910 38.462 15.79 0.00 33.98 2.10
180 181 6.946584 CGACTAAAACAATGCGTACTTTAGAC 59.053 38.462 15.79 11.10 33.98 2.59
181 182 6.814343 ACTAAAACAATGCGTACTTTAGACG 58.186 36.000 15.79 0.00 43.19 4.18
182 183 5.910637 AAAACAATGCGTACTTTAGACGA 57.089 34.783 0.00 0.00 42.98 4.20
183 184 6.476243 AAAACAATGCGTACTTTAGACGAT 57.524 33.333 0.00 0.00 42.98 3.73
184 185 5.450376 AACAATGCGTACTTTAGACGATG 57.550 39.130 0.00 0.00 42.98 3.84
185 186 4.740268 ACAATGCGTACTTTAGACGATGA 58.260 39.130 0.00 0.00 42.98 2.92
186 187 5.165676 ACAATGCGTACTTTAGACGATGAA 58.834 37.500 0.00 0.00 42.98 2.57
187 188 5.061808 ACAATGCGTACTTTAGACGATGAAC 59.938 40.000 0.00 0.00 42.98 3.18
188 189 3.504863 TGCGTACTTTAGACGATGAACC 58.495 45.455 0.00 0.00 42.98 3.62
189 190 2.856557 GCGTACTTTAGACGATGAACCC 59.143 50.000 0.00 0.00 42.98 4.11
190 191 3.103738 CGTACTTTAGACGATGAACCCG 58.896 50.000 0.00 0.00 42.98 5.28
191 192 3.181507 CGTACTTTAGACGATGAACCCGA 60.182 47.826 0.00 0.00 42.98 5.14
192 193 3.227810 ACTTTAGACGATGAACCCGAC 57.772 47.619 0.00 0.00 0.00 4.79
193 194 2.182825 CTTTAGACGATGAACCCGACG 58.817 52.381 0.00 0.00 0.00 5.12
194 195 1.452110 TTAGACGATGAACCCGACGA 58.548 50.000 0.00 0.00 0.00 4.20
195 196 1.452110 TAGACGATGAACCCGACGAA 58.548 50.000 0.00 0.00 0.00 3.85
196 197 0.599558 AGACGATGAACCCGACGAAA 59.400 50.000 0.00 0.00 0.00 3.46
197 198 1.000060 AGACGATGAACCCGACGAAAA 60.000 47.619 0.00 0.00 0.00 2.29
198 199 1.997606 GACGATGAACCCGACGAAAAT 59.002 47.619 0.00 0.00 0.00 1.82
199 200 3.119388 AGACGATGAACCCGACGAAAATA 60.119 43.478 0.00 0.00 0.00 1.40
200 201 3.587923 ACGATGAACCCGACGAAAATAA 58.412 40.909 0.00 0.00 0.00 1.40
201 202 4.186159 ACGATGAACCCGACGAAAATAAT 58.814 39.130 0.00 0.00 0.00 1.28
202 203 4.033587 ACGATGAACCCGACGAAAATAATG 59.966 41.667 0.00 0.00 0.00 1.90
203 204 4.269123 CGATGAACCCGACGAAAATAATGA 59.731 41.667 0.00 0.00 0.00 2.57
204 205 5.050363 CGATGAACCCGACGAAAATAATGAT 60.050 40.000 0.00 0.00 0.00 2.45
205 206 6.511121 CGATGAACCCGACGAAAATAATGATT 60.511 38.462 0.00 0.00 0.00 2.57
206 207 5.874831 TGAACCCGACGAAAATAATGATTG 58.125 37.500 0.00 0.00 0.00 2.67
207 208 4.287238 ACCCGACGAAAATAATGATTGC 57.713 40.909 0.00 0.00 0.00 3.56
208 209 3.945285 ACCCGACGAAAATAATGATTGCT 59.055 39.130 0.00 0.00 0.00 3.91
209 210 4.398044 ACCCGACGAAAATAATGATTGCTT 59.602 37.500 0.00 0.00 0.00 3.91
210 211 5.105917 ACCCGACGAAAATAATGATTGCTTT 60.106 36.000 0.00 0.00 0.00 3.51
211 212 6.094325 ACCCGACGAAAATAATGATTGCTTTA 59.906 34.615 0.00 0.00 0.00 1.85
212 213 7.138736 CCCGACGAAAATAATGATTGCTTTAT 58.861 34.615 0.00 0.00 0.00 1.40
213 214 7.647715 CCCGACGAAAATAATGATTGCTTTATT 59.352 33.333 0.00 0.00 36.47 1.40
214 215 9.658475 CCGACGAAAATAATGATTGCTTTATTA 57.342 29.630 0.00 0.00 34.88 0.98
334 337 0.686441 AAAATAGGGGAAAGGCGGCC 60.686 55.000 12.11 12.11 0.00 6.13
377 380 1.827789 GCCGGGCATGCAATTCCTA 60.828 57.895 21.36 0.00 0.00 2.94
402 405 1.073025 ACGCCTGGTGAAATGAGCA 59.927 52.632 15.34 0.00 0.00 4.26
404 407 1.236616 CGCCTGGTGAAATGAGCACA 61.237 55.000 0.00 0.00 37.99 4.57
406 409 0.518636 CCTGGTGAAATGAGCACACG 59.481 55.000 0.00 0.00 37.99 4.49
408 411 1.195448 CTGGTGAAATGAGCACACGAC 59.805 52.381 0.00 0.00 37.99 4.34
458 465 2.975799 GCCGCACCGTCCTTGAAA 60.976 61.111 0.00 0.00 0.00 2.69
461 468 0.040425 CCGCACCGTCCTTGAAAAAG 60.040 55.000 0.00 0.00 0.00 2.27
464 471 2.727777 GCACCGTCCTTGAAAAAGAAC 58.272 47.619 0.00 0.00 0.00 3.01
519 558 2.341846 AAGCAGTTCCTTTCGGTTCA 57.658 45.000 0.00 0.00 0.00 3.18
535 574 0.533491 TTCACCTCCCGACCGTATTG 59.467 55.000 0.00 0.00 0.00 1.90
550 589 3.059884 CGTATTGAGTCAGCACAACAGT 58.940 45.455 0.00 0.00 0.00 3.55
690 738 2.045926 CCGACTCCAAGGCCCAAG 60.046 66.667 0.00 0.00 0.00 3.61
727 775 1.671054 CCATTCCAGAACGCGTGGT 60.671 57.895 14.98 0.00 36.37 4.16
782 830 1.266178 CCACAAGATTTCCAACCCCC 58.734 55.000 0.00 0.00 0.00 5.40
783 831 1.203174 CCACAAGATTTCCAACCCCCT 60.203 52.381 0.00 0.00 0.00 4.79
784 832 2.171003 CACAAGATTTCCAACCCCCTC 58.829 52.381 0.00 0.00 0.00 4.30
785 833 2.073776 ACAAGATTTCCAACCCCCTCT 58.926 47.619 0.00 0.00 0.00 3.69
786 834 2.041755 ACAAGATTTCCAACCCCCTCTC 59.958 50.000 0.00 0.00 0.00 3.20
787 835 1.299939 AGATTTCCAACCCCCTCTCC 58.700 55.000 0.00 0.00 0.00 3.71
788 836 0.259065 GATTTCCAACCCCCTCTCCC 59.741 60.000 0.00 0.00 0.00 4.30
789 837 0.178801 ATTTCCAACCCCCTCTCCCT 60.179 55.000 0.00 0.00 0.00 4.20
790 838 0.845102 TTTCCAACCCCCTCTCCCTC 60.845 60.000 0.00 0.00 0.00 4.30
791 839 2.692741 CCAACCCCCTCTCCCTCC 60.693 72.222 0.00 0.00 0.00 4.30
792 840 2.456840 CAACCCCCTCTCCCTCCT 59.543 66.667 0.00 0.00 0.00 3.69
793 841 1.710341 CAACCCCCTCTCCCTCCTA 59.290 63.158 0.00 0.00 0.00 2.94
794 842 0.399233 CAACCCCCTCTCCCTCCTAG 60.399 65.000 0.00 0.00 0.00 3.02
795 843 2.202899 CCCCCTCTCCCTCCTAGC 59.797 72.222 0.00 0.00 0.00 3.42
796 844 2.408203 CCCCCTCTCCCTCCTAGCT 61.408 68.421 0.00 0.00 0.00 3.32
797 845 1.152355 CCCCTCTCCCTCCTAGCTG 60.152 68.421 0.00 0.00 0.00 4.24
798 846 1.660019 CCCCTCTCCCTCCTAGCTGA 61.660 65.000 0.00 0.00 0.00 4.26
807 855 1.454201 CTCCTAGCTGACACGACAGA 58.546 55.000 0.00 0.00 39.94 3.41
817 865 2.069273 GACACGACAGAACCATTCCTG 58.931 52.381 0.00 0.00 36.53 3.86
828 876 3.090532 ATTCCTGTCTCCCCGCCC 61.091 66.667 0.00 0.00 0.00 6.13
923 1202 0.961019 ACGCACACAAAGCATCCATT 59.039 45.000 0.00 0.00 0.00 3.16
942 1221 0.329261 TCGTCCCTCGGTTCCTAAGA 59.671 55.000 0.00 0.00 40.32 2.10
958 1237 3.430218 CCTAAGACAGCAGAGTTTGTTCG 59.570 47.826 0.00 0.00 0.00 3.95
959 1238 2.604046 AGACAGCAGAGTTTGTTCGT 57.396 45.000 0.00 0.00 0.00 3.85
962 1241 2.351726 GACAGCAGAGTTTGTTCGTGTT 59.648 45.455 0.00 0.00 0.00 3.32
963 1242 3.527533 ACAGCAGAGTTTGTTCGTGTTA 58.472 40.909 0.00 0.00 0.00 2.41
998 1280 2.429571 CGTTCCTTTCGTCGCCGA 60.430 61.111 0.00 0.00 42.41 5.54
1233 1524 2.282462 AAGAACGGCAAGCAGGGG 60.282 61.111 0.00 0.00 0.00 4.79
1283 1574 1.202268 ACCGATGATCCGAGACGTTTC 60.202 52.381 0.00 0.00 0.00 2.78
1285 1576 1.065701 CGATGATCCGAGACGTTTCCT 59.934 52.381 0.00 0.00 0.00 3.36
1351 2019 4.022464 TGTTCTTGTTTTAGTGTTGCGG 57.978 40.909 0.00 0.00 0.00 5.69
1354 2022 3.468770 TCTTGTTTTAGTGTTGCGGCTA 58.531 40.909 0.00 0.00 0.00 3.93
1393 2062 5.182001 TGCTCTGTTTTTAGCCTTTCTCATC 59.818 40.000 0.00 0.00 37.97 2.92
1394 2063 5.182001 GCTCTGTTTTTAGCCTTTCTCATCA 59.818 40.000 0.00 0.00 32.40 3.07
1395 2064 6.127786 GCTCTGTTTTTAGCCTTTCTCATCAT 60.128 38.462 0.00 0.00 32.40 2.45
1489 2163 2.300723 TGGTGCTGTGATTAACTACCGT 59.699 45.455 0.00 0.00 33.42 4.83
1490 2164 3.510753 TGGTGCTGTGATTAACTACCGTA 59.489 43.478 0.00 0.00 33.42 4.02
1491 2165 3.861689 GGTGCTGTGATTAACTACCGTAC 59.138 47.826 0.00 0.00 0.00 3.67
1492 2166 3.861689 GTGCTGTGATTAACTACCGTACC 59.138 47.826 0.00 0.00 0.00 3.34
1493 2167 3.111098 GCTGTGATTAACTACCGTACCG 58.889 50.000 0.00 0.00 0.00 4.02
1494 2168 3.181497 GCTGTGATTAACTACCGTACCGA 60.181 47.826 0.00 0.00 0.00 4.69
1495 2169 4.498682 GCTGTGATTAACTACCGTACCGAT 60.499 45.833 0.00 0.00 0.00 4.18
1496 2170 5.173774 TGTGATTAACTACCGTACCGATC 57.826 43.478 0.00 0.00 0.00 3.69
1530 2204 5.826737 CCTTGATTCATCTCCAGCAAACTAT 59.173 40.000 0.00 0.00 0.00 2.12
1612 2288 2.203832 ACCCCGACGGTAAACCCT 60.204 61.111 13.94 0.00 45.97 4.34
1714 2390 8.345565 GTCATAAATATCAATGAGTGGTTGACC 58.654 37.037 1.24 0.00 38.31 4.02
1729 2405 2.593346 TGACCTGCGTGCAAATTTTT 57.407 40.000 0.00 0.00 0.00 1.94
1787 2464 8.870075 AAAAAGTCTATGCTCCTAAAAGACAT 57.130 30.769 0.00 0.00 39.20 3.06
1873 2550 8.810652 TTCACAAATAGTTTGAATTGCTTACC 57.189 30.769 9.21 0.00 43.26 2.85
1874 2551 7.946207 TCACAAATAGTTTGAATTGCTTACCA 58.054 30.769 9.21 0.00 43.26 3.25
1875 2552 7.865385 TCACAAATAGTTTGAATTGCTTACCAC 59.135 33.333 9.21 0.00 43.26 4.16
1876 2553 7.651304 CACAAATAGTTTGAATTGCTTACCACA 59.349 33.333 9.21 0.00 43.26 4.17
1877 2554 8.367156 ACAAATAGTTTGAATTGCTTACCACAT 58.633 29.630 9.21 0.00 43.26 3.21
1878 2555 8.649841 CAAATAGTTTGAATTGCTTACCACATG 58.350 33.333 0.00 0.00 43.26 3.21
1879 2556 5.789643 AGTTTGAATTGCTTACCACATGT 57.210 34.783 0.00 0.00 0.00 3.21
1880 2557 5.531634 AGTTTGAATTGCTTACCACATGTG 58.468 37.500 19.31 19.31 0.00 3.21
1881 2558 5.068987 AGTTTGAATTGCTTACCACATGTGT 59.931 36.000 23.79 14.29 0.00 3.72
1882 2559 4.764679 TGAATTGCTTACCACATGTGTC 57.235 40.909 23.79 11.92 0.00 3.67
1883 2560 4.140536 TGAATTGCTTACCACATGTGTCA 58.859 39.130 23.79 14.25 0.00 3.58
1884 2561 4.766373 TGAATTGCTTACCACATGTGTCAT 59.234 37.500 23.79 11.74 0.00 3.06
1885 2562 4.707030 ATTGCTTACCACATGTGTCATG 57.293 40.909 23.79 11.29 0.00 3.07
1886 2563 3.138884 TGCTTACCACATGTGTCATGT 57.861 42.857 23.79 16.29 0.00 3.21
1887 2564 2.813172 TGCTTACCACATGTGTCATGTG 59.187 45.455 26.20 26.20 46.49 3.21
1894 2571 3.002791 CACATGTGTCATGTGGTAGACC 58.997 50.000 25.74 0.00 44.04 3.85
1895 2572 2.906389 ACATGTGTCATGTGGTAGACCT 59.094 45.455 13.47 0.00 36.82 3.85
1896 2573 3.055819 ACATGTGTCATGTGGTAGACCTC 60.056 47.826 13.47 0.00 36.82 3.85
1897 2574 1.899814 TGTGTCATGTGGTAGACCTCC 59.100 52.381 0.00 0.00 36.82 4.30
1898 2575 1.899814 GTGTCATGTGGTAGACCTCCA 59.100 52.381 0.00 0.00 36.82 3.86
1910 2587 6.356556 TGGTAGACCTCCACAAATATGATTG 58.643 40.000 0.00 0.00 36.82 2.67
1912 2589 7.054124 GGTAGACCTCCACAAATATGATTGAA 58.946 38.462 0.00 0.00 34.38 2.69
1913 2590 7.721399 GGTAGACCTCCACAAATATGATTGAAT 59.279 37.037 0.00 0.00 34.38 2.57
1914 2591 7.814264 AGACCTCCACAAATATGATTGAATC 57.186 36.000 0.00 0.00 34.38 2.52
1915 2592 7.348815 AGACCTCCACAAATATGATTGAATCA 58.651 34.615 10.65 10.65 44.55 2.57
1917 2594 6.322201 ACCTCCACAAATATGATTGAATCACC 59.678 38.462 10.45 0.00 43.01 4.02
1918 2595 6.321945 CCTCCACAAATATGATTGAATCACCA 59.678 38.462 10.45 1.87 43.01 4.17
1934 2611 2.028294 TCACCAAAATTTGCATGCGGAT 60.028 40.909 14.09 6.49 0.00 4.18
1942 2619 1.953559 TTGCATGCGGATAGAGAACC 58.046 50.000 14.09 0.00 0.00 3.62
1944 2621 1.209261 TGCATGCGGATAGAGAACCAA 59.791 47.619 14.09 0.00 0.00 3.67
2010 2688 9.809096 TCTTAGATTTTACTGTCATAGCAGAAG 57.191 33.333 0.00 0.00 39.62 2.85
2019 2697 6.940739 ACTGTCATAGCAGAAGTATTTGAGT 58.059 36.000 0.00 0.00 39.62 3.41
2029 2707 9.160496 AGCAGAAGTATTTGAGTTTGAGATTAG 57.840 33.333 0.00 0.00 0.00 1.73
2046 2724 5.810095 AGATTAGAAGGACACTTTTGGGAG 58.190 41.667 0.00 0.00 36.97 4.30
2047 2725 2.959465 AGAAGGACACTTTTGGGAGG 57.041 50.000 0.00 0.00 36.97 4.30
2061 2740 1.768870 TGGGAGGCTATTTAGAGGCAC 59.231 52.381 0.74 0.00 44.29 5.01
2064 2743 3.778954 GAGGCTATTTAGAGGCACCAT 57.221 47.619 0.74 0.00 44.29 3.55
2078 2757 2.354003 GGCACCATGGATCAACTTTTGG 60.354 50.000 21.47 0.00 0.00 3.28
2096 2775 3.695830 TGGTCACCTTCTCCAACATAC 57.304 47.619 0.00 0.00 0.00 2.39
2170 2849 3.527434 CCCGTTAGTGGGTCACTTC 57.473 57.895 5.86 0.54 42.59 3.01
2181 2860 2.306847 GGGTCACTTCTTTTGCTTCCA 58.693 47.619 0.00 0.00 0.00 3.53
2183 2862 2.952310 GGTCACTTCTTTTGCTTCCACT 59.048 45.455 0.00 0.00 0.00 4.00
2192 2871 2.727123 TTGCTTCCACTCCTTTGACA 57.273 45.000 0.00 0.00 0.00 3.58
2194 2873 3.228188 TGCTTCCACTCCTTTGACATT 57.772 42.857 0.00 0.00 0.00 2.71
2206 2885 2.408271 TTGACATTGGAGCTAGCTGG 57.592 50.000 24.99 8.59 0.00 4.85
2212 2891 3.922640 GGAGCTAGCTGGCCTCCG 61.923 72.222 24.99 0.00 0.00 4.63
2215 2894 4.906792 GCTAGCTGGCCTCCGCTG 62.907 72.222 20.26 13.03 35.69 5.18
2230 2909 1.331756 CCGCTGCCAATCATTGTCTAC 59.668 52.381 0.00 0.00 0.00 2.59
2232 2911 2.031314 CGCTGCCAATCATTGTCTACTG 59.969 50.000 0.00 0.00 0.00 2.74
2243 2922 3.138798 TCTACTGGAGACCCGCGC 61.139 66.667 0.00 0.00 34.29 6.86
2244 2923 4.554363 CTACTGGAGACCCGCGCG 62.554 72.222 25.67 25.67 34.29 6.86
2262 2941 4.314440 GCTGACGTGGGCAGTGGA 62.314 66.667 0.00 0.00 35.81 4.02
2263 2942 2.047844 CTGACGTGGGCAGTGGAG 60.048 66.667 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.202770 AGTCCCGTGCAGCTAGTTTTT 60.203 47.619 0.00 0.00 0.00 1.94
18 19 0.396811 AGTCCCGTGCAGCTAGTTTT 59.603 50.000 0.00 0.00 0.00 2.43
19 20 0.396811 AAGTCCCGTGCAGCTAGTTT 59.603 50.000 0.00 0.00 0.00 2.66
20 21 0.320771 CAAGTCCCGTGCAGCTAGTT 60.321 55.000 0.00 0.00 0.00 2.24
21 22 1.293498 CAAGTCCCGTGCAGCTAGT 59.707 57.895 0.00 0.00 0.00 2.57
22 23 0.737715 GACAAGTCCCGTGCAGCTAG 60.738 60.000 0.00 0.00 0.00 3.42
23 24 1.292223 GACAAGTCCCGTGCAGCTA 59.708 57.895 0.00 0.00 0.00 3.32
24 25 2.031163 GACAAGTCCCGTGCAGCT 59.969 61.111 0.00 0.00 0.00 4.24
25 26 3.414700 CGACAAGTCCCGTGCAGC 61.415 66.667 0.00 0.00 0.00 5.25
26 27 3.414700 GCGACAAGTCCCGTGCAG 61.415 66.667 0.00 0.00 0.00 4.41
27 28 4.980805 GGCGACAAGTCCCGTGCA 62.981 66.667 0.00 0.00 0.00 4.57
28 29 4.980805 TGGCGACAAGTCCCGTGC 62.981 66.667 0.00 0.00 37.44 5.34
29 30 2.738521 CTGGCGACAAGTCCCGTG 60.739 66.667 0.00 0.00 42.06 4.94
30 31 3.231736 ACTGGCGACAAGTCCCGT 61.232 61.111 0.00 0.00 42.06 5.28
31 32 2.738521 CACTGGCGACAAGTCCCG 60.739 66.667 0.00 0.00 42.06 5.14
32 33 3.050275 GCACTGGCGACAAGTCCC 61.050 66.667 0.00 0.00 42.06 4.46
50 51 3.539756 GATTGATTTTGATCGAGCGCTC 58.460 45.455 27.64 27.64 0.00 5.03
51 52 2.289002 GGATTGATTTTGATCGAGCGCT 59.711 45.455 11.27 11.27 0.00 5.92
52 53 2.644078 GGATTGATTTTGATCGAGCGC 58.356 47.619 0.00 0.00 0.00 5.92
53 54 2.539688 TCGGATTGATTTTGATCGAGCG 59.460 45.455 0.00 0.00 0.00 5.03
54 55 3.602491 CGTCGGATTGATTTTGATCGAGC 60.602 47.826 0.00 0.00 0.00 5.03
55 56 3.060272 CCGTCGGATTGATTTTGATCGAG 60.060 47.826 4.91 0.00 0.00 4.04
56 57 2.863740 CCGTCGGATTGATTTTGATCGA 59.136 45.455 4.91 0.00 0.00 3.59
57 58 2.599848 GCCGTCGGATTGATTTTGATCG 60.600 50.000 17.49 0.00 0.00 3.69
58 59 2.614057 AGCCGTCGGATTGATTTTGATC 59.386 45.455 17.49 0.00 0.00 2.92
59 60 2.643551 AGCCGTCGGATTGATTTTGAT 58.356 42.857 17.49 0.00 0.00 2.57
60 61 2.107950 AGCCGTCGGATTGATTTTGA 57.892 45.000 17.49 0.00 0.00 2.69
61 62 2.285602 CGTAGCCGTCGGATTGATTTTG 60.286 50.000 17.49 0.00 0.00 2.44
62 63 1.931172 CGTAGCCGTCGGATTGATTTT 59.069 47.619 17.49 0.00 0.00 1.82
63 64 1.567504 CGTAGCCGTCGGATTGATTT 58.432 50.000 17.49 0.00 0.00 2.17
64 65 3.267900 CGTAGCCGTCGGATTGATT 57.732 52.632 17.49 0.00 0.00 2.57
82 83 1.369091 CCACAACATCCGCTACCTGC 61.369 60.000 0.00 0.00 38.57 4.85
83 84 0.744414 CCCACAACATCCGCTACCTG 60.744 60.000 0.00 0.00 0.00 4.00
84 85 1.198759 ACCCACAACATCCGCTACCT 61.199 55.000 0.00 0.00 0.00 3.08
85 86 1.024579 CACCCACAACATCCGCTACC 61.025 60.000 0.00 0.00 0.00 3.18
86 87 1.644786 GCACCCACAACATCCGCTAC 61.645 60.000 0.00 0.00 0.00 3.58
87 88 1.376683 GCACCCACAACATCCGCTA 60.377 57.895 0.00 0.00 0.00 4.26
88 89 2.672996 GCACCCACAACATCCGCT 60.673 61.111 0.00 0.00 0.00 5.52
89 90 2.270297 GATGCACCCACAACATCCGC 62.270 60.000 0.00 0.00 35.27 5.54
90 91 0.959867 TGATGCACCCACAACATCCG 60.960 55.000 0.00 0.00 39.55 4.18
91 92 0.813184 CTGATGCACCCACAACATCC 59.187 55.000 0.00 0.00 39.55 3.51
92 93 0.171903 GCTGATGCACCCACAACATC 59.828 55.000 0.00 0.00 40.48 3.06
93 94 1.252904 GGCTGATGCACCCACAACAT 61.253 55.000 0.00 0.00 41.91 2.71
94 95 1.902918 GGCTGATGCACCCACAACA 60.903 57.895 0.00 0.00 41.91 3.33
95 96 2.964978 GGCTGATGCACCCACAAC 59.035 61.111 0.00 0.00 41.91 3.32
96 97 2.672651 CGGCTGATGCACCCACAA 60.673 61.111 0.00 0.00 41.91 3.33
97 98 4.720902 CCGGCTGATGCACCCACA 62.721 66.667 0.00 0.00 41.91 4.17
108 109 2.315925 TTCTAATCTTCAGCCGGCTG 57.684 50.000 44.24 44.24 44.86 4.85
109 110 3.567478 AATTCTAATCTTCAGCCGGCT 57.433 42.857 27.08 27.08 0.00 5.52
110 111 4.498177 GGAAAATTCTAATCTTCAGCCGGC 60.498 45.833 21.89 21.89 0.00 6.13
111 112 4.640201 TGGAAAATTCTAATCTTCAGCCGG 59.360 41.667 0.00 0.00 0.00 6.13
112 113 5.818136 TGGAAAATTCTAATCTTCAGCCG 57.182 39.130 0.00 0.00 0.00 5.52
113 114 7.872483 TGTTTTGGAAAATTCTAATCTTCAGCC 59.128 33.333 0.00 0.00 0.00 4.85
114 115 8.816640 TGTTTTGGAAAATTCTAATCTTCAGC 57.183 30.769 0.00 0.00 0.00 4.26
124 125 9.357652 CATCGTCATTATGTTTTGGAAAATTCT 57.642 29.630 0.00 0.00 0.00 2.40
125 126 9.352784 TCATCGTCATTATGTTTTGGAAAATTC 57.647 29.630 0.00 0.00 0.00 2.17
126 127 9.703892 TTCATCGTCATTATGTTTTGGAAAATT 57.296 25.926 0.00 0.00 0.00 1.82
127 128 9.874205 ATTCATCGTCATTATGTTTTGGAAAAT 57.126 25.926 0.00 0.00 0.00 1.82
128 129 9.352784 GATTCATCGTCATTATGTTTTGGAAAA 57.647 29.630 0.00 0.00 0.00 2.29
129 130 7.973388 GGATTCATCGTCATTATGTTTTGGAAA 59.027 33.333 0.00 0.00 0.00 3.13
130 131 7.479980 GGATTCATCGTCATTATGTTTTGGAA 58.520 34.615 0.00 0.00 0.00 3.53
131 132 6.238347 CGGATTCATCGTCATTATGTTTTGGA 60.238 38.462 0.00 0.00 0.00 3.53
132 133 5.909054 CGGATTCATCGTCATTATGTTTTGG 59.091 40.000 0.00 0.00 0.00 3.28
133 134 6.628856 GTCGGATTCATCGTCATTATGTTTTG 59.371 38.462 0.00 0.00 0.00 2.44
134 135 6.538742 AGTCGGATTCATCGTCATTATGTTTT 59.461 34.615 0.00 0.00 0.00 2.43
135 136 6.049149 AGTCGGATTCATCGTCATTATGTTT 58.951 36.000 0.00 0.00 0.00 2.83
136 137 5.601662 AGTCGGATTCATCGTCATTATGTT 58.398 37.500 0.00 0.00 0.00 2.71
137 138 5.201713 AGTCGGATTCATCGTCATTATGT 57.798 39.130 0.00 0.00 0.00 2.29
138 139 7.637709 TTTAGTCGGATTCATCGTCATTATG 57.362 36.000 0.00 0.00 0.00 1.90
139 140 7.709182 TGTTTTAGTCGGATTCATCGTCATTAT 59.291 33.333 0.00 0.00 0.00 1.28
140 141 7.036829 TGTTTTAGTCGGATTCATCGTCATTA 58.963 34.615 0.00 0.00 0.00 1.90
141 142 5.872617 TGTTTTAGTCGGATTCATCGTCATT 59.127 36.000 0.00 0.00 0.00 2.57
142 143 5.416083 TGTTTTAGTCGGATTCATCGTCAT 58.584 37.500 0.00 0.00 0.00 3.06
143 144 4.811908 TGTTTTAGTCGGATTCATCGTCA 58.188 39.130 0.00 0.00 0.00 4.35
144 145 5.773239 TTGTTTTAGTCGGATTCATCGTC 57.227 39.130 0.00 0.00 0.00 4.20
145 146 5.447279 GCATTGTTTTAGTCGGATTCATCGT 60.447 40.000 0.00 0.00 0.00 3.73
146 147 4.963953 GCATTGTTTTAGTCGGATTCATCG 59.036 41.667 0.00 0.00 0.00 3.84
147 148 4.963953 CGCATTGTTTTAGTCGGATTCATC 59.036 41.667 0.00 0.00 0.00 2.92
148 149 4.394920 ACGCATTGTTTTAGTCGGATTCAT 59.605 37.500 0.00 0.00 0.00 2.57
149 150 3.749088 ACGCATTGTTTTAGTCGGATTCA 59.251 39.130 0.00 0.00 0.00 2.57
150 151 4.336532 ACGCATTGTTTTAGTCGGATTC 57.663 40.909 0.00 0.00 0.00 2.52
151 152 4.933400 AGTACGCATTGTTTTAGTCGGATT 59.067 37.500 0.00 0.00 0.00 3.01
152 153 4.501071 AGTACGCATTGTTTTAGTCGGAT 58.499 39.130 0.00 0.00 0.00 4.18
153 154 3.916761 AGTACGCATTGTTTTAGTCGGA 58.083 40.909 0.00 0.00 0.00 4.55
154 155 4.657075 AAGTACGCATTGTTTTAGTCGG 57.343 40.909 0.00 0.00 0.00 4.79
155 156 6.946584 GTCTAAAGTACGCATTGTTTTAGTCG 59.053 38.462 7.84 0.00 34.58 4.18
156 157 6.946584 CGTCTAAAGTACGCATTGTTTTAGTC 59.053 38.462 7.84 3.57 34.58 2.59
157 158 6.642131 TCGTCTAAAGTACGCATTGTTTTAGT 59.358 34.615 7.84 0.00 40.12 2.24
158 159 7.041187 TCGTCTAAAGTACGCATTGTTTTAG 57.959 36.000 0.00 3.37 40.12 1.85
159 160 7.328982 TCATCGTCTAAAGTACGCATTGTTTTA 59.671 33.333 0.00 0.00 40.12 1.52
160 161 5.910637 TCGTCTAAAGTACGCATTGTTTT 57.089 34.783 0.00 0.00 40.12 2.43
161 162 5.636121 TCATCGTCTAAAGTACGCATTGTTT 59.364 36.000 0.00 0.00 40.12 2.83
162 163 5.165676 TCATCGTCTAAAGTACGCATTGTT 58.834 37.500 0.00 0.00 40.12 2.83
163 164 4.740268 TCATCGTCTAAAGTACGCATTGT 58.260 39.130 0.00 0.00 40.12 2.71
164 165 5.481472 GTTCATCGTCTAAAGTACGCATTG 58.519 41.667 0.00 0.00 40.12 2.82
165 166 4.565564 GGTTCATCGTCTAAAGTACGCATT 59.434 41.667 0.00 0.00 40.12 3.56
166 167 4.110482 GGTTCATCGTCTAAAGTACGCAT 58.890 43.478 0.00 0.00 40.12 4.73
167 168 3.504863 GGTTCATCGTCTAAAGTACGCA 58.495 45.455 0.00 0.00 40.12 5.24
168 169 2.856557 GGGTTCATCGTCTAAAGTACGC 59.143 50.000 0.00 0.00 40.12 4.42
169 170 3.103738 CGGGTTCATCGTCTAAAGTACG 58.896 50.000 0.00 0.00 41.64 3.67
170 171 4.101235 GTCGGGTTCATCGTCTAAAGTAC 58.899 47.826 0.00 0.00 0.00 2.73
171 172 3.181507 CGTCGGGTTCATCGTCTAAAGTA 60.182 47.826 0.00 0.00 0.00 2.24
172 173 2.415090 CGTCGGGTTCATCGTCTAAAGT 60.415 50.000 0.00 0.00 0.00 2.66
173 174 2.159476 TCGTCGGGTTCATCGTCTAAAG 60.159 50.000 0.00 0.00 0.00 1.85
174 175 1.811965 TCGTCGGGTTCATCGTCTAAA 59.188 47.619 0.00 0.00 0.00 1.85
175 176 1.452110 TCGTCGGGTTCATCGTCTAA 58.548 50.000 0.00 0.00 0.00 2.10
176 177 1.452110 TTCGTCGGGTTCATCGTCTA 58.548 50.000 0.00 0.00 0.00 2.59
177 178 0.599558 TTTCGTCGGGTTCATCGTCT 59.400 50.000 0.00 0.00 0.00 4.18
178 179 1.421382 TTTTCGTCGGGTTCATCGTC 58.579 50.000 0.00 0.00 0.00 4.20
179 180 2.088950 ATTTTCGTCGGGTTCATCGT 57.911 45.000 0.00 0.00 0.00 3.73
180 181 4.269123 TCATTATTTTCGTCGGGTTCATCG 59.731 41.667 0.00 0.00 0.00 3.84
181 182 5.728351 TCATTATTTTCGTCGGGTTCATC 57.272 39.130 0.00 0.00 0.00 2.92
182 183 6.494842 CAATCATTATTTTCGTCGGGTTCAT 58.505 36.000 0.00 0.00 0.00 2.57
183 184 5.675071 GCAATCATTATTTTCGTCGGGTTCA 60.675 40.000 0.00 0.00 0.00 3.18
184 185 4.733405 GCAATCATTATTTTCGTCGGGTTC 59.267 41.667 0.00 0.00 0.00 3.62
185 186 4.398044 AGCAATCATTATTTTCGTCGGGTT 59.602 37.500 0.00 0.00 0.00 4.11
186 187 3.945285 AGCAATCATTATTTTCGTCGGGT 59.055 39.130 0.00 0.00 0.00 5.28
187 188 4.552166 AGCAATCATTATTTTCGTCGGG 57.448 40.909 0.00 0.00 0.00 5.14
188 189 8.560576 AATAAAGCAATCATTATTTTCGTCGG 57.439 30.769 0.00 0.00 29.68 4.79
211 212 9.286946 GCACGCGTATCTTTATTATCTACTAAT 57.713 33.333 13.44 0.00 34.39 1.73
212 213 7.752239 GGCACGCGTATCTTTATTATCTACTAA 59.248 37.037 13.44 0.00 0.00 2.24
213 214 7.120285 AGGCACGCGTATCTTTATTATCTACTA 59.880 37.037 13.44 0.00 0.00 1.82
214 215 6.072064 AGGCACGCGTATCTTTATTATCTACT 60.072 38.462 13.44 0.00 0.00 2.57
215 216 6.091437 AGGCACGCGTATCTTTATTATCTAC 58.909 40.000 13.44 0.00 0.00 2.59
216 217 6.263516 AGGCACGCGTATCTTTATTATCTA 57.736 37.500 13.44 0.00 0.00 1.98
217 218 5.135508 AGGCACGCGTATCTTTATTATCT 57.864 39.130 13.44 0.00 0.00 1.98
218 219 5.003214 CGTAGGCACGCGTATCTTTATTATC 59.997 44.000 13.44 0.00 42.05 1.75
219 220 4.855388 CGTAGGCACGCGTATCTTTATTAT 59.145 41.667 13.44 0.00 42.05 1.28
220 221 4.221342 CGTAGGCACGCGTATCTTTATTA 58.779 43.478 13.44 0.00 42.05 0.98
221 222 3.047796 CGTAGGCACGCGTATCTTTATT 58.952 45.455 13.44 0.00 42.05 1.40
222 223 2.658285 CGTAGGCACGCGTATCTTTAT 58.342 47.619 13.44 0.00 42.05 1.40
223 224 2.109609 CGTAGGCACGCGTATCTTTA 57.890 50.000 13.44 0.00 42.05 1.85
224 225 2.953669 CGTAGGCACGCGTATCTTT 58.046 52.632 13.44 0.00 42.05 2.52
225 226 4.704007 CGTAGGCACGCGTATCTT 57.296 55.556 13.44 5.94 42.05 2.40
397 400 2.355837 GGCTTCGTCGTGTGCTCA 60.356 61.111 0.00 0.00 0.00 4.26
402 405 2.600769 AGGGAGGCTTCGTCGTGT 60.601 61.111 0.00 0.00 0.00 4.49
404 407 1.469335 TTTGAGGGAGGCTTCGTCGT 61.469 55.000 10.70 0.00 0.00 4.34
406 409 0.608640 TCTTTGAGGGAGGCTTCGTC 59.391 55.000 8.57 8.57 0.00 4.20
408 411 2.284190 GATTCTTTGAGGGAGGCTTCG 58.716 52.381 0.00 0.00 0.00 3.79
441 448 2.065906 TTTTTCAAGGACGGTGCGGC 62.066 55.000 0.00 0.00 0.00 6.53
454 461 0.316841 GGCGCATGGGTTCTTTTTCA 59.683 50.000 10.83 0.00 0.00 2.69
455 462 0.389817 GGGCGCATGGGTTCTTTTTC 60.390 55.000 10.83 0.00 0.00 2.29
458 465 3.061848 CGGGCGCATGGGTTCTTT 61.062 61.111 10.83 0.00 0.00 2.52
519 558 0.324091 ACTCAATACGGTCGGGAGGT 60.324 55.000 7.48 0.00 0.00 3.85
535 574 0.603975 GGGGACTGTTGTGCTGACTC 60.604 60.000 0.00 0.00 34.78 3.36
782 830 1.398692 GTGTCAGCTAGGAGGGAGAG 58.601 60.000 0.00 0.00 0.00 3.20
783 831 0.394488 CGTGTCAGCTAGGAGGGAGA 60.394 60.000 0.00 0.00 0.00 3.71
784 832 0.394488 TCGTGTCAGCTAGGAGGGAG 60.394 60.000 0.00 0.00 0.00 4.30
785 833 0.680280 GTCGTGTCAGCTAGGAGGGA 60.680 60.000 0.00 0.00 0.00 4.20
786 834 0.965866 TGTCGTGTCAGCTAGGAGGG 60.966 60.000 0.00 0.00 0.00 4.30
787 835 0.453793 CTGTCGTGTCAGCTAGGAGG 59.546 60.000 0.00 0.00 0.00 4.30
788 836 1.454201 TCTGTCGTGTCAGCTAGGAG 58.546 55.000 0.00 0.00 35.63 3.69
789 837 1.540267 GTTCTGTCGTGTCAGCTAGGA 59.460 52.381 0.00 0.00 35.63 2.94
790 838 1.402984 GGTTCTGTCGTGTCAGCTAGG 60.403 57.143 0.00 0.00 35.63 3.02
791 839 1.269723 TGGTTCTGTCGTGTCAGCTAG 59.730 52.381 0.00 0.00 35.63 3.42
792 840 1.324383 TGGTTCTGTCGTGTCAGCTA 58.676 50.000 0.00 0.00 35.63 3.32
793 841 0.681733 ATGGTTCTGTCGTGTCAGCT 59.318 50.000 0.00 0.00 35.63 4.24
794 842 1.461127 GAATGGTTCTGTCGTGTCAGC 59.539 52.381 0.00 0.00 35.63 4.26
795 843 2.069273 GGAATGGTTCTGTCGTGTCAG 58.931 52.381 0.00 0.00 36.85 3.51
796 844 1.691976 AGGAATGGTTCTGTCGTGTCA 59.308 47.619 0.00 0.00 0.00 3.58
797 845 2.069273 CAGGAATGGTTCTGTCGTGTC 58.931 52.381 0.00 0.00 0.00 3.67
798 846 1.416401 ACAGGAATGGTTCTGTCGTGT 59.584 47.619 0.00 0.00 39.77 4.49
807 855 1.991230 CGGGGAGACAGGAATGGTT 59.009 57.895 0.00 0.00 0.00 3.67
923 1202 0.329261 TCTTAGGAACCGAGGGACGA 59.671 55.000 0.00 0.00 45.77 4.20
942 1221 2.024176 ACACGAACAAACTCTGCTGT 57.976 45.000 0.00 0.00 0.00 4.40
958 1237 2.782192 CCGTCGATCGATCAACTAACAC 59.218 50.000 22.50 3.59 42.86 3.32
959 1238 2.421073 ACCGTCGATCGATCAACTAACA 59.579 45.455 22.50 0.00 42.86 2.41
962 1241 1.259770 CGACCGTCGATCGATCAACTA 59.740 52.381 22.50 4.58 43.74 2.24
963 1242 0.027716 CGACCGTCGATCGATCAACT 59.972 55.000 22.50 1.95 43.74 3.16
998 1280 2.033141 AGTTGCTCCGCTGCATGT 59.967 55.556 0.00 0.00 42.96 3.21
1145 1436 4.344865 TGCCGGCCTTGACCTTCC 62.345 66.667 26.77 0.00 0.00 3.46
1283 1574 2.502213 TATATCCACACGCACGAAGG 57.498 50.000 0.00 0.00 0.00 3.46
1285 1576 4.218852 TCCATATATATCCACACGCACGAA 59.781 41.667 0.00 0.00 0.00 3.85
1354 2022 0.390472 GAGCAAGCTAAGCAGTCCGT 60.390 55.000 12.91 0.00 0.00 4.69
1427 2096 8.514594 TGAAACAGTGATCAAATATGAAGAACC 58.485 33.333 0.00 0.00 39.49 3.62
1495 2169 7.616542 TGGAGATGAATCAAGGATCAATTTTGA 59.383 33.333 0.00 0.00 42.14 2.69
1496 2170 7.778083 TGGAGATGAATCAAGGATCAATTTTG 58.222 34.615 0.00 0.00 0.00 2.44
1610 2286 0.038343 CCGGGTGCACATTTTTCAGG 60.038 55.000 20.43 6.24 0.00 3.86
1612 2288 1.271934 CATCCGGGTGCACATTTTTCA 59.728 47.619 20.43 0.00 0.00 2.69
1708 2384 1.851658 AAATTTGCACGCAGGTCAAC 58.148 45.000 0.00 0.00 0.00 3.18
1714 2390 3.490155 TCATCACAAAAATTTGCACGCAG 59.510 39.130 5.82 0.00 41.79 5.18
1729 2405 9.227777 GATCTCCATGAATATGATTTCATCACA 57.772 33.333 0.00 0.00 42.90 3.58
1847 2524 9.255304 GGTAAGCAATTCAAACTATTTGTGAAA 57.745 29.630 1.50 0.00 41.36 2.69
1848 2525 8.417106 TGGTAAGCAATTCAAACTATTTGTGAA 58.583 29.630 1.50 0.00 41.36 3.18
1849 2526 7.865385 GTGGTAAGCAATTCAAACTATTTGTGA 59.135 33.333 1.50 0.00 41.36 3.58
1850 2527 7.651304 TGTGGTAAGCAATTCAAACTATTTGTG 59.349 33.333 1.50 0.00 41.36 3.33
1851 2528 7.721402 TGTGGTAAGCAATTCAAACTATTTGT 58.279 30.769 1.50 0.00 41.36 2.83
1852 2529 8.649841 CATGTGGTAAGCAATTCAAACTATTTG 58.350 33.333 0.00 0.00 41.96 2.32
1853 2530 8.367156 ACATGTGGTAAGCAATTCAAACTATTT 58.633 29.630 0.00 0.00 0.00 1.40
1854 2531 7.814107 CACATGTGGTAAGCAATTCAAACTATT 59.186 33.333 18.51 0.00 0.00 1.73
1855 2532 7.039784 ACACATGTGGTAAGCAATTCAAACTAT 60.040 33.333 28.64 0.00 34.19 2.12
1856 2533 6.264292 ACACATGTGGTAAGCAATTCAAACTA 59.736 34.615 28.64 0.00 34.19 2.24
1857 2534 5.068987 ACACATGTGGTAAGCAATTCAAACT 59.931 36.000 28.64 0.00 34.19 2.66
1858 2535 5.288804 ACACATGTGGTAAGCAATTCAAAC 58.711 37.500 28.64 0.00 34.19 2.93
1859 2536 5.068329 TGACACATGTGGTAAGCAATTCAAA 59.932 36.000 28.64 0.00 34.19 2.69
1860 2537 4.582240 TGACACATGTGGTAAGCAATTCAA 59.418 37.500 28.64 3.73 34.19 2.69
1861 2538 4.140536 TGACACATGTGGTAAGCAATTCA 58.859 39.130 28.64 16.61 34.19 2.57
1862 2539 4.764679 TGACACATGTGGTAAGCAATTC 57.235 40.909 28.64 14.32 34.19 2.17
1863 2540 4.523943 ACATGACACATGTGGTAAGCAATT 59.476 37.500 28.64 5.13 34.19 2.32
1864 2541 4.081406 ACATGACACATGTGGTAAGCAAT 58.919 39.130 28.64 5.90 34.19 3.56
1865 2542 3.252944 CACATGACACATGTGGTAAGCAA 59.747 43.478 28.64 7.21 44.04 3.91
1866 2543 2.813172 CACATGACACATGTGGTAAGCA 59.187 45.455 28.64 17.63 44.04 3.91
1867 2544 3.476295 CACATGACACATGTGGTAAGC 57.524 47.619 28.64 13.03 44.04 3.09
1873 2550 3.002791 GGTCTACCACATGACACATGTG 58.997 50.000 27.39 27.39 46.49 3.21
1874 2551 2.906389 AGGTCTACCACATGACACATGT 59.094 45.455 10.94 10.94 38.89 3.21
1875 2552 3.525537 GAGGTCTACCACATGACACATG 58.474 50.000 0.00 9.72 38.89 3.21
1876 2553 2.501723 GGAGGTCTACCACATGACACAT 59.498 50.000 0.00 0.00 38.89 3.21
1877 2554 1.899814 GGAGGTCTACCACATGACACA 59.100 52.381 0.00 0.00 38.89 3.72
1878 2555 1.899814 TGGAGGTCTACCACATGACAC 59.100 52.381 0.00 0.00 38.89 3.67
1879 2556 2.319025 TGGAGGTCTACCACATGACA 57.681 50.000 0.00 0.00 38.89 3.58
1886 2563 6.157820 TCAATCATATTTGTGGAGGTCTACCA 59.842 38.462 1.26 0.00 38.89 3.25
1887 2564 6.591935 TCAATCATATTTGTGGAGGTCTACC 58.408 40.000 0.00 0.00 0.00 3.18
1888 2565 8.682936 ATTCAATCATATTTGTGGAGGTCTAC 57.317 34.615 0.00 0.00 0.00 2.59
1889 2566 8.493607 TGATTCAATCATATTTGTGGAGGTCTA 58.506 33.333 0.00 0.00 33.59 2.59
1890 2567 7.284034 GTGATTCAATCATATTTGTGGAGGTCT 59.716 37.037 2.67 0.00 42.04 3.85
1891 2568 7.420800 GTGATTCAATCATATTTGTGGAGGTC 58.579 38.462 2.67 0.00 42.04 3.85
1892 2569 6.322201 GGTGATTCAATCATATTTGTGGAGGT 59.678 38.462 2.67 0.00 42.04 3.85
1893 2570 6.321945 TGGTGATTCAATCATATTTGTGGAGG 59.678 38.462 2.67 0.00 42.04 4.30
1894 2571 7.337480 TGGTGATTCAATCATATTTGTGGAG 57.663 36.000 2.67 0.00 42.04 3.86
1895 2572 7.715266 TTGGTGATTCAATCATATTTGTGGA 57.285 32.000 2.67 0.00 42.04 4.02
1896 2573 8.774890 TTTTGGTGATTCAATCATATTTGTGG 57.225 30.769 2.67 0.00 42.04 4.17
1910 2587 3.181518 CCGCATGCAAATTTTGGTGATTC 60.182 43.478 19.57 0.00 0.00 2.52
1912 2589 2.028294 TCCGCATGCAAATTTTGGTGAT 60.028 40.909 19.57 0.00 0.00 3.06
1913 2590 1.342496 TCCGCATGCAAATTTTGGTGA 59.658 42.857 19.57 0.00 0.00 4.02
1914 2591 1.793258 TCCGCATGCAAATTTTGGTG 58.207 45.000 19.57 0.00 0.00 4.17
1915 2592 2.766345 ATCCGCATGCAAATTTTGGT 57.234 40.000 19.57 0.00 0.00 3.67
1917 2594 4.923893 TCTCTATCCGCATGCAAATTTTG 58.076 39.130 19.57 4.72 0.00 2.44
1918 2595 5.343249 GTTCTCTATCCGCATGCAAATTTT 58.657 37.500 19.57 0.00 0.00 1.82
1985 2662 9.593134 ACTTCTGCTATGACAGTAAAATCTAAG 57.407 33.333 0.00 0.00 38.84 2.18
2000 2677 8.484641 TCTCAAACTCAAATACTTCTGCTATG 57.515 34.615 0.00 0.00 0.00 2.23
2001 2678 9.678260 AATCTCAAACTCAAATACTTCTGCTAT 57.322 29.630 0.00 0.00 0.00 2.97
2003 2680 7.992754 AATCTCAAACTCAAATACTTCTGCT 57.007 32.000 0.00 0.00 0.00 4.24
2004 2681 9.155975 TCTAATCTCAAACTCAAATACTTCTGC 57.844 33.333 0.00 0.00 0.00 4.26
2010 2688 9.436957 TGTCCTTCTAATCTCAAACTCAAATAC 57.563 33.333 0.00 0.00 0.00 1.89
2019 2697 6.490040 CCCAAAAGTGTCCTTCTAATCTCAAA 59.510 38.462 0.00 0.00 0.00 2.69
2029 2707 1.202940 AGCCTCCCAAAAGTGTCCTTC 60.203 52.381 0.00 0.00 0.00 3.46
2046 2724 2.106511 TCCATGGTGCCTCTAAATAGCC 59.893 50.000 12.58 0.00 0.00 3.93
2047 2725 3.492102 TCCATGGTGCCTCTAAATAGC 57.508 47.619 12.58 0.00 0.00 2.97
2061 2740 3.056607 GGTGACCAAAAGTTGATCCATGG 60.057 47.826 4.97 4.97 0.00 3.66
2063 2742 4.118168 AGGTGACCAAAAGTTGATCCAT 57.882 40.909 3.63 0.00 0.00 3.41
2064 2743 3.593442 AGGTGACCAAAAGTTGATCCA 57.407 42.857 3.63 0.00 0.00 3.41
2078 2757 6.472686 AGATAGTATGTTGGAGAAGGTGAC 57.527 41.667 0.00 0.00 0.00 3.67
2122 2801 0.320334 CATGGTACCACGTGTGCAGA 60.320 55.000 19.09 0.00 0.00 4.26
2124 2803 1.448069 ACATGGTACCACGTGTGCA 59.552 52.632 19.09 0.00 39.04 4.57
2169 2848 3.632145 GTCAAAGGAGTGGAAGCAAAAGA 59.368 43.478 0.00 0.00 0.00 2.52
2170 2849 3.381272 TGTCAAAGGAGTGGAAGCAAAAG 59.619 43.478 0.00 0.00 0.00 2.27
2183 2862 2.573462 AGCTAGCTCCAATGTCAAAGGA 59.427 45.455 12.68 0.00 0.00 3.36
2192 2871 1.704007 GGAGGCCAGCTAGCTCCAAT 61.704 60.000 21.22 6.94 33.11 3.16
2194 2873 2.765807 GGAGGCCAGCTAGCTCCA 60.766 66.667 21.22 0.00 33.11 3.86
2206 2885 2.123428 AATGATTGGCAGCGGAGGC 61.123 57.895 0.00 0.00 40.37 4.70
2212 2891 2.357009 CCAGTAGACAATGATTGGCAGC 59.643 50.000 14.31 5.29 42.71 5.25
2215 2894 4.142609 TCTCCAGTAGACAATGATTGGC 57.857 45.455 10.27 6.50 39.66 4.52
2245 2924 4.314440 TCCACTGCCCACGTCAGC 62.314 66.667 2.84 1.12 35.04 4.26
2246 2925 2.047844 CTCCACTGCCCACGTCAG 60.048 66.667 1.45 1.45 37.56 3.51


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

AutoCloner maintained by Alex Coulton.