Multiple sequence alignment - TraesCS4A01G270200

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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 TraesCS4A01G270200 chr4A 100.000 4184 0 0 1 4184 581480563 581484746 0.000000e+00 7727
1 TraesCS4A01G270200 chr4B 96.006 3630 114 20 548 4155 31878100 31874480 0.000000e+00 5871
2 TraesCS4A01G270200 chr4B 87.981 208 15 4 230 428 31878498 31878292 1.940000e-58 237
3 TraesCS4A01G270200 chr4D 94.595 3626 117 36 548 4104 19410447 19406832 0.000000e+00 5537
4 TraesCS4A01G270200 chr4D 86.547 223 20 6 231 444 19410843 19410622 1.940000e-58 237
5 TraesCS4A01G270200 chr5B 81.720 1860 297 25 1345 3187 96757741 96755908 0.000000e+00 1511
6 TraesCS4A01G270200 chr6B 81.307 1423 259 5 1772 3189 636212529 636213949 0.000000e+00 1147
7 TraesCS4A01G270200 chr6B 81.026 1423 263 5 1772 3189 636186101 636187521 0.000000e+00 1125
8 TraesCS4A01G270200 chr5A 83.445 1190 163 20 1345 2523 85148261 85147095 0.000000e+00 1075
9 TraesCS4A01G270200 chr5D 95.671 231 8 2 1 229 545994825 545995055 1.840000e-98 370
10 TraesCS4A01G270200 chr1A 78.909 275 33 12 1408 1668 574392957 574393220 3.350000e-36 163
11 TraesCS4A01G270200 chr1B 79.032 248 31 11 1432 1668 665437643 665437880 2.610000e-32 150


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 TraesCS4A01G270200 chr4A 581480563 581484746 4183 False 7727 7727 100.0000 1 4184 1 chr4A.!!$F1 4183
1 TraesCS4A01G270200 chr4B 31874480 31878498 4018 True 3054 5871 91.9935 230 4155 2 chr4B.!!$R1 3925
2 TraesCS4A01G270200 chr4D 19406832 19410843 4011 True 2887 5537 90.5710 231 4104 2 chr4D.!!$R1 3873
3 TraesCS4A01G270200 chr5B 96755908 96757741 1833 True 1511 1511 81.7200 1345 3187 1 chr5B.!!$R1 1842
4 TraesCS4A01G270200 chr6B 636212529 636213949 1420 False 1147 1147 81.3070 1772 3189 1 chr6B.!!$F2 1417
5 TraesCS4A01G270200 chr6B 636186101 636187521 1420 False 1125 1125 81.0260 1772 3189 1 chr6B.!!$F1 1417
6 TraesCS4A01G270200 chr5A 85147095 85148261 1166 True 1075 1075 83.4450 1345 2523 1 chr5A.!!$R1 1178

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
176 177 0.032540 GCTTGGCTTGTCACCCTTTG 59.967 55.000 0.00 0.0 0.00 2.77 F
188 189 0.258774 ACCCTTTGAAGTGTGGCTGT 59.741 50.000 0.00 0.0 0.00 4.40 F
213 214 0.401738 CAGAACTGGCCAGGAGGAAA 59.598 55.000 35.42 0.0 36.89 3.13 F
862 957 0.905809 TTACGGCCCAAGCTCCACTA 60.906 55.000 0.00 0.0 39.73 2.74 F
866 961 1.222113 GCCCAAGCTCCACTAGGTC 59.778 63.158 0.00 0.0 33.87 3.85 F
2448 2619 1.000274 GTTGTTGGTGTCCTTGATGCC 60.000 52.381 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 2097 0.035881 CAGTCCCAAGCTTGCTCTCA 59.964 55.000 21.43 0.00 0.00 3.27 R
2097 2268 0.600255 GCGGCAGGCGAGTAATGTAT 60.600 55.000 22.52 0.00 0.00 2.29 R
2289 2460 0.546122 TCACAACTTCACAGCCCTGT 59.454 50.000 0.00 0.00 46.17 4.00 R
2448 2619 2.093306 TCAGGTTACTTGACGGCATG 57.907 50.000 1.93 1.93 0.00 4.06 R
2721 2895 4.346129 CTGACTTCTTTGTGTTGCAGAAC 58.654 43.478 0.00 0.00 0.00 3.01 R
4161 4356 0.614812 GGCCAAATGGGTCAATTGCT 59.385 50.000 0.00 0.00 42.53 3.91 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
19 20 0.958091 TGGAACTGGAACGCAAATGG 59.042 50.000 0.00 0.00 0.00 3.16
20 21 1.243902 GGAACTGGAACGCAAATGGA 58.756 50.000 0.00 0.00 0.00 3.41
21 22 1.611491 GGAACTGGAACGCAAATGGAA 59.389 47.619 0.00 0.00 0.00 3.53
22 23 2.231235 GGAACTGGAACGCAAATGGAAT 59.769 45.455 0.00 0.00 0.00 3.01
23 24 3.306019 GGAACTGGAACGCAAATGGAATT 60.306 43.478 0.00 0.00 38.98 2.17
25 26 4.335400 ACTGGAACGCAAATGGAATTTT 57.665 36.364 0.00 0.00 46.10 1.82
26 27 4.306600 ACTGGAACGCAAATGGAATTTTC 58.693 39.130 0.00 0.00 46.10 2.29
27 28 4.039124 ACTGGAACGCAAATGGAATTTTCT 59.961 37.500 0.00 0.00 46.10 2.52
28 29 4.555262 TGGAACGCAAATGGAATTTTCTC 58.445 39.130 0.00 0.00 46.10 2.87
29 30 4.280677 TGGAACGCAAATGGAATTTTCTCT 59.719 37.500 0.00 0.00 46.10 3.10
30 31 4.622740 GGAACGCAAATGGAATTTTCTCTG 59.377 41.667 0.00 0.00 46.10 3.35
31 32 3.578688 ACGCAAATGGAATTTTCTCTGC 58.421 40.909 0.00 0.00 46.10 4.26
32 33 3.256631 ACGCAAATGGAATTTTCTCTGCT 59.743 39.130 0.00 0.00 46.10 4.24
33 34 4.458989 ACGCAAATGGAATTTTCTCTGCTA 59.541 37.500 0.00 0.00 46.10 3.49
34 35 5.048083 ACGCAAATGGAATTTTCTCTGCTAA 60.048 36.000 0.00 0.00 46.10 3.09
35 36 5.514204 CGCAAATGGAATTTTCTCTGCTAAG 59.486 40.000 0.00 0.00 46.10 2.18
36 37 6.393171 GCAAATGGAATTTTCTCTGCTAAGT 58.607 36.000 0.00 0.00 46.10 2.24
37 38 7.538575 GCAAATGGAATTTTCTCTGCTAAGTA 58.461 34.615 0.00 0.00 46.10 2.24
38 39 7.699812 GCAAATGGAATTTTCTCTGCTAAGTAG 59.300 37.037 0.00 0.00 46.10 2.57
39 40 7.872113 AATGGAATTTTCTCTGCTAAGTAGG 57.128 36.000 0.00 0.00 26.74 3.18
40 41 5.745227 TGGAATTTTCTCTGCTAAGTAGGG 58.255 41.667 0.00 0.00 0.00 3.53
41 42 5.250774 TGGAATTTTCTCTGCTAAGTAGGGT 59.749 40.000 0.00 0.00 0.00 4.34
42 43 6.442564 TGGAATTTTCTCTGCTAAGTAGGGTA 59.557 38.462 0.00 0.00 0.00 3.69
43 44 7.127339 TGGAATTTTCTCTGCTAAGTAGGGTAT 59.873 37.037 0.00 0.00 0.00 2.73
44 45 7.442666 GGAATTTTCTCTGCTAAGTAGGGTATG 59.557 40.741 0.00 0.00 0.00 2.39
45 46 7.676683 ATTTTCTCTGCTAAGTAGGGTATGA 57.323 36.000 0.00 0.00 0.00 2.15
46 47 7.490657 TTTTCTCTGCTAAGTAGGGTATGAA 57.509 36.000 0.00 0.00 0.00 2.57
47 48 7.676683 TTTCTCTGCTAAGTAGGGTATGAAT 57.323 36.000 0.00 0.00 0.00 2.57
48 49 8.777578 TTTCTCTGCTAAGTAGGGTATGAATA 57.222 34.615 0.00 0.00 0.00 1.75
49 50 8.958060 TTCTCTGCTAAGTAGGGTATGAATAT 57.042 34.615 0.00 0.00 0.00 1.28
50 51 8.958060 TCTCTGCTAAGTAGGGTATGAATATT 57.042 34.615 0.00 0.00 0.00 1.28
51 52 9.381038 TCTCTGCTAAGTAGGGTATGAATATTT 57.619 33.333 0.00 0.00 0.00 1.40
52 53 9.646427 CTCTGCTAAGTAGGGTATGAATATTTC 57.354 37.037 0.00 0.00 0.00 2.17
53 54 9.154632 TCTGCTAAGTAGGGTATGAATATTTCA 57.845 33.333 0.00 0.00 45.01 2.69
69 70 9.256477 TGAATATTTCATAATCAGTACGGACAC 57.744 33.333 0.00 0.00 34.08 3.67
70 71 8.603242 AATATTTCATAATCAGTACGGACACC 57.397 34.615 0.00 0.00 0.00 4.16
71 72 5.408880 TTTCATAATCAGTACGGACACCA 57.591 39.130 0.00 0.00 0.00 4.17
72 73 5.408880 TTCATAATCAGTACGGACACCAA 57.591 39.130 0.00 0.00 0.00 3.67
73 74 5.006153 TCATAATCAGTACGGACACCAAG 57.994 43.478 0.00 0.00 0.00 3.61
74 75 2.762535 AATCAGTACGGACACCAAGG 57.237 50.000 0.00 0.00 0.00 3.61
75 76 0.902531 ATCAGTACGGACACCAAGGG 59.097 55.000 0.00 0.00 0.00 3.95
76 77 0.470456 TCAGTACGGACACCAAGGGT 60.470 55.000 0.00 0.00 35.62 4.34
98 99 8.990163 GGGTGGATATTCATCTAACCTTAAAA 57.010 34.615 0.00 0.00 44.24 1.52
99 100 9.416284 GGGTGGATATTCATCTAACCTTAAAAA 57.584 33.333 0.00 0.00 44.24 1.94
102 103 9.983024 TGGATATTCATCTAACCTTAAAAACCA 57.017 29.630 0.00 0.00 0.00 3.67
112 113 8.527810 TCTAACCTTAAAAACCATAAATGCTGG 58.472 33.333 0.00 0.00 39.80 4.85
113 114 5.487433 ACCTTAAAAACCATAAATGCTGGC 58.513 37.500 0.00 0.00 37.27 4.85
114 115 5.248248 ACCTTAAAAACCATAAATGCTGGCT 59.752 36.000 0.00 0.00 37.27 4.75
115 116 5.581874 CCTTAAAAACCATAAATGCTGGCTG 59.418 40.000 0.00 0.00 37.27 4.85
116 117 4.888326 AAAAACCATAAATGCTGGCTGA 57.112 36.364 0.00 0.00 37.27 4.26
117 118 4.888326 AAAACCATAAATGCTGGCTGAA 57.112 36.364 0.00 0.00 37.27 3.02
118 119 4.888326 AAACCATAAATGCTGGCTGAAA 57.112 36.364 0.00 0.00 37.27 2.69
119 120 3.874392 ACCATAAATGCTGGCTGAAAC 57.126 42.857 0.00 0.00 37.27 2.78
120 121 3.434309 ACCATAAATGCTGGCTGAAACT 58.566 40.909 0.00 0.00 37.27 2.66
121 122 4.599041 ACCATAAATGCTGGCTGAAACTA 58.401 39.130 0.00 0.00 37.27 2.24
122 123 5.203528 ACCATAAATGCTGGCTGAAACTAT 58.796 37.500 0.00 0.00 37.27 2.12
123 124 5.068198 ACCATAAATGCTGGCTGAAACTATG 59.932 40.000 0.00 0.00 37.27 2.23
124 125 5.508489 CCATAAATGCTGGCTGAAACTATGG 60.508 44.000 8.03 8.03 0.00 2.74
125 126 3.370840 AATGCTGGCTGAAACTATGGA 57.629 42.857 0.00 0.00 0.00 3.41
126 127 2.408271 TGCTGGCTGAAACTATGGAG 57.592 50.000 0.00 0.00 0.00 3.86
127 128 1.630369 TGCTGGCTGAAACTATGGAGT 59.370 47.619 0.00 0.00 37.59 3.85
128 129 2.012673 GCTGGCTGAAACTATGGAGTG 58.987 52.381 0.00 0.00 35.52 3.51
129 130 2.616510 GCTGGCTGAAACTATGGAGTGT 60.617 50.000 0.00 0.00 35.52 3.55
130 131 3.005554 CTGGCTGAAACTATGGAGTGTG 58.994 50.000 0.00 0.00 35.52 3.82
131 132 2.637382 TGGCTGAAACTATGGAGTGTGA 59.363 45.455 0.00 0.00 35.52 3.58
132 133 3.072330 TGGCTGAAACTATGGAGTGTGAA 59.928 43.478 0.00 0.00 35.52 3.18
133 134 4.263462 TGGCTGAAACTATGGAGTGTGAAT 60.263 41.667 0.00 0.00 35.52 2.57
134 135 4.095483 GGCTGAAACTATGGAGTGTGAATG 59.905 45.833 0.00 0.00 35.52 2.67
135 136 4.437930 GCTGAAACTATGGAGTGTGAATGC 60.438 45.833 0.00 0.00 35.52 3.56
136 137 4.910195 TGAAACTATGGAGTGTGAATGCT 58.090 39.130 0.00 0.00 35.52 3.79
137 138 4.937620 TGAAACTATGGAGTGTGAATGCTC 59.062 41.667 0.00 0.00 35.52 4.26
163 164 3.814005 AAATGAAGATCCATGCTTGGC 57.186 42.857 13.75 1.11 43.29 4.52
164 165 2.750141 ATGAAGATCCATGCTTGGCT 57.250 45.000 13.75 4.03 43.29 4.75
165 166 2.519771 TGAAGATCCATGCTTGGCTT 57.480 45.000 13.75 11.70 43.29 4.35
166 167 2.097036 TGAAGATCCATGCTTGGCTTG 58.903 47.619 13.75 0.00 43.29 4.01
167 168 2.097825 GAAGATCCATGCTTGGCTTGT 58.902 47.619 13.75 0.01 43.29 3.16
168 169 1.760192 AGATCCATGCTTGGCTTGTC 58.240 50.000 13.75 8.84 43.29 3.18
169 170 1.005097 AGATCCATGCTTGGCTTGTCA 59.995 47.619 13.75 0.00 43.29 3.58
170 171 1.133790 GATCCATGCTTGGCTTGTCAC 59.866 52.381 13.75 0.00 43.29 3.67
171 172 0.895100 TCCATGCTTGGCTTGTCACC 60.895 55.000 13.75 0.00 43.29 4.02
172 173 1.588082 CATGCTTGGCTTGTCACCC 59.412 57.895 0.00 0.00 0.00 4.61
173 174 0.896940 CATGCTTGGCTTGTCACCCT 60.897 55.000 0.00 0.00 0.00 4.34
174 175 0.178953 ATGCTTGGCTTGTCACCCTT 60.179 50.000 0.00 0.00 0.00 3.95
175 176 0.396974 TGCTTGGCTTGTCACCCTTT 60.397 50.000 0.00 0.00 0.00 3.11
176 177 0.032540 GCTTGGCTTGTCACCCTTTG 59.967 55.000 0.00 0.00 0.00 2.77
177 178 1.691196 CTTGGCTTGTCACCCTTTGA 58.309 50.000 0.00 0.00 0.00 2.69
178 179 2.031120 CTTGGCTTGTCACCCTTTGAA 58.969 47.619 0.00 0.00 35.39 2.69
179 180 1.691196 TGGCTTGTCACCCTTTGAAG 58.309 50.000 0.00 0.00 35.39 3.02
180 181 1.064017 TGGCTTGTCACCCTTTGAAGT 60.064 47.619 0.00 0.00 35.39 3.01
181 182 1.338020 GGCTTGTCACCCTTTGAAGTG 59.662 52.381 0.00 0.00 35.39 3.16
182 183 2.024414 GCTTGTCACCCTTTGAAGTGT 58.976 47.619 0.00 0.00 35.39 3.55
183 184 2.223572 GCTTGTCACCCTTTGAAGTGTG 60.224 50.000 0.64 0.64 35.39 3.82
184 185 2.051334 TGTCACCCTTTGAAGTGTGG 57.949 50.000 6.53 0.00 35.48 4.17
185 186 0.668535 GTCACCCTTTGAAGTGTGGC 59.331 55.000 6.53 1.46 35.48 5.01
186 187 0.550914 TCACCCTTTGAAGTGTGGCT 59.449 50.000 6.53 0.00 35.48 4.75
187 188 0.670162 CACCCTTTGAAGTGTGGCTG 59.330 55.000 0.00 0.00 31.83 4.85
188 189 0.258774 ACCCTTTGAAGTGTGGCTGT 59.741 50.000 0.00 0.00 0.00 4.40
189 190 0.670162 CCCTTTGAAGTGTGGCTGTG 59.330 55.000 0.00 0.00 0.00 3.66
190 191 0.670162 CCTTTGAAGTGTGGCTGTGG 59.330 55.000 0.00 0.00 0.00 4.17
191 192 0.670162 CTTTGAAGTGTGGCTGTGGG 59.330 55.000 0.00 0.00 0.00 4.61
192 193 1.391157 TTTGAAGTGTGGCTGTGGGC 61.391 55.000 0.00 0.00 40.90 5.36
193 194 3.357079 GAAGTGTGGCTGTGGGCG 61.357 66.667 0.00 0.00 42.94 6.13
201 202 3.730761 GCTGTGGGCGCAGAACTG 61.731 66.667 10.83 9.19 38.70 3.16
202 203 3.052082 CTGTGGGCGCAGAACTGG 61.052 66.667 10.83 0.00 38.70 4.00
208 209 4.704833 GCGCAGAACTGGCCAGGA 62.705 66.667 35.42 0.00 0.00 3.86
209 210 2.435586 CGCAGAACTGGCCAGGAG 60.436 66.667 35.42 21.87 0.00 3.69
210 211 2.045536 GCAGAACTGGCCAGGAGG 60.046 66.667 35.42 21.94 38.23 4.30
211 212 2.596851 GCAGAACTGGCCAGGAGGA 61.597 63.158 35.42 0.00 36.89 3.71
212 213 2.069776 CAGAACTGGCCAGGAGGAA 58.930 57.895 35.42 0.00 36.89 3.36
213 214 0.401738 CAGAACTGGCCAGGAGGAAA 59.598 55.000 35.42 0.00 36.89 3.13
214 215 1.149101 AGAACTGGCCAGGAGGAAAA 58.851 50.000 35.42 0.00 36.89 2.29
215 216 1.713078 AGAACTGGCCAGGAGGAAAAT 59.287 47.619 35.42 10.21 36.89 1.82
216 217 2.919602 AGAACTGGCCAGGAGGAAAATA 59.080 45.455 35.42 0.00 36.89 1.40
217 218 3.333680 AGAACTGGCCAGGAGGAAAATAA 59.666 43.478 35.42 0.00 36.89 1.40
218 219 3.825908 ACTGGCCAGGAGGAAAATAAA 57.174 42.857 35.42 0.00 36.89 1.40
219 220 4.337264 ACTGGCCAGGAGGAAAATAAAT 57.663 40.909 35.42 7.81 36.89 1.40
220 221 4.687976 ACTGGCCAGGAGGAAAATAAATT 58.312 39.130 35.42 7.33 36.89 1.82
221 222 5.093677 ACTGGCCAGGAGGAAAATAAATTT 58.906 37.500 35.42 6.62 36.89 1.82
222 223 6.260663 ACTGGCCAGGAGGAAAATAAATTTA 58.739 36.000 35.42 0.00 36.89 1.40
223 224 6.728632 ACTGGCCAGGAGGAAAATAAATTTAA 59.271 34.615 35.42 0.00 36.89 1.52
224 225 7.402941 ACTGGCCAGGAGGAAAATAAATTTAAT 59.597 33.333 35.42 5.48 36.89 1.40
225 226 7.563906 TGGCCAGGAGGAAAATAAATTTAATG 58.436 34.615 0.00 0.00 36.89 1.90
226 227 7.181845 TGGCCAGGAGGAAAATAAATTTAATGT 59.818 33.333 0.00 0.00 36.89 2.71
227 228 7.495606 GGCCAGGAGGAAAATAAATTTAATGTG 59.504 37.037 0.00 0.00 36.89 3.21
228 229 8.257306 GCCAGGAGGAAAATAAATTTAATGTGA 58.743 33.333 1.21 0.00 36.89 3.58
249 250 9.874205 ATGTGAACTATTATTTGTTTCCATTGG 57.126 29.630 0.00 0.00 0.00 3.16
321 322 9.083080 GCAATATGTAAAACTATTTGTTGGGAC 57.917 33.333 0.00 0.00 39.13 4.46
335 336 5.864418 TGTTGGGACTAGTATATGTGGAC 57.136 43.478 0.00 0.00 0.00 4.02
344 345 8.150945 GGACTAGTATATGTGGACATGTTCATT 58.849 37.037 10.76 3.95 37.15 2.57
345 346 8.893219 ACTAGTATATGTGGACATGTTCATTG 57.107 34.615 10.76 0.00 37.15 2.82
471 481 8.262715 TGCTCACGACTTCAATAATAAAATGA 57.737 30.769 0.00 0.00 0.00 2.57
473 483 9.374960 GCTCACGACTTCAATAATAAAATGATC 57.625 33.333 0.00 0.00 0.00 2.92
509 544 5.674052 AAGATCTTCATGTACTCAGCACT 57.326 39.130 0.88 0.00 0.00 4.40
591 674 5.871396 AACTACTTCCTTCTCACACTCAA 57.129 39.130 0.00 0.00 0.00 3.02
627 710 2.121538 CGGCGAGGGAGAGACATCA 61.122 63.158 0.00 0.00 0.00 3.07
637 720 2.587194 AGACATCATCAGCGGCGC 60.587 61.111 26.86 26.86 0.00 6.53
672 755 2.094390 TCAGGACGAAGAACATAACCCG 60.094 50.000 0.00 0.00 0.00 5.28
708 791 2.389962 TTTCAGGCGTATGTACCACC 57.610 50.000 0.00 0.00 0.00 4.61
748 834 4.728534 CGAAGCCTCTTTCGGATATAGAG 58.271 47.826 0.52 0.00 44.56 2.43
781 872 4.524053 GCAAAGTACCTAGTTATTGGGCT 58.476 43.478 0.00 0.00 0.00 5.19
814 909 2.587194 CGCTCCAGGCTGATTCCG 60.587 66.667 17.94 9.11 39.13 4.30
860 955 1.745489 CTTACGGCCCAAGCTCCAC 60.745 63.158 0.00 0.00 39.73 4.02
861 956 2.185310 CTTACGGCCCAAGCTCCACT 62.185 60.000 0.00 0.00 39.73 4.00
862 957 0.905809 TTACGGCCCAAGCTCCACTA 60.906 55.000 0.00 0.00 39.73 2.74
863 958 1.327690 TACGGCCCAAGCTCCACTAG 61.328 60.000 0.00 0.00 39.73 2.57
865 960 2.301738 GGCCCAAGCTCCACTAGGT 61.302 63.158 0.00 0.00 39.73 3.08
866 961 1.222113 GCCCAAGCTCCACTAGGTC 59.778 63.158 0.00 0.00 33.87 3.85
867 962 1.517832 CCCAAGCTCCACTAGGTCG 59.482 63.158 0.00 0.00 33.87 4.79
868 963 1.517832 CCAAGCTCCACTAGGTCGG 59.482 63.158 0.00 0.00 33.87 4.79
869 964 1.258445 CCAAGCTCCACTAGGTCGGT 61.258 60.000 0.00 0.00 33.87 4.69
891 986 4.771114 TTTCTCTTTGGAGGAACAGTCA 57.229 40.909 0.00 0.00 39.86 3.41
898 993 1.249407 GGAGGAACAGTCAGTCTCGT 58.751 55.000 0.00 0.00 0.00 4.18
949 1045 3.268032 CAAACCCTCCCCCAGCCT 61.268 66.667 0.00 0.00 0.00 4.58
1698 1857 1.827399 TTGAGAAGGAGACCCGTGCC 61.827 60.000 0.00 0.00 37.58 5.01
2097 2268 2.857186 TTGTGCTTCCTATGCTGTCA 57.143 45.000 0.00 0.00 0.00 3.58
2289 2460 3.328931 AGGAGCAAGGTTTCAAGATCAGA 59.671 43.478 0.00 0.00 0.00 3.27
2448 2619 1.000274 GTTGTTGGTGTCCTTGATGCC 60.000 52.381 0.00 0.00 0.00 4.40
2454 2625 1.750018 TGTCCTTGATGCCATGCCG 60.750 57.895 0.00 0.00 0.00 5.69
2721 2895 1.586154 GGGACAAGACGGCCATTGTG 61.586 60.000 19.48 7.24 39.66 3.33
3205 3379 0.733729 CAATCTGCTGCAGAAGAGGC 59.266 55.000 33.31 8.52 44.04 4.70
3329 3503 3.640967 TGTTTGCAAACCAGCCTTTCTAT 59.359 39.130 33.33 0.00 38.11 1.98
3455 3637 4.096382 ACATCGACTGCTTTTGAAGTGTTT 59.904 37.500 0.00 0.00 38.76 2.83
3480 3662 5.652994 TGCAGGTTAAACAAACTGAGTTT 57.347 34.783 4.45 4.45 41.63 2.66
3654 3844 7.132694 TGTTATGCACTTCAGTATTCAGTTG 57.867 36.000 0.00 0.00 0.00 3.16
3660 3850 5.062809 GCACTTCAGTATTCAGTTGTAGAGC 59.937 44.000 0.00 0.00 0.00 4.09
3661 3851 6.393990 CACTTCAGTATTCAGTTGTAGAGCT 58.606 40.000 0.00 0.00 0.00 4.09
3668 3858 9.973450 CAGTATTCAGTTGTAGAGCTATGTATT 57.027 33.333 0.00 0.00 0.00 1.89
3811 4003 6.294508 GGATAGAAAGTGCTTTTGTTTGGCTA 60.295 38.462 0.00 0.00 32.11 3.93
3847 4039 8.615211 GTTCTAGACAATGATTATGAATGTGCA 58.385 33.333 0.00 0.00 0.00 4.57
3854 4046 4.334552 TGATTATGAATGTGCACAGGTGT 58.665 39.130 25.84 13.42 0.00 4.16
4040 4235 1.672881 GTGCTCTGCTCTGTGTTTTGT 59.327 47.619 0.00 0.00 0.00 2.83
4099 4294 6.000219 ACAATGTGCATGAGGGTAATATCTC 59.000 40.000 0.00 0.00 0.00 2.75
4149 4344 4.916041 TGGAAGTTCCATCTGATTGAGT 57.084 40.909 21.05 0.00 42.67 3.41
4153 4348 6.016024 TGGAAGTTCCATCTGATTGAGTTTTG 60.016 38.462 21.05 0.00 42.67 2.44
4156 4351 4.387026 TCCATCTGATTGAGTTTTGGGT 57.613 40.909 0.00 0.00 0.00 4.51
4157 4352 4.739793 TCCATCTGATTGAGTTTTGGGTT 58.260 39.130 0.00 0.00 0.00 4.11
4158 4353 5.886609 TCCATCTGATTGAGTTTTGGGTTA 58.113 37.500 0.00 0.00 0.00 2.85
4159 4354 6.493166 TCCATCTGATTGAGTTTTGGGTTAT 58.507 36.000 0.00 0.00 0.00 1.89
4160 4355 6.377996 TCCATCTGATTGAGTTTTGGGTTATG 59.622 38.462 0.00 0.00 0.00 1.90
4161 4356 6.377996 CCATCTGATTGAGTTTTGGGTTATGA 59.622 38.462 0.00 0.00 0.00 2.15
4162 4357 7.415989 CCATCTGATTGAGTTTTGGGTTATGAG 60.416 40.741 0.00 0.00 0.00 2.90
4163 4358 5.415701 TCTGATTGAGTTTTGGGTTATGAGC 59.584 40.000 0.00 0.00 0.00 4.26
4164 4359 5.076182 TGATTGAGTTTTGGGTTATGAGCA 58.924 37.500 0.00 0.00 0.00 4.26
4165 4360 5.538053 TGATTGAGTTTTGGGTTATGAGCAA 59.462 36.000 0.00 0.00 0.00 3.91
4166 4361 6.211184 TGATTGAGTTTTGGGTTATGAGCAAT 59.789 34.615 0.00 0.00 0.00 3.56
4167 4362 6.418057 TTGAGTTTTGGGTTATGAGCAATT 57.582 33.333 0.00 0.00 0.00 2.32
4168 4363 5.782047 TGAGTTTTGGGTTATGAGCAATTG 58.218 37.500 0.00 0.00 0.00 2.32
4169 4364 5.538053 TGAGTTTTGGGTTATGAGCAATTGA 59.462 36.000 10.34 0.00 0.00 2.57
4170 4365 5.783111 AGTTTTGGGTTATGAGCAATTGAC 58.217 37.500 10.34 2.82 0.00 3.18
4171 4366 4.799564 TTTGGGTTATGAGCAATTGACC 57.200 40.909 10.34 6.41 0.00 4.02
4172 4367 2.733956 TGGGTTATGAGCAATTGACCC 58.266 47.619 19.25 19.25 40.98 4.46
4173 4368 2.042297 TGGGTTATGAGCAATTGACCCA 59.958 45.455 23.05 23.05 44.78 4.51
4174 4369 3.299503 GGGTTATGAGCAATTGACCCAT 58.700 45.455 20.54 15.53 40.60 4.00
4175 4370 3.706086 GGGTTATGAGCAATTGACCCATT 59.294 43.478 20.54 0.09 40.60 3.16
4176 4371 4.162131 GGGTTATGAGCAATTGACCCATTT 59.838 41.667 20.54 1.40 40.60 2.32
4177 4372 5.111293 GGTTATGAGCAATTGACCCATTTG 58.889 41.667 10.34 0.00 0.00 2.32
4178 4373 3.899052 ATGAGCAATTGACCCATTTGG 57.101 42.857 10.34 0.00 41.37 3.28
4179 4374 1.275856 TGAGCAATTGACCCATTTGGC 59.724 47.619 10.34 0.00 37.83 4.52
4180 4375 0.614812 AGCAATTGACCCATTTGGCC 59.385 50.000 10.34 0.00 37.83 5.36
4181 4376 0.324285 GCAATTGACCCATTTGGCCA 59.676 50.000 10.34 0.00 37.83 5.36
4182 4377 1.065272 GCAATTGACCCATTTGGCCAT 60.065 47.619 6.09 0.00 37.83 4.40
4183 4378 2.618559 GCAATTGACCCATTTGGCCATT 60.619 45.455 6.09 0.00 37.83 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.958091 CCATTTGCGTTCCAGTTCCA 59.042 50.000 0.00 0.00 0.00 3.53
1 2 1.243902 TCCATTTGCGTTCCAGTTCC 58.756 50.000 0.00 0.00 0.00 3.62
2 3 3.575965 ATTCCATTTGCGTTCCAGTTC 57.424 42.857 0.00 0.00 0.00 3.01
3 4 4.335400 AAATTCCATTTGCGTTCCAGTT 57.665 36.364 0.00 0.00 0.00 3.16
4 5 4.039124 AGAAAATTCCATTTGCGTTCCAGT 59.961 37.500 0.00 0.00 32.86 4.00
5 6 4.559153 AGAAAATTCCATTTGCGTTCCAG 58.441 39.130 0.00 0.00 32.86 3.86
6 7 4.280677 AGAGAAAATTCCATTTGCGTTCCA 59.719 37.500 0.00 0.00 32.86 3.53
7 8 4.622740 CAGAGAAAATTCCATTTGCGTTCC 59.377 41.667 0.00 0.00 32.86 3.62
8 9 4.090498 GCAGAGAAAATTCCATTTGCGTTC 59.910 41.667 0.00 0.00 32.86 3.95
9 10 3.989817 GCAGAGAAAATTCCATTTGCGTT 59.010 39.130 0.00 0.00 32.86 4.84
10 11 3.256631 AGCAGAGAAAATTCCATTTGCGT 59.743 39.130 0.00 0.00 32.86 5.24
11 12 3.841643 AGCAGAGAAAATTCCATTTGCG 58.158 40.909 0.00 0.00 32.86 4.85
12 13 6.393171 ACTTAGCAGAGAAAATTCCATTTGC 58.607 36.000 0.00 0.00 31.77 3.68
13 14 8.186821 CCTACTTAGCAGAGAAAATTCCATTTG 58.813 37.037 0.00 0.00 31.77 2.32
14 15 7.340487 CCCTACTTAGCAGAGAAAATTCCATTT 59.660 37.037 0.00 0.00 0.00 2.32
15 16 6.830838 CCCTACTTAGCAGAGAAAATTCCATT 59.169 38.462 0.00 0.00 0.00 3.16
16 17 6.069381 ACCCTACTTAGCAGAGAAAATTCCAT 60.069 38.462 0.00 0.00 0.00 3.41
17 18 5.250774 ACCCTACTTAGCAGAGAAAATTCCA 59.749 40.000 0.00 0.00 0.00 3.53
18 19 5.746284 ACCCTACTTAGCAGAGAAAATTCC 58.254 41.667 0.00 0.00 0.00 3.01
19 20 8.204836 TCATACCCTACTTAGCAGAGAAAATTC 58.795 37.037 0.00 0.00 0.00 2.17
20 21 8.090788 TCATACCCTACTTAGCAGAGAAAATT 57.909 34.615 0.00 0.00 0.00 1.82
21 22 7.676683 TCATACCCTACTTAGCAGAGAAAAT 57.323 36.000 0.00 0.00 0.00 1.82
22 23 7.490657 TTCATACCCTACTTAGCAGAGAAAA 57.509 36.000 0.00 0.00 0.00 2.29
23 24 7.676683 ATTCATACCCTACTTAGCAGAGAAA 57.323 36.000 0.00 0.00 0.00 2.52
24 25 8.958060 ATATTCATACCCTACTTAGCAGAGAA 57.042 34.615 0.00 0.00 0.00 2.87
25 26 8.958060 AATATTCATACCCTACTTAGCAGAGA 57.042 34.615 0.00 0.00 0.00 3.10
26 27 9.646427 GAAATATTCATACCCTACTTAGCAGAG 57.354 37.037 0.00 0.00 0.00 3.35
27 28 9.154632 TGAAATATTCATACCCTACTTAGCAGA 57.845 33.333 0.00 0.00 34.08 4.26
43 44 9.256477 GTGTCCGTACTGATTATGAAATATTCA 57.744 33.333 0.00 0.00 45.01 2.57
44 45 8.709646 GGTGTCCGTACTGATTATGAAATATTC 58.290 37.037 0.00 0.00 31.55 1.75
45 46 8.208224 TGGTGTCCGTACTGATTATGAAATATT 58.792 33.333 0.00 0.00 0.00 1.28
46 47 7.732025 TGGTGTCCGTACTGATTATGAAATAT 58.268 34.615 0.00 0.00 0.00 1.28
47 48 7.114866 TGGTGTCCGTACTGATTATGAAATA 57.885 36.000 0.00 0.00 0.00 1.40
48 49 5.984725 TGGTGTCCGTACTGATTATGAAAT 58.015 37.500 0.00 0.00 0.00 2.17
49 50 5.408880 TGGTGTCCGTACTGATTATGAAA 57.591 39.130 0.00 0.00 0.00 2.69
50 51 5.408880 TTGGTGTCCGTACTGATTATGAA 57.591 39.130 0.00 0.00 0.00 2.57
51 52 4.142026 CCTTGGTGTCCGTACTGATTATGA 60.142 45.833 0.00 0.00 0.00 2.15
52 53 4.119862 CCTTGGTGTCCGTACTGATTATG 58.880 47.826 0.00 0.00 0.00 1.90
53 54 3.134081 CCCTTGGTGTCCGTACTGATTAT 59.866 47.826 0.00 0.00 0.00 1.28
54 55 2.498481 CCCTTGGTGTCCGTACTGATTA 59.502 50.000 0.00 0.00 0.00 1.75
55 56 1.278127 CCCTTGGTGTCCGTACTGATT 59.722 52.381 0.00 0.00 0.00 2.57
56 57 0.902531 CCCTTGGTGTCCGTACTGAT 59.097 55.000 0.00 0.00 0.00 2.90
57 58 0.470456 ACCCTTGGTGTCCGTACTGA 60.470 55.000 0.00 0.00 32.98 3.41
58 59 2.055299 ACCCTTGGTGTCCGTACTG 58.945 57.895 0.00 0.00 32.98 2.74
59 60 4.633547 ACCCTTGGTGTCCGTACT 57.366 55.556 0.00 0.00 32.98 2.73
68 69 5.163088 GGTTAGATGAATATCCACCCTTGGT 60.163 44.000 0.00 0.00 44.35 3.67
69 70 5.073691 AGGTTAGATGAATATCCACCCTTGG 59.926 44.000 0.00 0.00 45.56 3.61
70 71 6.192970 AGGTTAGATGAATATCCACCCTTG 57.807 41.667 0.00 0.00 37.66 3.61
71 72 6.848562 AAGGTTAGATGAATATCCACCCTT 57.151 37.500 0.00 0.00 37.66 3.95
72 73 7.947782 TTAAGGTTAGATGAATATCCACCCT 57.052 36.000 0.00 0.00 37.66 4.34
73 74 8.990163 TTTTAAGGTTAGATGAATATCCACCC 57.010 34.615 0.00 0.00 37.66 4.61
76 77 9.983024 TGGTTTTTAAGGTTAGATGAATATCCA 57.017 29.630 0.00 0.00 33.64 3.41
86 87 8.527810 CCAGCATTTATGGTTTTTAAGGTTAGA 58.472 33.333 0.00 0.00 36.17 2.10
87 88 7.277760 GCCAGCATTTATGGTTTTTAAGGTTAG 59.722 37.037 0.00 0.00 40.17 2.34
88 89 7.038658 AGCCAGCATTTATGGTTTTTAAGGTTA 60.039 33.333 0.00 0.00 40.17 2.85
89 90 5.937540 GCCAGCATTTATGGTTTTTAAGGTT 59.062 36.000 0.00 0.00 40.17 3.50
90 91 5.248248 AGCCAGCATTTATGGTTTTTAAGGT 59.752 36.000 0.00 0.00 40.17 3.50
91 92 5.581874 CAGCCAGCATTTATGGTTTTTAAGG 59.418 40.000 0.00 0.00 40.17 2.69
92 93 6.397272 TCAGCCAGCATTTATGGTTTTTAAG 58.603 36.000 0.00 0.00 40.17 1.85
93 94 6.352016 TCAGCCAGCATTTATGGTTTTTAA 57.648 33.333 0.00 0.00 40.17 1.52
94 95 5.991933 TCAGCCAGCATTTATGGTTTTTA 57.008 34.783 0.00 0.00 40.17 1.52
95 96 4.888326 TCAGCCAGCATTTATGGTTTTT 57.112 36.364 0.00 0.00 40.17 1.94
96 97 4.888326 TTCAGCCAGCATTTATGGTTTT 57.112 36.364 0.00 0.00 40.17 2.43
97 98 4.284234 AGTTTCAGCCAGCATTTATGGTTT 59.716 37.500 0.00 0.00 40.17 3.27
98 99 3.834231 AGTTTCAGCCAGCATTTATGGTT 59.166 39.130 0.00 0.00 40.17 3.67
99 100 3.434309 AGTTTCAGCCAGCATTTATGGT 58.566 40.909 0.00 0.00 40.17 3.55
100 101 5.508489 CCATAGTTTCAGCCAGCATTTATGG 60.508 44.000 0.00 0.00 41.04 2.74
101 102 5.300034 TCCATAGTTTCAGCCAGCATTTATG 59.700 40.000 0.00 0.00 0.00 1.90
102 103 5.448654 TCCATAGTTTCAGCCAGCATTTAT 58.551 37.500 0.00 0.00 0.00 1.40
103 104 4.854173 TCCATAGTTTCAGCCAGCATTTA 58.146 39.130 0.00 0.00 0.00 1.40
104 105 3.698040 CTCCATAGTTTCAGCCAGCATTT 59.302 43.478 0.00 0.00 0.00 2.32
105 106 3.285484 CTCCATAGTTTCAGCCAGCATT 58.715 45.455 0.00 0.00 0.00 3.56
106 107 2.240667 ACTCCATAGTTTCAGCCAGCAT 59.759 45.455 0.00 0.00 29.00 3.79
107 108 1.630369 ACTCCATAGTTTCAGCCAGCA 59.370 47.619 0.00 0.00 29.00 4.41
108 109 2.012673 CACTCCATAGTTTCAGCCAGC 58.987 52.381 0.00 0.00 31.97 4.85
109 110 3.005554 CACACTCCATAGTTTCAGCCAG 58.994 50.000 0.00 0.00 31.97 4.85
110 111 2.637382 TCACACTCCATAGTTTCAGCCA 59.363 45.455 0.00 0.00 31.97 4.75
111 112 3.334583 TCACACTCCATAGTTTCAGCC 57.665 47.619 0.00 0.00 31.97 4.85
112 113 4.437930 GCATTCACACTCCATAGTTTCAGC 60.438 45.833 0.00 0.00 31.97 4.26
113 114 4.940046 AGCATTCACACTCCATAGTTTCAG 59.060 41.667 0.00 0.00 31.97 3.02
114 115 4.910195 AGCATTCACACTCCATAGTTTCA 58.090 39.130 0.00 0.00 31.97 2.69
115 116 5.476752 GAGCATTCACACTCCATAGTTTC 57.523 43.478 0.00 0.00 31.97 2.78
141 142 4.224370 AGCCAAGCATGGATCTTCATTTTT 59.776 37.500 13.26 0.00 43.38 1.94
142 143 3.773119 AGCCAAGCATGGATCTTCATTTT 59.227 39.130 13.26 0.00 43.38 1.82
143 144 3.371965 AGCCAAGCATGGATCTTCATTT 58.628 40.909 13.26 0.00 43.38 2.32
144 145 3.028094 AGCCAAGCATGGATCTTCATT 57.972 42.857 13.26 0.00 43.38 2.57
145 146 2.750141 AGCCAAGCATGGATCTTCAT 57.250 45.000 13.26 0.00 43.38 2.57
154 155 1.588082 GGGTGACAAGCCAAGCATG 59.412 57.895 0.00 0.00 43.91 4.06
155 156 4.102113 GGGTGACAAGCCAAGCAT 57.898 55.556 0.00 0.00 43.91 3.79
161 162 1.338020 CACTTCAAAGGGTGACAAGCC 59.662 52.381 0.00 0.00 44.89 4.35
162 163 2.024414 ACACTTCAAAGGGTGACAAGC 58.976 47.619 0.00 0.00 42.11 4.01
169 170 0.258774 ACAGCCACACTTCAAAGGGT 59.741 50.000 0.00 0.00 45.28 4.34
170 171 0.670162 CACAGCCACACTTCAAAGGG 59.330 55.000 0.00 0.00 34.93 3.95
171 172 0.670162 CCACAGCCACACTTCAAAGG 59.330 55.000 0.00 0.00 0.00 3.11
172 173 0.670162 CCCACAGCCACACTTCAAAG 59.330 55.000 0.00 0.00 0.00 2.77
173 174 1.391157 GCCCACAGCCACACTTCAAA 61.391 55.000 0.00 0.00 34.35 2.69
174 175 1.827789 GCCCACAGCCACACTTCAA 60.828 57.895 0.00 0.00 34.35 2.69
175 176 2.203337 GCCCACAGCCACACTTCA 60.203 61.111 0.00 0.00 34.35 3.02
176 177 3.357079 CGCCCACAGCCACACTTC 61.357 66.667 0.00 0.00 38.78 3.01
184 185 3.730761 CAGTTCTGCGCCCACAGC 61.731 66.667 4.18 0.00 37.59 4.40
185 186 3.052082 CCAGTTCTGCGCCCACAG 61.052 66.667 4.18 0.00 39.12 3.66
191 192 4.704833 TCCTGGCCAGTTCTGCGC 62.705 66.667 30.63 0.00 0.00 6.09
192 193 2.435586 CTCCTGGCCAGTTCTGCG 60.436 66.667 30.63 14.69 0.00 5.18
193 194 2.045536 CCTCCTGGCCAGTTCTGC 60.046 66.667 30.63 0.00 0.00 4.26
194 195 0.401738 TTTCCTCCTGGCCAGTTCTG 59.598 55.000 30.63 15.82 0.00 3.02
195 196 1.149101 TTTTCCTCCTGGCCAGTTCT 58.851 50.000 30.63 0.00 0.00 3.01
196 197 2.222227 ATTTTCCTCCTGGCCAGTTC 57.778 50.000 30.63 0.00 0.00 3.01
197 198 3.825908 TTATTTTCCTCCTGGCCAGTT 57.174 42.857 30.63 7.78 0.00 3.16
198 199 3.825908 TTTATTTTCCTCCTGGCCAGT 57.174 42.857 30.63 12.56 0.00 4.00
199 200 5.682234 AAATTTATTTTCCTCCTGGCCAG 57.318 39.130 26.87 26.87 0.00 4.85
200 201 7.181845 ACATTAAATTTATTTTCCTCCTGGCCA 59.818 33.333 4.71 4.71 0.00 5.36
201 202 7.495606 CACATTAAATTTATTTTCCTCCTGGCC 59.504 37.037 0.00 0.00 0.00 5.36
202 203 8.257306 TCACATTAAATTTATTTTCCTCCTGGC 58.743 33.333 0.00 0.00 0.00 4.85
266 267 6.378710 TTTGGTGTGTGATTTATTCGTGAA 57.621 33.333 0.00 0.00 0.00 3.18
283 284 8.772705 AGTTTTACATATTGCACAAATTTGGTG 58.227 29.630 21.74 16.86 39.25 4.17
295 296 9.083080 GTCCCAACAAATAGTTTTACATATTGC 57.917 33.333 0.00 0.00 38.74 3.56
311 312 6.213802 TGTCCACATATACTAGTCCCAACAAA 59.786 38.462 0.00 0.00 0.00 2.83
314 315 5.864418 TGTCCACATATACTAGTCCCAAC 57.136 43.478 0.00 0.00 0.00 3.77
321 322 9.546428 TTCAATGAACATGTCCACATATACTAG 57.454 33.333 0.00 0.00 34.26 2.57
441 451 9.906660 TTTATTATTGAAGTCGTGAGCATTTTT 57.093 25.926 0.00 0.00 0.00 1.94
591 674 1.227853 GAAGCCACCCAGTCGTTGT 60.228 57.895 0.00 0.00 0.00 3.32
637 720 2.885644 CTGAACCGGTCGATGGCG 60.886 66.667 8.04 0.00 39.35 5.69
658 741 2.007608 GTCCTGCGGGTTATGTTCTTC 58.992 52.381 12.43 0.00 0.00 2.87
672 755 5.449725 GCCTGAAAATAGATCAAAGTCCTGC 60.450 44.000 0.00 0.00 0.00 4.85
708 791 5.973565 GGCTTCGGATTTATTGATCAAACTG 59.026 40.000 13.09 7.22 0.00 3.16
781 872 2.045438 CGTGGTGCTATTGGGCCA 60.045 61.111 0.00 0.00 0.00 5.36
814 909 3.050275 GCCGGGCCGCATTAGATC 61.050 66.667 23.20 0.00 0.00 2.75
833 928 0.177141 TGGGCCGTAAGAGGAATTCG 59.823 55.000 0.00 0.00 43.02 3.34
860 955 4.246458 CTCCAAAGAGAAAACCGACCTAG 58.754 47.826 0.00 0.00 43.39 3.02
861 956 3.007614 CCTCCAAAGAGAAAACCGACCTA 59.992 47.826 0.00 0.00 43.39 3.08
862 957 2.224548 CCTCCAAAGAGAAAACCGACCT 60.225 50.000 0.00 0.00 43.39 3.85
863 958 2.152016 CCTCCAAAGAGAAAACCGACC 58.848 52.381 0.00 0.00 43.39 4.79
865 960 3.118186 TGTTCCTCCAAAGAGAAAACCGA 60.118 43.478 0.00 0.00 43.39 4.69
866 961 3.211045 TGTTCCTCCAAAGAGAAAACCG 58.789 45.455 0.00 0.00 43.39 4.44
867 962 4.207955 ACTGTTCCTCCAAAGAGAAAACC 58.792 43.478 0.00 0.00 43.39 3.27
868 963 4.881850 TGACTGTTCCTCCAAAGAGAAAAC 59.118 41.667 0.00 0.00 43.39 2.43
869 964 5.110814 TGACTGTTCCTCCAAAGAGAAAA 57.889 39.130 0.00 0.00 43.39 2.29
891 986 3.027412 AGATCAGGTTGCATACGAGACT 58.973 45.455 0.00 0.00 0.00 3.24
1232 1337 3.009714 GGTCCCTGTCCCTGTCCC 61.010 72.222 0.00 0.00 0.00 4.46
1233 1338 3.391382 CGGTCCCTGTCCCTGTCC 61.391 72.222 0.00 0.00 0.00 4.02
1234 1339 3.391382 CCGGTCCCTGTCCCTGTC 61.391 72.222 0.00 0.00 0.00 3.51
1237 1342 4.716977 GTCCCGGTCCCTGTCCCT 62.717 72.222 0.00 0.00 0.00 4.20
1734 1905 3.969312 TCTTATCAGCCACATCATCCTCA 59.031 43.478 0.00 0.00 0.00 3.86
1926 2097 0.035881 CAGTCCCAAGCTTGCTCTCA 59.964 55.000 21.43 0.00 0.00 3.27
2097 2268 0.600255 GCGGCAGGCGAGTAATGTAT 60.600 55.000 22.52 0.00 0.00 2.29
2289 2460 0.546122 TCACAACTTCACAGCCCTGT 59.454 50.000 0.00 0.00 46.17 4.00
2448 2619 2.093306 TCAGGTTACTTGACGGCATG 57.907 50.000 1.93 1.93 0.00 4.06
2454 2625 4.957296 TCTCAGGTTTCAGGTTACTTGAC 58.043 43.478 0.00 0.00 0.00 3.18
2721 2895 4.346129 CTGACTTCTTTGTGTTGCAGAAC 58.654 43.478 0.00 0.00 0.00 3.01
3194 3368 1.680522 GGATCTCCGCCTCTTCTGCA 61.681 60.000 0.00 0.00 0.00 4.41
3205 3379 2.108168 TGTACCCAAGAAGGATCTCCG 58.892 52.381 0.00 0.00 41.22 4.63
3280 3454 9.750125 GGAAAGGATAATGGTTCAATTGTTATC 57.250 33.333 5.13 10.49 33.27 1.75
3301 3475 2.204237 GCTGGTTTGCAAACAGGAAAG 58.796 47.619 35.95 25.33 38.28 2.62
3455 3637 6.031751 ACTCAGTTTGTTTAACCTGCAAAA 57.968 33.333 0.00 0.00 37.46 2.44
3507 3689 9.373603 TGCAAAAATGATAGAAAATGAATCTGG 57.626 29.630 0.00 0.00 0.00 3.86
3688 3878 7.917505 GCTCGGTCATTTCAAATCTCATTTTAT 59.082 33.333 0.00 0.00 0.00 1.40
3699 3890 3.410631 TGGTAGCTCGGTCATTTCAAA 57.589 42.857 0.00 0.00 0.00 2.69
3841 4033 0.670162 GCTTCAACACCTGTGCACAT 59.330 50.000 22.00 2.92 0.00 3.21
3854 4046 4.700213 GGCTAGTTATTCAACAGGCTTCAA 59.300 41.667 0.00 0.00 37.10 2.69
3962 4157 9.587772 ACATATAAACACTTAACTCTAGCTGTG 57.412 33.333 0.00 0.00 0.00 3.66
4040 4235 2.164422 TCAACGTGGCAATCAACAAACA 59.836 40.909 0.00 0.00 0.00 2.83
4099 4294 9.574458 TCTCTCTGAAAATTCATTACTCTTACG 57.426 33.333 0.00 0.00 36.46 3.18
4113 4308 7.006509 TGGAACTTCCAATTCTCTCTGAAAAT 58.993 34.615 8.15 0.00 45.00 1.82
4116 4311 5.567037 TGGAACTTCCAATTCTCTCTGAA 57.433 39.130 8.15 0.00 45.00 3.02
4148 4343 4.929211 GGTCAATTGCTCATAACCCAAAAC 59.071 41.667 0.00 0.00 0.00 2.43
4149 4344 4.020662 GGGTCAATTGCTCATAACCCAAAA 60.021 41.667 20.54 0.00 44.72 2.44
4153 4348 2.733956 TGGGTCAATTGCTCATAACCC 58.266 47.619 19.25 19.25 45.41 4.11
4156 4351 4.382901 GCCAAATGGGTCAATTGCTCATAA 60.383 41.667 13.38 0.00 39.65 1.90
4157 4352 3.132646 GCCAAATGGGTCAATTGCTCATA 59.867 43.478 13.38 0.00 39.65 2.15
4158 4353 2.093341 GCCAAATGGGTCAATTGCTCAT 60.093 45.455 8.80 8.80 39.65 2.90
4159 4354 1.275856 GCCAAATGGGTCAATTGCTCA 59.724 47.619 0.00 2.62 39.65 4.26
4160 4355 1.405933 GGCCAAATGGGTCAATTGCTC 60.406 52.381 0.00 0.00 42.53 4.26
4161 4356 0.614812 GGCCAAATGGGTCAATTGCT 59.385 50.000 0.00 0.00 42.53 3.91
4162 4357 3.157727 GGCCAAATGGGTCAATTGC 57.842 52.632 0.00 0.00 42.53 3.56


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

AutoCloner maintained by Alex Coulton.