Multiple sequence alignment - TraesCS2A01G155000

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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 TraesCS2A01G155000 chr2A 100.000 2237 0 0 1 2237 102133671 102131435 0.000000e+00 4132
1 TraesCS2A01G155000 chr2A 87.500 256 24 6 267 517 102679395 102679143 2.810000e-74 289
2 TraesCS2A01G155000 chr2A 84.397 282 30 12 267 538 102043424 102043701 4.740000e-67 265
3 TraesCS2A01G155000 chr2A 96.855 159 4 1 1 158 585678752 585678910 4.740000e-67 265
4 TraesCS2A01G155000 chr2D 94.088 1573 69 10 644 2216 103129733 103128185 0.000000e+00 2368
5 TraesCS2A01G155000 chr2D 89.412 255 21 4 267 517 106265626 106265374 1.290000e-82 316
6 TraesCS2A01G155000 chr2D 81.842 380 44 16 267 637 103130164 103129801 1.680000e-76 296
7 TraesCS2A01G155000 chr2D 87.764 237 18 8 288 518 102944005 102944236 1.320000e-67 267
8 TraesCS2A01G155000 chr2D 85.950 242 27 6 280 517 181440375 181440613 3.690000e-63 252
9 TraesCS2A01G155000 chr2B 93.215 1577 94 10 644 2217 154595168 154593602 0.000000e+00 2307
10 TraesCS2A01G155000 chr2B 84.564 298 34 8 267 555 154595637 154595343 3.640000e-73 285
11 TraesCS2A01G155000 chr2B 88.841 233 21 4 288 517 154907063 154906833 4.700000e-72 281
12 TraesCS2A01G155000 chr2B 85.098 255 31 6 267 517 154930240 154929989 1.030000e-63 254
13 TraesCS2A01G155000 chr5A 96.226 159 5 1 1 158 115628633 115628791 2.200000e-65 259


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 TraesCS2A01G155000 chr2A 102131435 102133671 2236 True 4132 4132 100.0000 1 2237 1 chr2A.!!$R1 2236
1 TraesCS2A01G155000 chr2D 103128185 103130164 1979 True 1332 2368 87.9650 267 2216 2 chr2D.!!$R2 1949
2 TraesCS2A01G155000 chr2B 154593602 154595637 2035 True 1296 2307 88.8895 267 2217 2 chr2B.!!$R3 1950

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
94 95 0.034059 CGGGCTGATAGGATCACCAC 59.966 60.0 0.0 0.0 38.94 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1241 1361 1.202867 GGAGAAGATCATTGGGAGGGC 60.203 57.143 0.0 0.0 0.0 5.19 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.840831 TTGAGCTGATCTTGTCCGG 57.159 52.632 0.00 0.00 0.00 5.14
19 20 0.391661 TTGAGCTGATCTTGTCCGGC 60.392 55.000 0.00 0.00 0.00 6.13
20 21 1.522580 GAGCTGATCTTGTCCGGCC 60.523 63.158 0.00 0.00 0.00 6.13
21 22 2.514824 GCTGATCTTGTCCGGCCC 60.515 66.667 0.00 0.00 0.00 5.80
22 23 2.190578 CTGATCTTGTCCGGCCCC 59.809 66.667 0.00 0.00 0.00 5.80
23 24 2.609299 TGATCTTGTCCGGCCCCA 60.609 61.111 0.00 0.00 0.00 4.96
24 25 2.196997 CTGATCTTGTCCGGCCCCAA 62.197 60.000 0.00 0.00 0.00 4.12
25 26 1.227383 GATCTTGTCCGGCCCCAAT 59.773 57.895 0.00 0.00 0.00 3.16
26 27 0.819666 GATCTTGTCCGGCCCCAATC 60.820 60.000 0.00 0.00 0.00 2.67
27 28 1.281925 ATCTTGTCCGGCCCCAATCT 61.282 55.000 0.00 0.00 0.00 2.40
28 29 1.000896 CTTGTCCGGCCCCAATCTT 60.001 57.895 0.00 0.00 0.00 2.40
29 30 0.611896 CTTGTCCGGCCCCAATCTTT 60.612 55.000 0.00 0.00 0.00 2.52
30 31 0.610785 TTGTCCGGCCCCAATCTTTC 60.611 55.000 0.00 0.00 0.00 2.62
31 32 1.303282 GTCCGGCCCCAATCTTTCT 59.697 57.895 0.00 0.00 0.00 2.52
32 33 0.748367 GTCCGGCCCCAATCTTTCTC 60.748 60.000 0.00 0.00 0.00 2.87
33 34 1.453928 CCGGCCCCAATCTTTCTCC 60.454 63.158 0.00 0.00 0.00 3.71
34 35 1.453928 CGGCCCCAATCTTTCTCCC 60.454 63.158 0.00 0.00 0.00 4.30
35 36 1.926426 CGGCCCCAATCTTTCTCCCT 61.926 60.000 0.00 0.00 0.00 4.20
36 37 0.396278 GGCCCCAATCTTTCTCCCTG 60.396 60.000 0.00 0.00 0.00 4.45
37 38 0.332972 GCCCCAATCTTTCTCCCTGT 59.667 55.000 0.00 0.00 0.00 4.00
38 39 1.272704 GCCCCAATCTTTCTCCCTGTT 60.273 52.381 0.00 0.00 0.00 3.16
39 40 2.450476 CCCCAATCTTTCTCCCTGTTG 58.550 52.381 0.00 0.00 0.00 3.33
40 41 2.450476 CCCAATCTTTCTCCCTGTTGG 58.550 52.381 0.00 0.00 36.68 3.77
41 42 1.821136 CCAATCTTTCTCCCTGTTGGC 59.179 52.381 0.00 0.00 30.91 4.52
42 43 1.821136 CAATCTTTCTCCCTGTTGGCC 59.179 52.381 0.00 0.00 0.00 5.36
43 44 1.376649 ATCTTTCTCCCTGTTGGCCT 58.623 50.000 3.32 0.00 0.00 5.19
44 45 0.401738 TCTTTCTCCCTGTTGGCCTG 59.598 55.000 3.32 0.00 0.00 4.85
45 46 0.111253 CTTTCTCCCTGTTGGCCTGT 59.889 55.000 3.32 0.00 0.00 4.00
46 47 0.110486 TTTCTCCCTGTTGGCCTGTC 59.890 55.000 3.32 0.00 0.00 3.51
47 48 1.779061 TTCTCCCTGTTGGCCTGTCC 61.779 60.000 3.32 0.00 0.00 4.02
48 49 2.121963 TCCCTGTTGGCCTGTCCT 60.122 61.111 3.32 0.00 35.26 3.85
49 50 2.034687 CCCTGTTGGCCTGTCCTG 59.965 66.667 3.32 0.00 35.26 3.86
50 51 2.528818 CCCTGTTGGCCTGTCCTGA 61.529 63.158 3.32 0.00 35.26 3.86
51 52 1.302832 CCTGTTGGCCTGTCCTGAC 60.303 63.158 3.32 0.00 35.26 3.51
52 53 1.302832 CTGTTGGCCTGTCCTGACC 60.303 63.158 3.32 0.00 35.26 4.02
53 54 2.034221 GTTGGCCTGTCCTGACCC 59.966 66.667 3.32 0.00 35.26 4.46
54 55 2.121963 TTGGCCTGTCCTGACCCT 60.122 61.111 3.32 0.00 35.26 4.34
55 56 2.224159 TTGGCCTGTCCTGACCCTC 61.224 63.158 3.32 0.00 35.26 4.30
56 57 2.284995 GGCCTGTCCTGACCCTCT 60.285 66.667 0.00 0.00 0.00 3.69
57 58 1.920835 GGCCTGTCCTGACCCTCTT 60.921 63.158 0.00 0.00 0.00 2.85
58 59 1.599576 GCCTGTCCTGACCCTCTTC 59.400 63.158 0.00 0.00 0.00 2.87
59 60 1.893786 CCTGTCCTGACCCTCTTCG 59.106 63.158 0.00 0.00 0.00 3.79
60 61 1.608717 CCTGTCCTGACCCTCTTCGG 61.609 65.000 0.00 0.00 0.00 4.30
61 62 0.900647 CTGTCCTGACCCTCTTCGGT 60.901 60.000 0.00 0.00 39.49 4.69
71 72 3.951663 ACCCTCTTCGGTCTTATTTTGG 58.048 45.455 0.00 0.00 0.00 3.28
72 73 2.683362 CCCTCTTCGGTCTTATTTTGGC 59.317 50.000 0.00 0.00 0.00 4.52
73 74 2.351726 CCTCTTCGGTCTTATTTTGGCG 59.648 50.000 0.00 0.00 0.00 5.69
74 75 2.351726 CTCTTCGGTCTTATTTTGGCGG 59.648 50.000 0.00 0.00 0.00 6.13
75 76 0.806241 TTCGGTCTTATTTTGGCGGC 59.194 50.000 0.00 0.00 0.00 6.53
76 77 1.061887 CGGTCTTATTTTGGCGGCG 59.938 57.895 0.51 0.51 0.00 6.46
77 78 1.431845 GGTCTTATTTTGGCGGCGG 59.568 57.895 9.78 0.00 0.00 6.13
78 79 1.431845 GTCTTATTTTGGCGGCGGG 59.568 57.895 9.78 0.00 0.00 6.13
79 80 2.104132 CTTATTTTGGCGGCGGGC 59.896 61.111 9.78 11.16 42.51 6.13
80 81 2.361865 TTATTTTGGCGGCGGGCT 60.362 55.556 18.59 1.06 42.94 5.19
81 82 2.612219 CTTATTTTGGCGGCGGGCTG 62.612 60.000 18.59 0.00 42.94 4.85
82 83 3.630298 TATTTTGGCGGCGGGCTGA 62.630 57.895 18.59 5.01 42.94 4.26
83 84 2.902423 TATTTTGGCGGCGGGCTGAT 62.902 55.000 18.59 11.58 42.94 2.90
84 85 2.902423 ATTTTGGCGGCGGGCTGATA 62.902 55.000 18.59 3.84 42.94 2.15
85 86 4.545706 TTGGCGGCGGGCTGATAG 62.546 66.667 18.59 0.00 42.94 2.08
88 89 4.008933 GCGGCGGGCTGATAGGAT 62.009 66.667 9.78 0.00 39.11 3.24
89 90 2.262915 CGGCGGGCTGATAGGATC 59.737 66.667 0.00 0.00 0.00 3.36
90 91 2.574018 CGGCGGGCTGATAGGATCA 61.574 63.158 0.00 0.00 37.76 2.92
91 92 1.004440 GGCGGGCTGATAGGATCAC 60.004 63.158 0.00 0.00 35.06 3.06
92 93 1.004440 GCGGGCTGATAGGATCACC 60.004 63.158 0.00 0.00 35.06 4.02
93 94 1.758440 GCGGGCTGATAGGATCACCA 61.758 60.000 0.00 0.00 38.94 4.17
94 95 0.034059 CGGGCTGATAGGATCACCAC 59.966 60.000 0.00 0.00 38.94 4.16
95 96 1.428869 GGGCTGATAGGATCACCACT 58.571 55.000 0.00 0.00 38.94 4.00
96 97 1.071385 GGGCTGATAGGATCACCACTG 59.929 57.143 0.00 0.00 38.94 3.66
97 98 1.542108 GGCTGATAGGATCACCACTGC 60.542 57.143 0.00 0.00 38.94 4.40
98 99 1.542108 GCTGATAGGATCACCACTGCC 60.542 57.143 0.00 0.00 38.94 4.85
99 100 2.045524 CTGATAGGATCACCACTGCCT 58.954 52.381 0.00 0.00 38.94 4.75
100 101 2.036992 CTGATAGGATCACCACTGCCTC 59.963 54.545 0.00 0.00 38.94 4.70
101 102 1.346068 GATAGGATCACCACTGCCTCC 59.654 57.143 0.00 0.00 38.94 4.30
102 103 0.339859 TAGGATCACCACTGCCTCCT 59.660 55.000 0.00 0.00 39.60 3.69
103 104 0.339859 AGGATCACCACTGCCTCCTA 59.660 55.000 0.00 0.00 34.59 2.94
104 105 1.061812 AGGATCACCACTGCCTCCTAT 60.062 52.381 0.00 0.00 34.59 2.57
105 106 1.071385 GGATCACCACTGCCTCCTATG 59.929 57.143 0.00 0.00 35.97 2.23
106 107 1.071385 GATCACCACTGCCTCCTATGG 59.929 57.143 0.00 0.00 38.26 2.74
116 117 2.058593 CCTCCTATGGCTTTTCCCAC 57.941 55.000 0.00 0.00 37.79 4.61
117 118 1.284785 CCTCCTATGGCTTTTCCCACA 59.715 52.381 0.00 0.00 37.79 4.17
118 119 2.648059 CTCCTATGGCTTTTCCCACAG 58.352 52.381 0.00 0.00 37.79 3.66
119 120 1.767759 CCTATGGCTTTTCCCACAGG 58.232 55.000 0.00 0.00 42.75 4.00
120 121 2.806945 CTATGGCTTTTCCCACAGGA 57.193 50.000 0.00 0.00 41.88 3.86
142 143 6.183309 GAACTATTTCCAAGCCAGTAGTTG 57.817 41.667 0.00 0.00 33.82 3.16
160 161 4.406001 GTTGGAGCTACAACTACTTTGC 57.594 45.455 30.83 5.26 45.49 3.68
161 162 4.065789 GTTGGAGCTACAACTACTTTGCT 58.934 43.478 30.83 0.00 45.49 3.91
162 163 3.664107 TGGAGCTACAACTACTTTGCTG 58.336 45.455 0.00 0.00 39.01 4.41
163 164 3.003480 GGAGCTACAACTACTTTGCTGG 58.997 50.000 0.00 0.00 39.01 4.85
164 165 3.306780 GGAGCTACAACTACTTTGCTGGA 60.307 47.826 0.00 0.00 39.01 3.86
165 166 4.315803 GAGCTACAACTACTTTGCTGGAA 58.684 43.478 0.00 0.00 39.01 3.53
166 167 4.911390 AGCTACAACTACTTTGCTGGAAT 58.089 39.130 0.00 0.00 39.01 3.01
167 168 4.697352 AGCTACAACTACTTTGCTGGAATG 59.303 41.667 0.00 0.00 39.01 2.67
168 169 4.142600 GCTACAACTACTTTGCTGGAATGG 60.143 45.833 0.30 0.00 39.01 3.16
169 170 2.558359 ACAACTACTTTGCTGGAATGGC 59.442 45.455 0.30 0.00 39.01 4.40
170 171 2.557924 CAACTACTTTGCTGGAATGGCA 59.442 45.455 0.00 0.00 37.97 4.92
171 172 3.091633 ACTACTTTGCTGGAATGGCAT 57.908 42.857 0.00 0.00 39.54 4.40
172 173 4.235079 ACTACTTTGCTGGAATGGCATA 57.765 40.909 0.00 0.00 39.54 3.14
173 174 4.796606 ACTACTTTGCTGGAATGGCATAT 58.203 39.130 0.00 0.00 39.54 1.78
174 175 5.940617 ACTACTTTGCTGGAATGGCATATA 58.059 37.500 0.00 0.00 39.54 0.86
175 176 6.000219 ACTACTTTGCTGGAATGGCATATAG 59.000 40.000 0.00 0.63 39.54 1.31
176 177 4.796606 ACTTTGCTGGAATGGCATATAGT 58.203 39.130 0.00 0.00 39.54 2.12
177 178 5.940617 ACTTTGCTGGAATGGCATATAGTA 58.059 37.500 0.00 0.00 39.54 1.82
178 179 5.765182 ACTTTGCTGGAATGGCATATAGTAC 59.235 40.000 0.00 0.00 39.54 2.73
179 180 5.567037 TTGCTGGAATGGCATATAGTACT 57.433 39.130 0.00 0.00 39.54 2.73
180 181 6.680148 TTGCTGGAATGGCATATAGTACTA 57.320 37.500 4.77 4.77 39.54 1.82
181 182 6.037786 TGCTGGAATGGCATATAGTACTAC 57.962 41.667 4.31 0.00 34.56 2.73
182 183 5.780282 TGCTGGAATGGCATATAGTACTACT 59.220 40.000 4.31 0.00 34.56 2.57
183 184 6.102663 GCTGGAATGGCATATAGTACTACTG 58.897 44.000 4.31 7.29 0.00 2.74
184 185 6.037786 TGGAATGGCATATAGTACTACTGC 57.962 41.667 22.43 22.43 0.00 4.40
185 186 5.780282 TGGAATGGCATATAGTACTACTGCT 59.220 40.000 26.36 14.83 33.43 4.24
186 187 6.270000 TGGAATGGCATATAGTACTACTGCTT 59.730 38.462 26.36 18.73 33.43 3.91
187 188 7.162082 GGAATGGCATATAGTACTACTGCTTT 58.838 38.462 26.36 21.76 33.43 3.51
188 189 7.118390 GGAATGGCATATAGTACTACTGCTTTG 59.882 40.741 26.36 11.22 33.43 2.77
189 190 6.479972 TGGCATATAGTACTACTGCTTTGT 57.520 37.500 26.36 6.47 33.43 2.83
190 191 6.884832 TGGCATATAGTACTACTGCTTTGTT 58.115 36.000 26.36 5.88 33.43 2.83
191 192 7.335627 TGGCATATAGTACTACTGCTTTGTTT 58.664 34.615 26.36 5.29 33.43 2.83
192 193 7.279981 TGGCATATAGTACTACTGCTTTGTTTG 59.720 37.037 26.36 9.35 33.43 2.93
193 194 7.254795 GGCATATAGTACTACTGCTTTGTTTGG 60.255 40.741 26.36 2.44 33.43 3.28
194 195 7.254795 GCATATAGTACTACTGCTTTGTTTGGG 60.255 40.741 22.91 0.00 0.00 4.12
195 196 3.146847 AGTACTACTGCTTTGTTTGGGC 58.853 45.455 0.00 0.00 0.00 5.36
196 197 1.328279 ACTACTGCTTTGTTTGGGCC 58.672 50.000 0.00 0.00 0.00 5.80
197 198 1.327303 CTACTGCTTTGTTTGGGCCA 58.673 50.000 0.00 0.00 0.00 5.36
198 199 1.895131 CTACTGCTTTGTTTGGGCCAT 59.105 47.619 7.26 0.00 0.00 4.40
199 200 1.130777 ACTGCTTTGTTTGGGCCATT 58.869 45.000 7.26 0.00 0.00 3.16
200 201 1.202675 ACTGCTTTGTTTGGGCCATTG 60.203 47.619 7.26 0.00 0.00 2.82
201 202 0.108207 TGCTTTGTTTGGGCCATTGG 59.892 50.000 7.26 0.00 0.00 3.16
211 212 3.354678 GCCATTGGCGTCACTGTT 58.645 55.556 12.82 0.00 39.62 3.16
212 213 1.081242 GCCATTGGCGTCACTGTTG 60.081 57.895 12.82 0.00 39.62 3.33
213 214 1.795170 GCCATTGGCGTCACTGTTGT 61.795 55.000 12.82 0.00 39.62 3.32
214 215 0.040157 CCATTGGCGTCACTGTTGTG 60.040 55.000 6.61 0.00 45.07 3.33
215 216 0.661187 CATTGGCGTCACTGTTGTGC 60.661 55.000 0.00 0.00 43.49 4.57
216 217 1.795170 ATTGGCGTCACTGTTGTGCC 61.795 55.000 0.00 6.92 43.49 5.01
217 218 2.591715 GGCGTCACTGTTGTGCCT 60.592 61.111 6.67 0.00 43.49 4.75
218 219 1.301401 GGCGTCACTGTTGTGCCTA 60.301 57.895 6.67 0.00 43.49 3.93
219 220 0.673644 GGCGTCACTGTTGTGCCTAT 60.674 55.000 6.67 0.00 43.49 2.57
220 221 0.443869 GCGTCACTGTTGTGCCTATG 59.556 55.000 0.00 0.00 43.49 2.23
221 222 1.078709 CGTCACTGTTGTGCCTATGG 58.921 55.000 0.00 0.00 43.49 2.74
222 223 1.453155 GTCACTGTTGTGCCTATGGG 58.547 55.000 0.00 0.00 43.49 4.00
239 240 4.777384 GCCTTTTGCCTGTTTGGG 57.223 55.556 0.00 0.00 36.00 4.12
246 247 2.743060 GCCTGTTTGGGCCTTTGG 59.257 61.111 4.53 1.04 45.92 3.28
259 260 3.339731 TTTGGCGTCAAAGGCGAG 58.660 55.556 11.91 0.00 37.89 5.03
260 261 2.258013 TTTGGCGTCAAAGGCGAGG 61.258 57.895 11.91 0.00 37.89 4.63
261 262 2.668185 TTTGGCGTCAAAGGCGAGGA 62.668 55.000 11.91 0.00 37.89 3.71
262 263 2.815647 GGCGTCAAAGGCGAGGAG 60.816 66.667 0.00 0.00 0.00 3.69
263 264 2.815647 GCGTCAAAGGCGAGGAGG 60.816 66.667 0.00 0.00 0.00 4.30
264 265 2.125512 CGTCAAAGGCGAGGAGGG 60.126 66.667 0.00 0.00 0.00 4.30
265 266 2.436824 GTCAAAGGCGAGGAGGGC 60.437 66.667 0.00 0.00 0.00 5.19
269 270 4.722535 AAGGCGAGGAGGGCAGGA 62.723 66.667 0.00 0.00 34.40 3.86
297 298 1.129811 GCCGTTTTGATTAGTCCCACG 59.870 52.381 0.00 0.00 0.00 4.94
319 320 2.373707 CCTGGGCAAGGGAGAGAGG 61.374 68.421 0.00 0.00 43.15 3.69
322 323 2.041265 GGCAAGGGAGAGAGGGGA 59.959 66.667 0.00 0.00 0.00 4.81
323 324 1.616628 GGCAAGGGAGAGAGGGGAA 60.617 63.158 0.00 0.00 0.00 3.97
329 332 1.313129 GGAGAGAGGGGAAGGAGCT 59.687 63.158 0.00 0.00 0.00 4.09
342 346 1.428869 AGGAGCTGGGCTACATAAGG 58.571 55.000 4.51 0.00 42.99 2.69
344 348 0.398318 GAGCTGGGCTACATAAGGGG 59.602 60.000 0.00 0.00 39.88 4.79
346 350 1.456287 CTGGGCTACATAAGGGGGC 59.544 63.158 0.00 0.00 0.00 5.80
349 353 1.123246 GGGCTACATAAGGGGGCGTA 61.123 60.000 0.00 0.00 0.00 4.42
378 382 3.663176 GAAAGGCACGCAGCTGCA 61.663 61.111 36.03 0.00 44.79 4.41
380 384 2.482296 GAAAGGCACGCAGCTGCATT 62.482 55.000 36.03 21.01 44.79 3.56
503 510 1.149133 AGAAGGCCCCACCAATCCTT 61.149 55.000 0.00 0.00 43.14 3.36
509 516 2.434336 GGCCCCACCAATCCTTAATTTC 59.566 50.000 0.00 0.00 38.86 2.17
522 533 6.683090 TCCTTAATTTCAAATTTTGTCGCG 57.317 33.333 0.00 0.00 0.00 5.87
528 539 4.785669 TTCAAATTTTGTCGCGCATTTT 57.214 31.818 8.75 1.60 0.00 1.82
538 549 4.480541 TGTCGCGCATTTTGACAAAATAT 58.519 34.783 22.46 3.63 38.97 1.28
540 551 3.856521 TCGCGCATTTTGACAAAATATGG 59.143 39.130 22.46 15.88 38.97 2.74
545 556 6.183360 GCGCATTTTGACAAAATATGGTGATT 60.183 34.615 22.46 0.00 38.97 2.57
562 573 8.831715 ATGGTGATTTTGAAGGTTTTATGTTC 57.168 30.769 0.00 0.00 0.00 3.18
563 574 8.017418 TGGTGATTTTGAAGGTTTTATGTTCT 57.983 30.769 0.00 0.00 0.00 3.01
564 575 8.141268 TGGTGATTTTGAAGGTTTTATGTTCTC 58.859 33.333 0.00 0.00 0.00 2.87
565 576 8.360390 GGTGATTTTGAAGGTTTTATGTTCTCT 58.640 33.333 0.00 0.00 0.00 3.10
566 577 9.750125 GTGATTTTGAAGGTTTTATGTTCTCTT 57.250 29.630 0.00 0.00 0.00 2.85
578 589 9.928236 GTTTTATGTTCTCTTTGATATGCTCTC 57.072 33.333 0.00 0.00 0.00 3.20
592 603 0.037447 GCTCTCTTTGAAGGCCCTGT 59.963 55.000 0.00 0.00 0.00 4.00
593 604 1.948144 GCTCTCTTTGAAGGCCCTGTC 60.948 57.143 0.00 0.00 0.00 3.51
595 606 1.988107 TCTCTTTGAAGGCCCTGTCAT 59.012 47.619 0.00 0.00 0.00 3.06
601 612 1.272092 TGAAGGCCCTGTCATTTCTGG 60.272 52.381 0.00 0.00 0.00 3.86
603 614 0.329596 AGGCCCTGTCATTTCTGGAC 59.670 55.000 0.00 0.00 35.83 4.02
609 620 4.338879 CCCTGTCATTTCTGGACTTCAAT 58.661 43.478 0.00 0.00 36.26 2.57
610 621 4.768968 CCCTGTCATTTCTGGACTTCAATT 59.231 41.667 0.00 0.00 36.26 2.32
674 785 0.177836 AACAAGTTTTGGCTGGGCAC 59.822 50.000 0.00 0.00 34.12 5.01
701 813 5.859205 ATGAGATAAAACCTTGGCATTCC 57.141 39.130 0.00 0.00 0.00 3.01
702 814 3.694072 TGAGATAAAACCTTGGCATTCCG 59.306 43.478 0.00 0.00 34.14 4.30
718 830 2.781681 TCCGAAGTTCCATTCCTTCC 57.218 50.000 0.00 0.00 34.85 3.46
726 838 3.713764 AGTTCCATTCCTTCCGATGAGAT 59.286 43.478 0.00 0.00 0.00 2.75
743 862 5.964958 TGAGATTGCCTTAAAACTCCAAG 57.035 39.130 0.00 0.00 0.00 3.61
744 863 4.766891 TGAGATTGCCTTAAAACTCCAAGG 59.233 41.667 0.00 0.00 43.58 3.61
749 868 3.643159 CCTTAAAACTCCAAGGCACAC 57.357 47.619 0.00 0.00 35.24 3.82
750 869 2.296190 CCTTAAAACTCCAAGGCACACC 59.704 50.000 0.00 0.00 35.24 4.16
751 870 1.989706 TAAAACTCCAAGGCACACCC 58.010 50.000 0.00 0.00 36.11 4.61
760 879 0.250166 AAGGCACACCCGTTCTGTAC 60.250 55.000 0.00 0.00 39.21 2.90
785 904 3.691609 GGAAATTGCATTCTCTCGGAAGT 59.308 43.478 0.36 0.00 37.36 3.01
795 914 6.128007 GCATTCTCTCGGAAGTGGAATAAAAA 60.128 38.462 0.00 0.00 37.36 1.94
829 948 9.798994 AATGAAAGAATTTGTATTGATCTCTGC 57.201 29.630 0.00 0.00 39.27 4.26
883 1002 7.418408 ACATACATCACTACAAGATCTACACG 58.582 38.462 0.00 0.00 0.00 4.49
884 1003 5.250235 ACATCACTACAAGATCTACACGG 57.750 43.478 0.00 0.00 0.00 4.94
885 1004 4.098044 ACATCACTACAAGATCTACACGGG 59.902 45.833 0.00 0.00 0.00 5.28
886 1005 3.021695 TCACTACAAGATCTACACGGGG 58.978 50.000 0.00 0.00 0.00 5.73
947 1067 5.894298 TCCTCTATCCATATGCACAACTT 57.106 39.130 0.00 0.00 0.00 2.66
1241 1361 1.770658 TCCCCAGCTGATATGAGTTGG 59.229 52.381 17.39 16.52 42.48 3.77
1321 1441 3.272574 TGATCTTCAGGCATGGAAGTC 57.727 47.619 0.00 3.45 41.88 3.01
1372 1492 2.096496 CGATGAATCCAGCCTTGTGAAC 59.904 50.000 0.00 0.00 0.00 3.18
1549 1669 1.449956 GCTTCTGAGCCTGCTCCAG 60.450 63.158 16.06 12.81 43.29 3.86
1599 1719 7.543172 GCTCATCTGCAATCATACAAAAAGAAA 59.457 33.333 0.00 0.00 0.00 2.52
1601 1721 9.195411 TCATCTGCAATCATACAAAAAGAAAAC 57.805 29.630 0.00 0.00 0.00 2.43
1641 1761 9.927668 AATTGGATAACTTTATTTTCACCACAG 57.072 29.630 0.00 0.00 0.00 3.66
1644 1764 9.575868 TGGATAACTTTATTTTCACCACAGTTA 57.424 29.630 0.00 0.00 31.61 2.24
1650 1770 7.230712 ACTTTATTTTCACCACAGTTAGGGAAG 59.769 37.037 0.00 0.00 0.00 3.46
1680 1800 3.304829 TCTATCCCAATCATCGGTCACA 58.695 45.455 0.00 0.00 0.00 3.58
1686 1806 1.332686 CAATCATCGGTCACAGGCATG 59.667 52.381 0.00 0.00 0.00 4.06
1714 1834 2.791560 CACCTTAACATCGCTGAGATCG 59.208 50.000 0.00 0.00 37.52 3.69
1822 1942 2.663602 CAGAACTCCATCTTCGACAACG 59.336 50.000 0.00 0.00 41.26 4.10
1926 2046 9.052759 GTAGAGTTTTGGACAAAGTTAGATGAA 57.947 33.333 0.00 0.00 0.00 2.57
1928 2048 7.775561 AGAGTTTTGGACAAAGTTAGATGAAGT 59.224 33.333 0.00 0.00 0.00 3.01
1959 2079 4.033709 ACATAGGTGACAGGTCTAATGCT 58.966 43.478 0.65 0.00 0.00 3.79
2121 2241 1.742761 ACATGAACTTGCCATCCTCG 58.257 50.000 0.00 0.00 0.00 4.63
2170 2290 3.096489 TCTGCAGGCACAACAAAAATC 57.904 42.857 15.13 0.00 0.00 2.17
2208 2328 3.513515 GTCCTTCTGAACTCTCATGGACT 59.486 47.826 12.77 0.00 40.03 3.85
2217 2337 3.871485 ACTCTCATGGACTTGCATTCTC 58.129 45.455 0.00 0.00 0.00 2.87
2218 2338 3.518705 ACTCTCATGGACTTGCATTCTCT 59.481 43.478 0.00 0.00 0.00 3.10
2219 2339 4.713814 ACTCTCATGGACTTGCATTCTCTA 59.286 41.667 0.00 0.00 0.00 2.43
2220 2340 5.188555 ACTCTCATGGACTTGCATTCTCTAA 59.811 40.000 0.00 0.00 0.00 2.10
2221 2341 6.053632 TCTCATGGACTTGCATTCTCTAAA 57.946 37.500 0.00 0.00 0.00 1.85
2222 2342 6.656902 TCTCATGGACTTGCATTCTCTAAAT 58.343 36.000 0.00 0.00 0.00 1.40
2223 2343 7.114754 TCTCATGGACTTGCATTCTCTAAATT 58.885 34.615 0.00 0.00 0.00 1.82
2224 2344 7.613022 TCTCATGGACTTGCATTCTCTAAATTT 59.387 33.333 0.00 0.00 0.00 1.82
2225 2345 8.806429 TCATGGACTTGCATTCTCTAAATTTA 57.194 30.769 0.00 0.00 0.00 1.40
2226 2346 9.412460 TCATGGACTTGCATTCTCTAAATTTAT 57.588 29.630 0.00 0.00 0.00 1.40
2227 2347 9.674824 CATGGACTTGCATTCTCTAAATTTATC 57.325 33.333 0.00 0.00 0.00 1.75
2228 2348 8.225603 TGGACTTGCATTCTCTAAATTTATCC 57.774 34.615 0.00 0.00 0.00 2.59
2229 2349 7.285401 TGGACTTGCATTCTCTAAATTTATCCC 59.715 37.037 0.00 0.00 0.00 3.85
2230 2350 7.285401 GGACTTGCATTCTCTAAATTTATCCCA 59.715 37.037 0.00 0.00 0.00 4.37
2231 2351 8.773033 ACTTGCATTCTCTAAATTTATCCCAT 57.227 30.769 0.00 0.00 0.00 4.00
2232 2352 8.636213 ACTTGCATTCTCTAAATTTATCCCATG 58.364 33.333 0.00 1.70 0.00 3.66
2233 2353 8.537728 TTGCATTCTCTAAATTTATCCCATGT 57.462 30.769 0.00 0.00 0.00 3.21
2234 2354 9.639563 TTGCATTCTCTAAATTTATCCCATGTA 57.360 29.630 0.00 0.00 0.00 2.29
2235 2355 9.066892 TGCATTCTCTAAATTTATCCCATGTAC 57.933 33.333 0.00 0.00 0.00 2.90
2236 2356 9.289782 GCATTCTCTAAATTTATCCCATGTACT 57.710 33.333 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.391661 GCCGGACAAGATCAGCTCAA 60.392 55.000 5.05 0.00 0.00 3.02
1 2 1.219124 GCCGGACAAGATCAGCTCA 59.781 57.895 5.05 0.00 0.00 4.26
2 3 1.522580 GGCCGGACAAGATCAGCTC 60.523 63.158 5.05 0.00 0.00 4.09
3 4 2.586792 GGCCGGACAAGATCAGCT 59.413 61.111 5.05 0.00 0.00 4.24
4 5 2.514824 GGGCCGGACAAGATCAGC 60.515 66.667 11.00 0.00 0.00 4.26
5 6 2.190578 GGGGCCGGACAAGATCAG 59.809 66.667 11.00 0.00 0.00 2.90
6 7 1.570857 ATTGGGGCCGGACAAGATCA 61.571 55.000 11.00 0.00 0.00 2.92
7 8 0.819666 GATTGGGGCCGGACAAGATC 60.820 60.000 11.00 4.77 0.00 2.75
8 9 1.227383 GATTGGGGCCGGACAAGAT 59.773 57.895 11.00 0.00 0.00 2.40
9 10 1.497309 AAGATTGGGGCCGGACAAGA 61.497 55.000 11.00 0.00 0.00 3.02
10 11 0.611896 AAAGATTGGGGCCGGACAAG 60.612 55.000 11.00 0.00 0.00 3.16
11 12 0.610785 GAAAGATTGGGGCCGGACAA 60.611 55.000 11.00 9.57 0.00 3.18
12 13 1.001393 GAAAGATTGGGGCCGGACA 60.001 57.895 11.00 0.00 0.00 4.02
13 14 0.748367 GAGAAAGATTGGGGCCGGAC 60.748 60.000 5.05 0.00 0.00 4.79
14 15 1.607612 GAGAAAGATTGGGGCCGGA 59.392 57.895 5.05 0.00 0.00 5.14
15 16 1.453928 GGAGAAAGATTGGGGCCGG 60.454 63.158 0.00 0.00 0.00 6.13
16 17 1.453928 GGGAGAAAGATTGGGGCCG 60.454 63.158 0.00 0.00 0.00 6.13
17 18 0.396278 CAGGGAGAAAGATTGGGGCC 60.396 60.000 0.00 0.00 0.00 5.80
18 19 0.332972 ACAGGGAGAAAGATTGGGGC 59.667 55.000 0.00 0.00 0.00 5.80
19 20 2.450476 CAACAGGGAGAAAGATTGGGG 58.550 52.381 0.00 0.00 0.00 4.96
20 21 2.450476 CCAACAGGGAGAAAGATTGGG 58.550 52.381 0.00 0.00 40.01 4.12
21 22 1.821136 GCCAACAGGGAGAAAGATTGG 59.179 52.381 0.00 0.00 40.01 3.16
22 23 1.821136 GGCCAACAGGGAGAAAGATTG 59.179 52.381 0.00 0.00 40.01 2.67
23 24 1.713078 AGGCCAACAGGGAGAAAGATT 59.287 47.619 5.01 0.00 40.01 2.40
24 25 1.005215 CAGGCCAACAGGGAGAAAGAT 59.995 52.381 5.01 0.00 40.01 2.40
25 26 0.401738 CAGGCCAACAGGGAGAAAGA 59.598 55.000 5.01 0.00 40.01 2.52
26 27 0.111253 ACAGGCCAACAGGGAGAAAG 59.889 55.000 5.01 0.00 40.01 2.62
27 28 0.110486 GACAGGCCAACAGGGAGAAA 59.890 55.000 5.01 0.00 40.01 2.52
28 29 1.761174 GACAGGCCAACAGGGAGAA 59.239 57.895 5.01 0.00 40.01 2.87
29 30 2.224159 GGACAGGCCAACAGGGAGA 61.224 63.158 5.01 0.00 40.01 3.71
30 31 2.227036 AGGACAGGCCAACAGGGAG 61.227 63.158 5.01 0.00 40.01 4.30
31 32 2.121963 AGGACAGGCCAACAGGGA 60.122 61.111 5.01 0.00 40.01 4.20
32 33 2.034687 CAGGACAGGCCAACAGGG 59.965 66.667 5.01 0.00 40.02 4.45
33 34 1.302832 GTCAGGACAGGCCAACAGG 60.303 63.158 5.01 0.00 40.02 4.00
34 35 1.302832 GGTCAGGACAGGCCAACAG 60.303 63.158 5.01 0.00 40.02 3.16
35 36 2.829384 GGGTCAGGACAGGCCAACA 61.829 63.158 5.01 0.00 40.02 3.33
36 37 2.034221 GGGTCAGGACAGGCCAAC 59.966 66.667 5.01 0.00 40.02 3.77
37 38 2.121963 AGGGTCAGGACAGGCCAA 60.122 61.111 5.01 0.00 40.02 4.52
38 39 2.607750 GAGGGTCAGGACAGGCCA 60.608 66.667 5.01 0.00 40.02 5.36
39 40 1.904990 GAAGAGGGTCAGGACAGGCC 61.905 65.000 0.00 0.00 0.00 5.19
40 41 1.599576 GAAGAGGGTCAGGACAGGC 59.400 63.158 1.41 0.00 0.00 4.85
41 42 1.608717 CCGAAGAGGGTCAGGACAGG 61.609 65.000 1.41 0.00 35.97 4.00
42 43 0.900647 ACCGAAGAGGGTCAGGACAG 60.901 60.000 1.41 0.00 46.96 3.51
43 44 1.155390 ACCGAAGAGGGTCAGGACA 59.845 57.895 1.41 0.00 46.96 4.02
44 45 4.115270 ACCGAAGAGGGTCAGGAC 57.885 61.111 0.00 0.00 46.96 3.85
50 51 3.872630 GCCAAAATAAGACCGAAGAGGGT 60.873 47.826 0.00 0.00 46.96 4.34
51 52 2.683362 GCCAAAATAAGACCGAAGAGGG 59.317 50.000 0.00 0.00 46.96 4.30
53 54 2.351726 CCGCCAAAATAAGACCGAAGAG 59.648 50.000 0.00 0.00 0.00 2.85
54 55 2.352388 CCGCCAAAATAAGACCGAAGA 58.648 47.619 0.00 0.00 0.00 2.87
55 56 1.202143 GCCGCCAAAATAAGACCGAAG 60.202 52.381 0.00 0.00 0.00 3.79
56 57 0.806241 GCCGCCAAAATAAGACCGAA 59.194 50.000 0.00 0.00 0.00 4.30
57 58 1.363145 CGCCGCCAAAATAAGACCGA 61.363 55.000 0.00 0.00 0.00 4.69
58 59 1.061887 CGCCGCCAAAATAAGACCG 59.938 57.895 0.00 0.00 0.00 4.79
59 60 1.431845 CCGCCGCCAAAATAAGACC 59.568 57.895 0.00 0.00 0.00 3.85
60 61 1.431845 CCCGCCGCCAAAATAAGAC 59.568 57.895 0.00 0.00 0.00 3.01
61 62 2.411504 GCCCGCCGCCAAAATAAGA 61.412 57.895 0.00 0.00 0.00 2.10
62 63 2.104132 GCCCGCCGCCAAAATAAG 59.896 61.111 0.00 0.00 0.00 1.73
63 64 2.361865 AGCCCGCCGCCAAAATAA 60.362 55.556 0.00 0.00 38.78 1.40
64 65 2.902423 ATCAGCCCGCCGCCAAAATA 62.902 55.000 0.00 0.00 38.78 1.40
65 66 2.902423 TATCAGCCCGCCGCCAAAAT 62.902 55.000 0.00 0.00 38.78 1.82
66 67 3.630298 TATCAGCCCGCCGCCAAAA 62.630 57.895 0.00 0.00 38.78 2.44
67 68 4.102815 TATCAGCCCGCCGCCAAA 62.103 61.111 0.00 0.00 38.78 3.28
68 69 4.545706 CTATCAGCCCGCCGCCAA 62.546 66.667 0.00 0.00 38.78 4.52
71 72 3.941657 GATCCTATCAGCCCGCCGC 62.942 68.421 0.00 0.00 37.98 6.53
72 73 2.262915 GATCCTATCAGCCCGCCG 59.737 66.667 0.00 0.00 0.00 6.46
73 74 1.004440 GTGATCCTATCAGCCCGCC 60.004 63.158 0.00 0.00 40.53 6.13
74 75 4.683432 GTGATCCTATCAGCCCGC 57.317 61.111 0.00 0.00 40.53 6.13
79 80 2.036992 GAGGCAGTGGTGATCCTATCAG 59.963 54.545 0.00 0.00 40.53 2.90
80 81 2.042464 GAGGCAGTGGTGATCCTATCA 58.958 52.381 0.00 0.00 36.84 2.15
81 82 1.346068 GGAGGCAGTGGTGATCCTATC 59.654 57.143 0.00 0.00 31.39 2.08
82 83 1.061812 AGGAGGCAGTGGTGATCCTAT 60.062 52.381 0.00 0.00 38.83 2.57
83 84 0.339859 AGGAGGCAGTGGTGATCCTA 59.660 55.000 0.00 0.00 38.83 2.94
84 85 0.339859 TAGGAGGCAGTGGTGATCCT 59.660 55.000 0.00 0.00 41.75 3.24
85 86 1.071385 CATAGGAGGCAGTGGTGATCC 59.929 57.143 0.00 0.00 33.30 3.36
86 87 1.071385 CCATAGGAGGCAGTGGTGATC 59.929 57.143 0.00 0.00 0.00 2.92
87 88 1.135094 CCATAGGAGGCAGTGGTGAT 58.865 55.000 0.00 0.00 0.00 3.06
88 89 2.607811 CCATAGGAGGCAGTGGTGA 58.392 57.895 0.00 0.00 0.00 4.02
97 98 1.284785 TGTGGGAAAAGCCATAGGAGG 59.715 52.381 0.00 0.00 38.95 4.30
98 99 2.648059 CTGTGGGAAAAGCCATAGGAG 58.352 52.381 0.00 0.00 38.95 3.69
99 100 1.284785 CCTGTGGGAAAAGCCATAGGA 59.715 52.381 0.00 0.00 44.53 2.94
100 101 1.284785 TCCTGTGGGAAAAGCCATAGG 59.715 52.381 0.00 0.00 43.59 2.57
101 102 2.806945 TCCTGTGGGAAAAGCCATAG 57.193 50.000 0.00 0.00 38.93 2.23
117 118 9.858384 CCAACTACTGGCTTGGAAATAGTTCCT 62.858 44.444 21.69 3.43 45.41 3.36
118 119 7.794203 CCAACTACTGGCTTGGAAATAGTTCC 61.794 46.154 15.06 15.06 45.40 3.62
119 120 5.123979 CCAACTACTGGCTTGGAAATAGTTC 59.876 44.000 0.00 0.00 39.58 3.01
120 121 5.010282 CCAACTACTGGCTTGGAAATAGTT 58.990 41.667 0.00 0.00 39.58 2.24
121 122 4.288626 TCCAACTACTGGCTTGGAAATAGT 59.711 41.667 2.92 0.00 45.98 2.12
122 123 4.843728 TCCAACTACTGGCTTGGAAATAG 58.156 43.478 2.92 0.00 45.98 1.73
123 124 4.843728 CTCCAACTACTGGCTTGGAAATA 58.156 43.478 6.61 0.00 44.29 1.40
124 125 3.690460 CTCCAACTACTGGCTTGGAAAT 58.310 45.455 6.61 0.00 44.29 2.17
125 126 2.814097 GCTCCAACTACTGGCTTGGAAA 60.814 50.000 6.61 0.00 44.29 3.13
126 127 1.271379 GCTCCAACTACTGGCTTGGAA 60.271 52.381 6.61 0.00 44.29 3.53
127 128 0.324943 GCTCCAACTACTGGCTTGGA 59.675 55.000 5.21 5.21 45.98 3.53
128 129 0.326264 AGCTCCAACTACTGGCTTGG 59.674 55.000 0.00 0.00 45.98 3.61
129 130 2.028112 TGTAGCTCCAACTACTGGCTTG 60.028 50.000 0.00 0.00 45.98 4.01
130 131 2.257207 TGTAGCTCCAACTACTGGCTT 58.743 47.619 0.00 0.00 45.98 4.35
131 132 1.938585 TGTAGCTCCAACTACTGGCT 58.061 50.000 0.00 0.00 45.98 4.75
132 133 2.347731 GTTGTAGCTCCAACTACTGGC 58.652 52.381 14.40 0.00 45.98 4.85
139 140 4.065789 AGCAAAGTAGTTGTAGCTCCAAC 58.934 43.478 13.88 13.88 44.00 3.77
140 141 4.065088 CAGCAAAGTAGTTGTAGCTCCAA 58.935 43.478 0.00 0.00 39.63 3.53
141 142 3.557054 CCAGCAAAGTAGTTGTAGCTCCA 60.557 47.826 0.00 0.00 39.63 3.86
142 143 3.003480 CCAGCAAAGTAGTTGTAGCTCC 58.997 50.000 0.00 0.00 39.63 4.70
143 144 3.926616 TCCAGCAAAGTAGTTGTAGCTC 58.073 45.455 0.00 0.00 39.63 4.09
144 145 4.351874 TTCCAGCAAAGTAGTTGTAGCT 57.648 40.909 0.00 0.00 39.63 3.32
145 146 4.142600 CCATTCCAGCAAAGTAGTTGTAGC 60.143 45.833 0.00 0.00 39.63 3.58
146 147 4.142600 GCCATTCCAGCAAAGTAGTTGTAG 60.143 45.833 0.00 0.00 39.63 2.74
147 148 3.756434 GCCATTCCAGCAAAGTAGTTGTA 59.244 43.478 0.00 0.00 39.63 2.41
148 149 2.558359 GCCATTCCAGCAAAGTAGTTGT 59.442 45.455 0.00 0.00 39.63 3.32
149 150 2.557924 TGCCATTCCAGCAAAGTAGTTG 59.442 45.455 0.00 0.00 37.28 3.16
150 151 2.875296 TGCCATTCCAGCAAAGTAGTT 58.125 42.857 0.00 0.00 37.28 2.24
151 152 2.584835 TGCCATTCCAGCAAAGTAGT 57.415 45.000 0.00 0.00 37.28 2.73
152 153 6.000219 ACTATATGCCATTCCAGCAAAGTAG 59.000 40.000 0.00 0.00 44.83 2.57
153 154 5.940617 ACTATATGCCATTCCAGCAAAGTA 58.059 37.500 0.00 0.00 44.83 2.24
154 155 4.796606 ACTATATGCCATTCCAGCAAAGT 58.203 39.130 0.00 0.00 44.83 2.66
155 156 6.000219 AGTACTATATGCCATTCCAGCAAAG 59.000 40.000 0.00 0.00 44.83 2.77
156 157 5.940617 AGTACTATATGCCATTCCAGCAAA 58.059 37.500 0.00 0.00 44.83 3.68
157 158 5.567037 AGTACTATATGCCATTCCAGCAA 57.433 39.130 0.00 0.00 44.83 3.91
158 159 5.780282 AGTAGTACTATATGCCATTCCAGCA 59.220 40.000 5.75 0.00 45.94 4.41
159 160 6.102663 CAGTAGTACTATATGCCATTCCAGC 58.897 44.000 5.75 0.00 0.00 4.85
160 161 6.071108 AGCAGTAGTACTATATGCCATTCCAG 60.071 42.308 26.82 4.43 37.61 3.86
161 162 5.780282 AGCAGTAGTACTATATGCCATTCCA 59.220 40.000 26.82 0.00 37.61 3.53
162 163 6.287589 AGCAGTAGTACTATATGCCATTCC 57.712 41.667 26.82 9.61 37.61 3.01
163 164 7.657761 ACAAAGCAGTAGTACTATATGCCATTC 59.342 37.037 26.82 10.11 37.61 2.67
164 165 7.509546 ACAAAGCAGTAGTACTATATGCCATT 58.490 34.615 26.82 21.69 37.61 3.16
165 166 7.067496 ACAAAGCAGTAGTACTATATGCCAT 57.933 36.000 26.82 18.68 37.61 4.40
166 167 6.479972 ACAAAGCAGTAGTACTATATGCCA 57.520 37.500 26.82 0.00 37.61 4.92
167 168 7.254795 CCAAACAAAGCAGTAGTACTATATGCC 60.255 40.741 26.82 15.90 37.61 4.40
168 169 7.254795 CCCAAACAAAGCAGTAGTACTATATGC 60.255 40.741 24.76 24.76 37.15 3.14
169 170 7.254795 GCCCAAACAAAGCAGTAGTACTATATG 60.255 40.741 5.75 9.45 0.00 1.78
170 171 6.766467 GCCCAAACAAAGCAGTAGTACTATAT 59.234 38.462 5.75 0.00 0.00 0.86
171 172 6.110707 GCCCAAACAAAGCAGTAGTACTATA 58.889 40.000 5.75 0.00 0.00 1.31
172 173 4.941873 GCCCAAACAAAGCAGTAGTACTAT 59.058 41.667 5.75 0.00 0.00 2.12
173 174 4.320870 GCCCAAACAAAGCAGTAGTACTA 58.679 43.478 1.57 0.00 0.00 1.82
174 175 3.146847 GCCCAAACAAAGCAGTAGTACT 58.853 45.455 0.00 0.00 0.00 2.73
175 176 2.228103 GGCCCAAACAAAGCAGTAGTAC 59.772 50.000 0.00 0.00 0.00 2.73
176 177 2.158593 TGGCCCAAACAAAGCAGTAGTA 60.159 45.455 0.00 0.00 0.00 1.82
177 178 1.328279 GGCCCAAACAAAGCAGTAGT 58.672 50.000 0.00 0.00 0.00 2.73
178 179 1.327303 TGGCCCAAACAAAGCAGTAG 58.673 50.000 0.00 0.00 0.00 2.57
179 180 2.008242 ATGGCCCAAACAAAGCAGTA 57.992 45.000 0.00 0.00 0.00 2.74
180 181 1.130777 AATGGCCCAAACAAAGCAGT 58.869 45.000 0.00 0.00 0.00 4.40
181 182 1.515081 CAATGGCCCAAACAAAGCAG 58.485 50.000 0.00 0.00 0.00 4.24
182 183 0.108207 CCAATGGCCCAAACAAAGCA 59.892 50.000 0.00 0.00 0.00 3.91
183 184 1.236616 GCCAATGGCCCAAACAAAGC 61.237 55.000 14.47 0.00 44.06 3.51
184 185 2.931246 GCCAATGGCCCAAACAAAG 58.069 52.632 14.47 0.00 44.06 2.77
194 195 1.081242 CAACAGTGACGCCAATGGC 60.081 57.895 15.52 15.52 46.75 4.40
195 196 0.040157 CACAACAGTGACGCCAATGG 60.040 55.000 3.82 0.00 42.19 3.16
196 197 0.661187 GCACAACAGTGACGCCAATG 60.661 55.000 0.00 0.00 43.39 2.82
197 198 1.654220 GCACAACAGTGACGCCAAT 59.346 52.632 0.00 0.00 35.24 3.16
198 199 2.477176 GGCACAACAGTGACGCCAA 61.477 57.895 0.00 0.00 42.71 4.52
199 200 2.034048 TAGGCACAACAGTGACGCCA 62.034 55.000 15.58 3.65 46.11 5.69
200 201 0.673644 ATAGGCACAACAGTGACGCC 60.674 55.000 0.00 2.85 46.11 5.68
201 202 0.443869 CATAGGCACAACAGTGACGC 59.556 55.000 0.00 0.00 46.11 5.19
202 203 1.078709 CCATAGGCACAACAGTGACG 58.921 55.000 0.00 0.00 46.11 4.35
203 204 1.453155 CCCATAGGCACAACAGTGAC 58.547 55.000 0.00 0.00 41.76 3.67
204 205 3.955145 CCCATAGGCACAACAGTGA 57.045 52.632 0.00 0.00 35.24 3.41
222 223 4.777384 CCCAAACAGGCAAAAGGC 57.223 55.556 0.00 0.00 43.74 4.35
230 231 2.743060 GCCAAAGGCCCAAACAGG 59.257 61.111 0.00 0.00 44.06 4.00
242 243 2.258013 CCTCGCCTTTGACGCCAAA 61.258 57.895 0.00 0.00 39.74 3.28
243 244 2.668212 CCTCGCCTTTGACGCCAA 60.668 61.111 0.00 0.00 0.00 4.52
244 245 3.589654 CTCCTCGCCTTTGACGCCA 62.590 63.158 0.00 0.00 0.00 5.69
245 246 2.815647 CTCCTCGCCTTTGACGCC 60.816 66.667 0.00 0.00 0.00 5.68
246 247 2.815647 CCTCCTCGCCTTTGACGC 60.816 66.667 0.00 0.00 0.00 5.19
247 248 2.125512 CCCTCCTCGCCTTTGACG 60.126 66.667 0.00 0.00 0.00 4.35
248 249 2.436824 GCCCTCCTCGCCTTTGAC 60.437 66.667 0.00 0.00 0.00 3.18
249 250 2.927856 TGCCCTCCTCGCCTTTGA 60.928 61.111 0.00 0.00 0.00 2.69
250 251 2.437359 CTGCCCTCCTCGCCTTTG 60.437 66.667 0.00 0.00 0.00 2.77
251 252 3.721706 CCTGCCCTCCTCGCCTTT 61.722 66.667 0.00 0.00 0.00 3.11
252 253 4.722535 TCCTGCCCTCCTCGCCTT 62.723 66.667 0.00 0.00 0.00 4.35
256 257 2.837291 CTCCTCCTGCCCTCCTCG 60.837 72.222 0.00 0.00 0.00 4.63
257 258 3.160748 GCTCCTCCTGCCCTCCTC 61.161 72.222 0.00 0.00 0.00 3.71
258 259 4.814041 GGCTCCTCCTGCCCTCCT 62.814 72.222 0.00 0.00 44.32 3.69
265 266 2.754664 AAAACGGCTGGCTCCTCCTG 62.755 60.000 0.00 0.00 36.91 3.86
269 270 0.251341 AATCAAAACGGCTGGCTCCT 60.251 50.000 0.00 0.00 0.00 3.69
297 298 4.785453 CTCCCTTGCCCAGGCGAC 62.785 72.222 3.83 0.00 42.29 5.19
319 320 1.348775 ATGTAGCCCAGCTCCTTCCC 61.349 60.000 0.00 0.00 40.44 3.97
322 323 1.771255 CCTTATGTAGCCCAGCTCCTT 59.229 52.381 0.00 0.00 40.44 3.36
323 324 1.428869 CCTTATGTAGCCCAGCTCCT 58.571 55.000 0.00 0.00 40.44 3.69
329 332 2.448582 CGCCCCCTTATGTAGCCCA 61.449 63.158 0.00 0.00 0.00 5.36
342 346 2.895372 CCATTCGCACTACGCCCC 60.895 66.667 0.00 0.00 43.23 5.80
344 348 1.017177 TTCACCATTCGCACTACGCC 61.017 55.000 0.00 0.00 43.23 5.68
346 350 1.393539 CCTTTCACCATTCGCACTACG 59.606 52.381 0.00 0.00 45.62 3.51
349 353 0.537143 TGCCTTTCACCATTCGCACT 60.537 50.000 0.00 0.00 0.00 4.40
357 361 3.286751 GCTGCGTGCCTTTCACCA 61.287 61.111 0.00 0.00 42.69 4.17
380 384 2.232756 TAGTTCGCTTTGTGCTCACA 57.767 45.000 0.00 0.00 40.11 3.58
479 486 2.067932 TTGGTGGGGCCTTCTCACAG 62.068 60.000 0.84 0.00 38.35 3.66
503 510 6.459257 AATGCGCGACAAAATTTGAAATTA 57.541 29.167 12.10 0.00 0.00 1.40
509 516 3.893709 GTCAAAATGCGCGACAAAATTTG 59.106 39.130 12.10 18.18 34.36 2.32
519 530 3.611986 ACCATATTTTGTCAAAATGCGCG 59.388 39.130 26.74 16.10 41.01 6.86
522 533 9.332301 CAAAATCACCATATTTTGTCAAAATGC 57.668 29.630 26.74 0.00 45.46 3.56
538 549 8.017418 AGAACATAAAACCTTCAAAATCACCA 57.983 30.769 0.00 0.00 0.00 4.17
540 551 9.750125 AAGAGAACATAAAACCTTCAAAATCAC 57.250 29.630 0.00 0.00 0.00 3.06
555 566 9.896645 AAAGAGAGCATATCAAAGAGAACATAA 57.103 29.630 0.00 0.00 0.00 1.90
557 568 8.045507 TCAAAGAGAGCATATCAAAGAGAACAT 58.954 33.333 0.00 0.00 0.00 2.71
558 569 7.389232 TCAAAGAGAGCATATCAAAGAGAACA 58.611 34.615 0.00 0.00 0.00 3.18
559 570 7.840342 TCAAAGAGAGCATATCAAAGAGAAC 57.160 36.000 0.00 0.00 0.00 3.01
560 571 7.551974 CCTTCAAAGAGAGCATATCAAAGAGAA 59.448 37.037 0.00 0.00 0.00 2.87
561 572 7.046652 CCTTCAAAGAGAGCATATCAAAGAGA 58.953 38.462 0.00 0.00 0.00 3.10
562 573 6.238429 GCCTTCAAAGAGAGCATATCAAAGAG 60.238 42.308 0.00 0.00 0.00 2.85
563 574 5.587844 GCCTTCAAAGAGAGCATATCAAAGA 59.412 40.000 0.00 0.00 0.00 2.52
564 575 5.221009 GGCCTTCAAAGAGAGCATATCAAAG 60.221 44.000 0.00 0.00 0.00 2.77
565 576 4.641989 GGCCTTCAAAGAGAGCATATCAAA 59.358 41.667 0.00 0.00 0.00 2.69
566 577 4.202441 GGCCTTCAAAGAGAGCATATCAA 58.798 43.478 0.00 0.00 0.00 2.57
567 578 3.434167 GGGCCTTCAAAGAGAGCATATCA 60.434 47.826 0.84 0.00 0.00 2.15
568 579 3.145286 GGGCCTTCAAAGAGAGCATATC 58.855 50.000 0.84 0.00 0.00 1.63
569 580 2.782341 AGGGCCTTCAAAGAGAGCATAT 59.218 45.455 0.00 0.00 0.00 1.78
570 581 2.092753 CAGGGCCTTCAAAGAGAGCATA 60.093 50.000 1.32 0.00 0.00 3.14
571 582 0.998145 AGGGCCTTCAAAGAGAGCAT 59.002 50.000 0.00 0.00 0.00 3.79
573 584 0.037447 ACAGGGCCTTCAAAGAGAGC 59.963 55.000 1.32 0.00 0.00 4.09
578 589 3.057033 CAGAAATGACAGGGCCTTCAAAG 60.057 47.826 18.11 4.62 0.00 2.77
674 785 7.814264 ATGCCAAGGTTTTATCTCATAGAAG 57.186 36.000 0.00 0.00 0.00 2.85
701 813 2.380084 TCGGAAGGAATGGAACTTCG 57.620 50.000 0.00 0.00 0.00 3.79
702 814 3.873910 TCATCGGAAGGAATGGAACTTC 58.126 45.455 0.00 0.00 0.00 3.01
718 830 4.635765 TGGAGTTTTAAGGCAATCTCATCG 59.364 41.667 0.00 0.00 0.00 3.84
743 862 0.250166 AAGTACAGAACGGGTGTGCC 60.250 55.000 0.00 0.00 31.43 5.01
744 863 0.865769 CAAGTACAGAACGGGTGTGC 59.134 55.000 0.00 0.00 0.00 4.57
745 864 1.069513 TCCAAGTACAGAACGGGTGTG 59.930 52.381 0.00 0.00 0.00 3.82
746 865 1.416243 TCCAAGTACAGAACGGGTGT 58.584 50.000 0.00 0.00 0.00 4.16
747 866 2.536761 TTCCAAGTACAGAACGGGTG 57.463 50.000 0.00 0.00 0.00 4.61
748 867 3.782656 ATTTCCAAGTACAGAACGGGT 57.217 42.857 0.00 0.00 0.00 5.28
749 868 3.365969 GCAATTTCCAAGTACAGAACGGG 60.366 47.826 0.00 0.00 0.00 5.28
750 869 3.252215 TGCAATTTCCAAGTACAGAACGG 59.748 43.478 0.00 0.00 0.00 4.44
751 870 4.481930 TGCAATTTCCAAGTACAGAACG 57.518 40.909 0.00 0.00 0.00 3.95
760 879 3.691118 TCCGAGAGAATGCAATTTCCAAG 59.309 43.478 0.00 0.00 36.07 3.61
829 948 5.459762 GTGATGTTCAAATTGGACACAAGTG 59.540 40.000 9.58 0.00 40.49 3.16
1147 1267 4.208686 GACTACCCGCCGGAGCTG 62.209 72.222 5.05 0.00 36.60 4.24
1241 1361 1.202867 GGAGAAGATCATTGGGAGGGC 60.203 57.143 0.00 0.00 0.00 5.19
1275 1395 3.432592 GGAAGACAGCGATGATGATCATG 59.567 47.826 14.30 2.27 37.20 3.07
1321 1441 4.028648 GCCGTAAACATCGAAAAATCAACG 59.971 41.667 0.00 0.00 0.00 4.10
1372 1492 2.301296 AGATCATAGCCAACCGGAGATG 59.699 50.000 9.46 3.78 0.00 2.90
1549 1669 4.502962 CAACTGAAGAGGATGAGGAGTTC 58.497 47.826 0.00 0.00 0.00 3.01
1599 1719 8.992073 GTTATCCAATTTGCATTTTCTCAAGTT 58.008 29.630 0.00 0.00 0.00 2.66
1601 1721 8.767478 AGTTATCCAATTTGCATTTTCTCAAG 57.233 30.769 0.00 0.00 0.00 3.02
1632 1752 4.165372 AGAAACTTCCCTAACTGTGGTGAA 59.835 41.667 0.00 0.00 0.00 3.18
1641 1761 6.993308 GGGATAGAATGAGAAACTTCCCTAAC 59.007 42.308 0.00 0.00 38.81 2.34
1644 1764 5.039645 TGGGATAGAATGAGAAACTTCCCT 58.960 41.667 6.26 0.00 41.77 4.20
1650 1770 6.148480 CCGATGATTGGGATAGAATGAGAAAC 59.852 42.308 0.00 0.00 0.00 2.78
1714 1834 3.576550 ACTTCCTCAGAGAGAACAAGGTC 59.423 47.826 0.00 0.00 0.00 3.85
1926 2046 4.157246 TGTCACCTATGTGTACTGGAACT 58.843 43.478 0.00 0.00 43.26 3.01
1928 2048 3.513912 CCTGTCACCTATGTGTACTGGAA 59.486 47.826 14.77 0.00 43.26 3.53
1947 2067 4.937620 ACACACAACATAGCATTAGACCTG 59.062 41.667 0.00 0.00 0.00 4.00
2073 2193 1.739049 CAGGCAGATCCTCGACTCC 59.261 63.158 0.00 0.00 45.52 3.85
2075 2195 1.381056 AGCAGGCAGATCCTCGACT 60.381 57.895 0.00 0.00 45.52 4.18
2085 2205 1.882912 TGTACAAGAACAGCAGGCAG 58.117 50.000 0.00 0.00 0.00 4.85
2121 2241 6.267471 AGAGAGAGGAATATGAGGTTGTGATC 59.733 42.308 0.00 0.00 0.00 2.92
2170 2290 6.881065 TCAGAAGGACTAATGATTCAAACTGG 59.119 38.462 0.00 0.00 0.00 4.00
2208 2328 8.537728 ACATGGGATAAATTTAGAGAATGCAA 57.462 30.769 3.94 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.