Multiple sequence alignment - TraesCS5B01G162000

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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 TraesCS5B01G162000 chr5B 100.000 1505 0 0 625 2129 299015308 299016812 0.000000e+00 2780.0
1 TraesCS5B01G162000 chr5B 100.000 353 0 0 1 353 299014684 299015036 0.000000e+00 652.0
2 TraesCS5B01G162000 chr5B 81.818 352 41 15 1442 1780 509092746 509092405 7.480000e-70 274.0
3 TraesCS5B01G162000 chr5B 78.571 238 43 7 1421 1652 693879033 693879268 1.320000e-32 150.0
4 TraesCS5B01G162000 chr5B 81.731 104 13 5 1 101 604155553 604155653 4.870000e-12 82.4
5 TraesCS5B01G162000 chr5D 92.914 1496 61 15 645 2129 265662345 265663806 0.000000e+00 2134.0
6 TraesCS5B01G162000 chr5A 96.731 520 15 1 645 1164 353169862 353170379 0.000000e+00 865.0
7 TraesCS5B01G162000 chr5A 85.825 515 45 14 1626 2129 353171605 353172102 2.420000e-144 521.0
8 TraesCS5B01G162000 chr5A 87.425 334 26 10 1156 1481 353171261 353171586 9.280000e-99 370.0
9 TraesCS5B01G162000 chr3A 84.409 372 40 14 1421 1779 654323273 654323639 1.210000e-92 350.0
10 TraesCS5B01G162000 chr3A 78.836 378 52 17 1421 1780 396022711 396023078 1.640000e-56 230.0
11 TraesCS5B01G162000 chr3A 82.000 100 15 2 1 99 550115193 550115096 4.870000e-12 82.4
12 TraesCS5B01G162000 chr3A 77.982 109 18 4 154 261 508519813 508519710 1.760000e-06 63.9
13 TraesCS5B01G162000 chr7B 81.742 356 44 17 1432 1778 610350955 610350612 5.790000e-71 278.0
14 TraesCS5B01G162000 chr7B 76.350 389 40 31 1408 1780 395204391 395204743 6.080000e-36 161.0
15 TraesCS5B01G162000 chr1D 84.053 301 34 9 1421 1711 483356203 483355907 5.790000e-71 278.0
16 TraesCS5B01G162000 chr1D 77.483 151 25 5 151 297 88222453 88222598 4.870000e-12 82.4
17 TraesCS5B01G162000 chr4A 79.167 384 34 19 1421 1778 565835943 565836306 7.650000e-55 224.0
18 TraesCS5B01G162000 chr3B 81.362 279 34 8 1512 1778 545811392 545811120 5.950000e-51 211.0
19 TraesCS5B01G162000 chr3B 75.748 301 48 12 1430 1714 803649914 803649623 6.170000e-26 128.0
20 TraesCS5B01G162000 chr3B 82.105 95 13 3 1680 1770 452422997 452423091 6.300000e-11 78.7
21 TraesCS5B01G162000 chr3B 83.333 84 11 2 1690 1770 452422094 452422177 8.150000e-10 75.0
22 TraesCS5B01G162000 chr2D 85.644 202 21 4 1428 1629 208613526 208613333 2.770000e-49 206.0
23 TraesCS5B01G162000 chr2B 79.167 240 32 13 1485 1711 657466676 657466910 1.320000e-32 150.0
24 TraesCS5B01G162000 chr2B 87.838 74 8 1 154 227 110040240 110040168 3.760000e-13 86.1
25 TraesCS5B01G162000 chr6A 74.570 291 59 10 1 278 83331567 83331855 1.730000e-21 113.0
26 TraesCS5B01G162000 chrUn 88.750 80 8 1 3 81 295507253 295507332 1.740000e-16 97.1
27 TraesCS5B01G162000 chr7A 88.750 80 8 1 3 81 163111412 163111491 1.740000e-16 97.1
28 TraesCS5B01G162000 chr7A 78.082 146 17 12 154 294 166762743 166762608 6.300000e-11 78.7
29 TraesCS5B01G162000 chr6B 78.000 150 23 6 151 295 40071587 40071731 3.760000e-13 86.1
30 TraesCS5B01G162000 chr2A 93.023 43 2 1 249 291 234119314 234119273 6.340000e-06 62.1
31 TraesCS5B01G162000 chr4B 96.875 32 1 0 1381 1412 510827783 510827814 1.000000e-03 54.7


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 TraesCS5B01G162000 chr5B 299014684 299016812 2128 False 1716.000000 2780 100.000000 1 2129 2 chr5B.!!$F3 2128
1 TraesCS5B01G162000 chr5D 265662345 265663806 1461 False 2134.000000 2134 92.914000 645 2129 1 chr5D.!!$F1 1484
2 TraesCS5B01G162000 chr5A 353169862 353172102 2240 False 585.333333 865 89.993667 645 2129 3 chr5A.!!$F1 1484

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
164 165 0.035317 TGTGCTGCCTTCGTCAATCT 59.965 50.0 0.0 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1236 2132 0.041535 TGAGGGCAATCTTTGGGCAT 59.958 50.0 0.0 0.0 0.0 4.4 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
23 24 6.059787 AGCTCAGATGGTTAGATTCTTTGT 57.940 37.500 0.00 0.00 0.00 2.83
24 25 5.879223 AGCTCAGATGGTTAGATTCTTTGTG 59.121 40.000 0.00 0.00 0.00 3.33
25 26 5.065731 GCTCAGATGGTTAGATTCTTTGTGG 59.934 44.000 0.00 0.00 0.00 4.17
26 27 6.126863 TCAGATGGTTAGATTCTTTGTGGT 57.873 37.500 0.00 0.00 0.00 4.16
27 28 5.939883 TCAGATGGTTAGATTCTTTGTGGTG 59.060 40.000 0.00 0.00 0.00 4.17
28 29 5.124457 CAGATGGTTAGATTCTTTGTGGTGG 59.876 44.000 0.00 0.00 0.00 4.61
29 30 4.715534 TGGTTAGATTCTTTGTGGTGGA 57.284 40.909 0.00 0.00 0.00 4.02
30 31 5.055265 TGGTTAGATTCTTTGTGGTGGAA 57.945 39.130 0.00 0.00 0.00 3.53
31 32 4.825085 TGGTTAGATTCTTTGTGGTGGAAC 59.175 41.667 0.00 0.00 0.00 3.62
32 33 5.070685 GGTTAGATTCTTTGTGGTGGAACT 58.929 41.667 0.00 0.00 36.74 3.01
33 34 6.183361 TGGTTAGATTCTTTGTGGTGGAACTA 60.183 38.462 0.00 0.00 36.74 2.24
34 35 6.884836 GGTTAGATTCTTTGTGGTGGAACTAT 59.115 38.462 0.00 0.00 36.74 2.12
35 36 7.065923 GGTTAGATTCTTTGTGGTGGAACTATC 59.934 40.741 0.00 0.00 36.74 2.08
36 37 5.501156 AGATTCTTTGTGGTGGAACTATCC 58.499 41.667 0.00 0.00 46.76 2.59
50 51 6.002653 GGAACTATCCATTAGGGTTCAAGT 57.997 41.667 0.00 0.00 45.79 3.16
51 52 6.056236 GGAACTATCCATTAGGGTTCAAGTC 58.944 44.000 0.00 0.00 45.79 3.01
52 53 6.126739 GGAACTATCCATTAGGGTTCAAGTCT 60.127 42.308 0.00 0.00 45.79 3.24
53 54 6.893020 ACTATCCATTAGGGTTCAAGTCTT 57.107 37.500 0.00 0.00 38.11 3.01
54 55 7.989947 ACTATCCATTAGGGTTCAAGTCTTA 57.010 36.000 0.00 0.00 38.11 2.10
55 56 8.024145 ACTATCCATTAGGGTTCAAGTCTTAG 57.976 38.462 0.00 0.00 38.11 2.18
56 57 7.844779 ACTATCCATTAGGGTTCAAGTCTTAGA 59.155 37.037 0.00 0.00 38.11 2.10
57 58 6.295719 TCCATTAGGGTTCAAGTCTTAGAC 57.704 41.667 3.85 3.85 38.11 2.59
58 59 6.023603 TCCATTAGGGTTCAAGTCTTAGACT 58.976 40.000 9.37 9.37 40.48 3.24
59 60 6.500751 TCCATTAGGGTTCAAGTCTTAGACTT 59.499 38.462 20.62 20.62 44.67 3.01
68 69 2.330216 AGTCTTAGACTTGGCACTGGT 58.670 47.619 9.37 0.00 40.28 4.00
69 70 2.037772 AGTCTTAGACTTGGCACTGGTG 59.962 50.000 9.37 0.00 40.28 4.17
105 106 8.751302 TTTTAATTTATTTCAGGCTTTCCGAC 57.249 30.769 0.00 0.00 37.47 4.79
106 107 5.975693 AATTTATTTCAGGCTTTCCGACA 57.024 34.783 0.00 0.00 37.47 4.35
107 108 5.975693 ATTTATTTCAGGCTTTCCGACAA 57.024 34.783 0.00 0.00 37.47 3.18
108 109 5.975693 TTTATTTCAGGCTTTCCGACAAT 57.024 34.783 0.00 0.00 37.47 2.71
109 110 7.639113 ATTTATTTCAGGCTTTCCGACAATA 57.361 32.000 0.00 0.00 37.47 1.90
110 111 7.639113 TTTATTTCAGGCTTTCCGACAATAT 57.361 32.000 0.00 0.00 37.47 1.28
111 112 7.639113 TTATTTCAGGCTTTCCGACAATATT 57.361 32.000 0.00 0.00 37.47 1.28
112 113 5.560966 TTTCAGGCTTTCCGACAATATTC 57.439 39.130 0.00 0.00 37.47 1.75
113 114 4.214986 TCAGGCTTTCCGACAATATTCA 57.785 40.909 0.00 0.00 37.47 2.57
114 115 4.780815 TCAGGCTTTCCGACAATATTCAT 58.219 39.130 0.00 0.00 37.47 2.57
115 116 5.192927 TCAGGCTTTCCGACAATATTCATT 58.807 37.500 0.00 0.00 37.47 2.57
116 117 5.296780 TCAGGCTTTCCGACAATATTCATTC 59.703 40.000 0.00 0.00 37.47 2.67
117 118 5.066375 CAGGCTTTCCGACAATATTCATTCA 59.934 40.000 0.00 0.00 37.47 2.57
118 119 5.297776 AGGCTTTCCGACAATATTCATTCAG 59.702 40.000 0.00 0.00 37.47 3.02
119 120 5.066505 GGCTTTCCGACAATATTCATTCAGT 59.933 40.000 0.00 0.00 0.00 3.41
120 121 5.967674 GCTTTCCGACAATATTCATTCAGTG 59.032 40.000 0.00 0.00 0.00 3.66
121 122 6.435430 TTTCCGACAATATTCATTCAGTGG 57.565 37.500 0.00 0.00 0.00 4.00
122 123 4.450976 TCCGACAATATTCATTCAGTGGG 58.549 43.478 0.00 0.00 0.00 4.61
123 124 4.163268 TCCGACAATATTCATTCAGTGGGA 59.837 41.667 2.28 2.28 32.61 4.37
124 125 4.512944 CCGACAATATTCATTCAGTGGGAG 59.487 45.833 0.00 0.00 0.00 4.30
125 126 5.118990 CGACAATATTCATTCAGTGGGAGT 58.881 41.667 0.00 0.00 0.00 3.85
126 127 5.586243 CGACAATATTCATTCAGTGGGAGTT 59.414 40.000 0.00 0.00 0.00 3.01
127 128 6.094048 CGACAATATTCATTCAGTGGGAGTTT 59.906 38.462 0.00 0.00 0.00 2.66
128 129 7.362056 CGACAATATTCATTCAGTGGGAGTTTT 60.362 37.037 0.00 0.00 0.00 2.43
129 130 8.193953 ACAATATTCATTCAGTGGGAGTTTTT 57.806 30.769 0.00 0.00 0.00 1.94
130 131 9.308000 ACAATATTCATTCAGTGGGAGTTTTTA 57.692 29.630 0.00 0.00 0.00 1.52
133 134 7.839680 ATTCATTCAGTGGGAGTTTTTAACT 57.160 32.000 0.00 0.00 46.38 2.24
134 135 8.934023 ATTCATTCAGTGGGAGTTTTTAACTA 57.066 30.769 0.00 0.00 43.03 2.24
135 136 8.934023 TTCATTCAGTGGGAGTTTTTAACTAT 57.066 30.769 0.00 0.00 43.03 2.12
136 137 8.335532 TCATTCAGTGGGAGTTTTTAACTATG 57.664 34.615 0.00 0.00 43.03 2.23
137 138 8.160765 TCATTCAGTGGGAGTTTTTAACTATGA 58.839 33.333 0.00 0.00 43.03 2.15
138 139 8.792633 CATTCAGTGGGAGTTTTTAACTATGAA 58.207 33.333 0.00 0.00 43.03 2.57
139 140 7.979444 TCAGTGGGAGTTTTTAACTATGAAG 57.021 36.000 0.00 0.00 43.03 3.02
140 141 6.940298 TCAGTGGGAGTTTTTAACTATGAAGG 59.060 38.462 0.00 0.00 43.03 3.46
141 142 5.710567 AGTGGGAGTTTTTAACTATGAAGGC 59.289 40.000 0.00 0.00 43.03 4.35
142 143 5.475564 GTGGGAGTTTTTAACTATGAAGGCA 59.524 40.000 0.00 0.00 43.03 4.75
143 144 6.015772 GTGGGAGTTTTTAACTATGAAGGCAA 60.016 38.462 0.00 0.00 43.03 4.52
144 145 6.015772 TGGGAGTTTTTAACTATGAAGGCAAC 60.016 38.462 0.00 0.00 43.03 4.17
146 147 7.084486 GGAGTTTTTAACTATGAAGGCAACTG 58.916 38.462 0.00 0.00 45.82 3.16
147 148 7.255486 GGAGTTTTTAACTATGAAGGCAACTGT 60.255 37.037 0.00 0.00 45.82 3.55
148 149 7.425606 AGTTTTTAACTATGAAGGCAACTGTG 58.574 34.615 0.00 0.00 44.35 3.66
149 150 7.947284 AGTTTTTAACTATGAAGGCAACTGTGC 60.947 37.037 0.00 0.00 44.35 4.57
158 159 3.736483 CAACTGTGCTGCCTTCGT 58.264 55.556 0.00 0.00 0.00 3.85
159 160 1.571460 CAACTGTGCTGCCTTCGTC 59.429 57.895 0.00 0.00 0.00 4.20
160 161 1.146041 AACTGTGCTGCCTTCGTCA 59.854 52.632 0.00 0.00 0.00 4.35
161 162 0.463654 AACTGTGCTGCCTTCGTCAA 60.464 50.000 0.00 0.00 0.00 3.18
162 163 0.250467 ACTGTGCTGCCTTCGTCAAT 60.250 50.000 0.00 0.00 0.00 2.57
163 164 0.445436 CTGTGCTGCCTTCGTCAATC 59.555 55.000 0.00 0.00 0.00 2.67
164 165 0.035317 TGTGCTGCCTTCGTCAATCT 59.965 50.000 0.00 0.00 0.00 2.40
165 166 0.723981 GTGCTGCCTTCGTCAATCTC 59.276 55.000 0.00 0.00 0.00 2.75
166 167 0.321346 TGCTGCCTTCGTCAATCTCA 59.679 50.000 0.00 0.00 0.00 3.27
167 168 1.005340 GCTGCCTTCGTCAATCTCAG 58.995 55.000 0.00 0.00 0.00 3.35
168 169 1.649664 CTGCCTTCGTCAATCTCAGG 58.350 55.000 0.00 0.00 0.00 3.86
169 170 1.205655 CTGCCTTCGTCAATCTCAGGA 59.794 52.381 0.00 0.00 0.00 3.86
170 171 1.833630 TGCCTTCGTCAATCTCAGGAT 59.166 47.619 0.00 0.00 0.00 3.24
171 172 2.208431 GCCTTCGTCAATCTCAGGATG 58.792 52.381 0.00 0.00 37.54 3.51
182 183 2.764007 TCAGGATGATATGCCGGCT 58.236 52.632 29.70 15.76 42.56 5.52
183 184 0.610174 TCAGGATGATATGCCGGCTC 59.390 55.000 29.70 17.89 42.56 4.70
184 185 0.322648 CAGGATGATATGCCGGCTCA 59.677 55.000 29.70 23.34 39.69 4.26
185 186 1.059098 AGGATGATATGCCGGCTCAA 58.941 50.000 29.70 13.42 0.00 3.02
186 187 1.632409 AGGATGATATGCCGGCTCAAT 59.368 47.619 29.70 17.87 0.00 2.57
187 188 2.012673 GGATGATATGCCGGCTCAATC 58.987 52.381 29.70 24.84 0.00 2.67
188 189 2.355513 GGATGATATGCCGGCTCAATCT 60.356 50.000 29.70 15.51 0.00 2.40
189 190 2.936919 TGATATGCCGGCTCAATCTT 57.063 45.000 29.70 4.14 0.00 2.40
190 191 3.213206 TGATATGCCGGCTCAATCTTT 57.787 42.857 29.70 3.35 0.00 2.52
191 192 3.141398 TGATATGCCGGCTCAATCTTTC 58.859 45.455 29.70 12.91 0.00 2.62
192 193 1.581934 TATGCCGGCTCAATCTTTCG 58.418 50.000 29.70 0.00 0.00 3.46
193 194 0.107703 ATGCCGGCTCAATCTTTCGA 60.108 50.000 29.70 1.81 0.00 3.71
194 195 0.321210 TGCCGGCTCAATCTTTCGAA 60.321 50.000 29.70 0.00 0.00 3.71
195 196 0.375106 GCCGGCTCAATCTTTCGAAG 59.625 55.000 22.15 0.00 0.00 3.79
196 197 2.007049 GCCGGCTCAATCTTTCGAAGA 61.007 52.381 22.15 0.00 42.69 2.87
211 212 7.631822 TCTTTCGAAGATACTCATAAGAGTCG 58.368 38.462 3.43 2.06 44.89 4.18
212 213 7.254829 TCTTTCGAAGATACTCATAAGAGTCGG 60.255 40.741 3.43 0.00 44.89 4.79
219 220 1.920574 CTCATAAGAGTCGGTTGTGCG 59.079 52.381 0.00 0.00 37.11 5.34
220 221 1.271379 TCATAAGAGTCGGTTGTGCGT 59.729 47.619 0.00 0.00 0.00 5.24
221 222 1.390123 CATAAGAGTCGGTTGTGCGTG 59.610 52.381 0.00 0.00 0.00 5.34
222 223 0.942410 TAAGAGTCGGTTGTGCGTGC 60.942 55.000 0.00 0.00 0.00 5.34
223 224 4.059459 GAGTCGGTTGTGCGTGCG 62.059 66.667 0.00 0.00 0.00 5.34
224 225 4.884257 AGTCGGTTGTGCGTGCGT 62.884 61.111 0.00 0.00 0.00 5.24
225 226 4.643385 GTCGGTTGTGCGTGCGTG 62.643 66.667 0.00 0.00 0.00 5.34
245 246 4.921547 GTGCACACGTTCATAGAGATAGA 58.078 43.478 13.17 0.00 0.00 1.98
246 247 5.524284 GTGCACACGTTCATAGAGATAGAT 58.476 41.667 13.17 0.00 0.00 1.98
247 248 5.400782 GTGCACACGTTCATAGAGATAGATG 59.599 44.000 13.17 0.00 0.00 2.90
248 249 5.067805 TGCACACGTTCATAGAGATAGATGT 59.932 40.000 0.00 0.00 0.00 3.06
249 250 5.400782 GCACACGTTCATAGAGATAGATGTG 59.599 44.000 0.00 0.00 37.39 3.21
250 251 6.499172 CACACGTTCATAGAGATAGATGTGT 58.501 40.000 0.00 0.00 37.32 3.72
251 252 6.416161 CACACGTTCATAGAGATAGATGTGTG 59.584 42.308 10.91 10.91 44.75 3.82
252 253 5.400782 CACGTTCATAGAGATAGATGTGTGC 59.599 44.000 0.00 0.00 0.00 4.57
253 254 4.614702 CGTTCATAGAGATAGATGTGTGCG 59.385 45.833 0.00 0.00 0.00 5.34
254 255 4.166187 TCATAGAGATAGATGTGTGCGC 57.834 45.455 0.00 0.00 0.00 6.09
255 256 3.569701 TCATAGAGATAGATGTGTGCGCA 59.430 43.478 5.66 5.66 0.00 6.09
256 257 4.219288 TCATAGAGATAGATGTGTGCGCAT 59.781 41.667 15.91 0.00 0.00 4.73
257 258 2.752121 AGAGATAGATGTGTGCGCATG 58.248 47.619 15.91 0.00 0.00 4.06
258 259 2.102084 AGAGATAGATGTGTGCGCATGT 59.898 45.455 15.91 0.00 0.00 3.21
259 260 3.319122 AGAGATAGATGTGTGCGCATGTA 59.681 43.478 15.91 0.00 0.00 2.29
260 261 4.021632 AGAGATAGATGTGTGCGCATGTAT 60.022 41.667 15.91 5.63 37.82 2.29
261 262 3.992427 AGATAGATGTGTGCGCATGTATG 59.008 43.478 15.91 0.00 36.06 2.39
262 263 2.314323 AGATGTGTGCGCATGTATGA 57.686 45.000 15.91 0.00 0.00 2.15
263 264 2.207590 AGATGTGTGCGCATGTATGAG 58.792 47.619 15.91 0.00 0.00 2.90
264 265 1.935873 GATGTGTGCGCATGTATGAGT 59.064 47.619 15.91 0.00 0.00 3.41
265 266 1.077915 TGTGTGCGCATGTATGAGTG 58.922 50.000 15.91 0.00 0.00 3.51
266 267 1.078709 GTGTGCGCATGTATGAGTGT 58.921 50.000 15.91 0.00 0.00 3.55
267 268 1.061131 GTGTGCGCATGTATGAGTGTC 59.939 52.381 15.91 0.00 0.00 3.67
268 269 1.066929 TGTGCGCATGTATGAGTGTCT 60.067 47.619 15.91 0.00 0.00 3.41
269 270 1.325640 GTGCGCATGTATGAGTGTCTG 59.674 52.381 15.91 0.00 0.00 3.51
270 271 0.302890 GCGCATGTATGAGTGTCTGC 59.697 55.000 0.30 0.00 0.00 4.26
271 272 0.573987 CGCATGTATGAGTGTCTGCG 59.426 55.000 0.11 0.11 45.05 5.18
272 273 1.645034 GCATGTATGAGTGTCTGCGT 58.355 50.000 0.00 0.00 0.00 5.24
273 274 2.002586 GCATGTATGAGTGTCTGCGTT 58.997 47.619 0.00 0.00 0.00 4.84
274 275 2.416547 GCATGTATGAGTGTCTGCGTTT 59.583 45.455 0.00 0.00 0.00 3.60
275 276 3.725895 GCATGTATGAGTGTCTGCGTTTG 60.726 47.826 0.00 0.00 0.00 2.93
276 277 3.106242 TGTATGAGTGTCTGCGTTTGT 57.894 42.857 0.00 0.00 0.00 2.83
277 278 4.245845 TGTATGAGTGTCTGCGTTTGTA 57.754 40.909 0.00 0.00 0.00 2.41
278 279 4.816392 TGTATGAGTGTCTGCGTTTGTAT 58.184 39.130 0.00 0.00 0.00 2.29
279 280 5.234752 TGTATGAGTGTCTGCGTTTGTATT 58.765 37.500 0.00 0.00 0.00 1.89
280 281 4.668576 ATGAGTGTCTGCGTTTGTATTG 57.331 40.909 0.00 0.00 0.00 1.90
281 282 3.723260 TGAGTGTCTGCGTTTGTATTGA 58.277 40.909 0.00 0.00 0.00 2.57
282 283 3.740832 TGAGTGTCTGCGTTTGTATTGAG 59.259 43.478 0.00 0.00 0.00 3.02
283 284 3.728845 AGTGTCTGCGTTTGTATTGAGT 58.271 40.909 0.00 0.00 0.00 3.41
284 285 4.127171 AGTGTCTGCGTTTGTATTGAGTT 58.873 39.130 0.00 0.00 0.00 3.01
285 286 5.294356 AGTGTCTGCGTTTGTATTGAGTTA 58.706 37.500 0.00 0.00 0.00 2.24
286 287 5.405571 AGTGTCTGCGTTTGTATTGAGTTAG 59.594 40.000 0.00 0.00 0.00 2.34
287 288 5.404366 GTGTCTGCGTTTGTATTGAGTTAGA 59.596 40.000 0.00 0.00 0.00 2.10
288 289 5.986741 TGTCTGCGTTTGTATTGAGTTAGAA 59.013 36.000 0.00 0.00 0.00 2.10
289 290 6.480651 TGTCTGCGTTTGTATTGAGTTAGAAA 59.519 34.615 0.00 0.00 0.00 2.52
290 291 7.011576 TGTCTGCGTTTGTATTGAGTTAGAAAA 59.988 33.333 0.00 0.00 0.00 2.29
291 292 7.853929 GTCTGCGTTTGTATTGAGTTAGAAAAA 59.146 33.333 0.00 0.00 0.00 1.94
317 318 5.934935 AGTTGGGAAATTAGTTGTGTACG 57.065 39.130 0.00 0.00 0.00 3.67
318 319 5.370679 AGTTGGGAAATTAGTTGTGTACGT 58.629 37.500 0.00 0.00 0.00 3.57
319 320 6.523840 AGTTGGGAAATTAGTTGTGTACGTA 58.476 36.000 0.00 0.00 0.00 3.57
320 321 6.424812 AGTTGGGAAATTAGTTGTGTACGTAC 59.575 38.462 18.90 18.90 0.00 3.67
321 322 5.851720 TGGGAAATTAGTTGTGTACGTACA 58.148 37.500 24.10 24.10 0.00 2.90
335 336 4.799949 TGTACGTACACTGAAATATTCCGC 59.200 41.667 24.10 0.00 0.00 5.54
336 337 3.852286 ACGTACACTGAAATATTCCGCA 58.148 40.909 0.00 0.00 0.00 5.69
337 338 4.247258 ACGTACACTGAAATATTCCGCAA 58.753 39.130 0.00 0.00 0.00 4.85
338 339 4.691685 ACGTACACTGAAATATTCCGCAAA 59.308 37.500 0.00 0.00 0.00 3.68
339 340 5.179742 ACGTACACTGAAATATTCCGCAAAA 59.820 36.000 0.00 0.00 0.00 2.44
340 341 6.128117 ACGTACACTGAAATATTCCGCAAAAT 60.128 34.615 0.00 0.00 0.00 1.82
341 342 7.064847 ACGTACACTGAAATATTCCGCAAAATA 59.935 33.333 0.00 0.00 0.00 1.40
342 343 7.906010 CGTACACTGAAATATTCCGCAAAATAA 59.094 33.333 0.00 0.00 0.00 1.40
343 344 9.730420 GTACACTGAAATATTCCGCAAAATAAT 57.270 29.630 0.00 0.00 0.00 1.28
345 346 9.086336 ACACTGAAATATTCCGCAAAATAATTG 57.914 29.630 0.00 0.00 0.00 2.32
346 347 8.542132 CACTGAAATATTCCGCAAAATAATTGG 58.458 33.333 0.00 0.00 0.00 3.16
347 348 8.257306 ACTGAAATATTCCGCAAAATAATTGGT 58.743 29.630 0.00 0.00 0.00 3.67
348 349 8.417780 TGAAATATTCCGCAAAATAATTGGTG 57.582 30.769 0.00 0.00 0.00 4.17
349 350 8.037758 TGAAATATTCCGCAAAATAATTGGTGT 58.962 29.630 0.00 0.00 0.00 4.16
350 351 8.419076 AAATATTCCGCAAAATAATTGGTGTC 57.581 30.769 0.00 0.00 0.00 3.67
351 352 4.855715 TTCCGCAAAATAATTGGTGTCA 57.144 36.364 0.00 0.00 0.00 3.58
352 353 4.167554 TCCGCAAAATAATTGGTGTCAC 57.832 40.909 0.00 0.00 0.00 3.67
642 643 3.220447 ATTCCACGTTACCACCACG 57.780 52.632 0.00 0.00 43.52 4.94
643 644 0.320946 ATTCCACGTTACCACCACGG 60.321 55.000 0.00 0.00 42.14 4.94
673 674 2.858344 CACGTTGTCATAATCGAGGTCC 59.142 50.000 0.00 0.00 0.00 4.46
742 743 5.283294 CCATTGATGCGCAAAATTATCTCA 58.717 37.500 17.11 8.28 40.48 3.27
751 752 4.214971 CGCAAAATTATCTCATCCTCCCAG 59.785 45.833 0.00 0.00 0.00 4.45
836 837 1.593006 GTGAATCATTGTACGCCTCCG 59.407 52.381 0.00 0.00 41.14 4.63
944 945 1.468520 ACATGCACTTGGTGTATTCGC 59.531 47.619 0.00 0.00 36.79 4.70
998 999 0.533032 GTAGAAGCTCCGACCTTGCT 59.467 55.000 0.00 0.00 38.87 3.91
1236 2132 4.771577 TCTTTTCATGCATTCCTAAAGCCA 59.228 37.500 0.00 0.00 0.00 4.75
1237 2133 5.422970 TCTTTTCATGCATTCCTAAAGCCAT 59.577 36.000 0.00 0.00 0.00 4.40
1238 2134 4.659111 TTCATGCATTCCTAAAGCCATG 57.341 40.909 0.00 0.00 32.37 3.66
1239 2135 2.363038 TCATGCATTCCTAAAGCCATGC 59.637 45.455 0.00 0.00 42.07 4.06
1240 2136 1.113788 TGCATTCCTAAAGCCATGCC 58.886 50.000 0.00 0.00 41.20 4.40
1247 2143 2.024080 TCCTAAAGCCATGCCCAAAGAT 60.024 45.455 0.00 0.00 0.00 2.40
1316 2214 6.942532 TCCATATCATAAAAGTGAGTTGGC 57.057 37.500 0.00 0.00 35.58 4.52
1317 2215 6.422333 TCCATATCATAAAAGTGAGTTGGCA 58.578 36.000 0.00 0.00 35.58 4.92
1364 2266 4.151867 GTGTTTAGCTTTACACTTCCTCCG 59.848 45.833 18.55 0.00 41.05 4.63
1473 2375 3.074412 AGCTCGGGTGAACAGTAAAATG 58.926 45.455 0.00 0.00 0.00 2.32
1519 2425 7.791949 TGACAAACATTGACAAAAGTTTCAAC 58.208 30.769 15.26 11.39 35.58 3.18
1563 2469 0.179111 TCACATTCCTAGAAGGCGCG 60.179 55.000 0.00 0.00 34.61 6.86
1564 2470 1.144057 ACATTCCTAGAAGGCGCGG 59.856 57.895 8.83 0.00 34.61 6.46
1565 2471 2.109181 ATTCCTAGAAGGCGCGGC 59.891 61.111 27.06 27.06 34.61 6.53
1566 2472 2.731571 ATTCCTAGAAGGCGCGGCA 61.732 57.895 34.94 13.18 34.61 5.69
1567 2473 2.252072 ATTCCTAGAAGGCGCGGCAA 62.252 55.000 34.94 18.28 34.61 4.52
1568 2474 2.435938 CCTAGAAGGCGCGGCAAA 60.436 61.111 34.94 15.13 0.00 3.68
1569 2475 2.038269 CCTAGAAGGCGCGGCAAAA 61.038 57.895 34.94 15.49 0.00 2.44
1570 2476 1.582610 CCTAGAAGGCGCGGCAAAAA 61.583 55.000 34.94 15.87 0.00 1.94
1598 2504 8.612619 ACAAAATCGGTACTATGAAAATGCTAG 58.387 33.333 0.00 0.00 0.00 3.42
1603 2509 7.324935 TCGGTACTATGAAAATGCTAGTTTCA 58.675 34.615 11.97 11.97 46.12 2.69
1675 2587 4.218200 TCCATGACGATTTGTTTCAAGCAT 59.782 37.500 0.00 0.00 0.00 3.79
1676 2588 5.414144 TCCATGACGATTTGTTTCAAGCATA 59.586 36.000 0.00 0.00 0.00 3.14
1807 2726 5.326283 AGTACTCATATCTAGGACTGCCA 57.674 43.478 0.00 0.00 36.75 4.92
1813 2732 6.728164 ACTCATATCTAGGACTGCCATTACAT 59.272 38.462 0.00 0.00 36.29 2.29
1877 2796 2.699954 TGCTAGCTTGAACAACTAGGC 58.300 47.619 17.23 7.10 35.09 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.879223 CACAAAGAATCTAACCATCTGAGCT 59.121 40.000 0.00 0.00 0.00 4.09
1 2 5.065731 CCACAAAGAATCTAACCATCTGAGC 59.934 44.000 0.00 0.00 0.00 4.26
2 3 6.093219 CACCACAAAGAATCTAACCATCTGAG 59.907 42.308 0.00 0.00 0.00 3.35
3 4 5.939883 CACCACAAAGAATCTAACCATCTGA 59.060 40.000 0.00 0.00 0.00 3.27
4 5 5.124457 CCACCACAAAGAATCTAACCATCTG 59.876 44.000 0.00 0.00 0.00 2.90
5 6 5.014123 TCCACCACAAAGAATCTAACCATCT 59.986 40.000 0.00 0.00 0.00 2.90
6 7 5.253330 TCCACCACAAAGAATCTAACCATC 58.747 41.667 0.00 0.00 0.00 3.51
7 8 5.255397 TCCACCACAAAGAATCTAACCAT 57.745 39.130 0.00 0.00 0.00 3.55
8 9 4.715534 TCCACCACAAAGAATCTAACCA 57.284 40.909 0.00 0.00 0.00 3.67
9 10 5.070685 AGTTCCACCACAAAGAATCTAACC 58.929 41.667 0.00 0.00 0.00 2.85
10 11 7.065923 GGATAGTTCCACCACAAAGAATCTAAC 59.934 40.741 0.00 0.00 42.12 2.34
11 12 7.110155 GGATAGTTCCACCACAAAGAATCTAA 58.890 38.462 0.00 0.00 42.12 2.10
12 13 6.650120 GGATAGTTCCACCACAAAGAATCTA 58.350 40.000 0.00 0.00 42.12 1.98
13 14 5.501156 GGATAGTTCCACCACAAAGAATCT 58.499 41.667 0.00 0.00 42.12 2.40
14 15 5.819825 GGATAGTTCCACCACAAAGAATC 57.180 43.478 0.00 0.00 42.12 2.52
27 28 6.002653 ACTTGAACCCTAATGGATAGTTCC 57.997 41.667 0.00 0.00 42.94 3.62
28 29 6.890293 AGACTTGAACCCTAATGGATAGTTC 58.110 40.000 0.00 0.00 37.83 3.01
29 30 6.893020 AGACTTGAACCCTAATGGATAGTT 57.107 37.500 0.00 0.00 38.00 2.24
30 31 6.893020 AAGACTTGAACCCTAATGGATAGT 57.107 37.500 0.00 0.00 38.00 2.12
31 32 8.145122 GTCTAAGACTTGAACCCTAATGGATAG 58.855 40.741 0.00 0.00 38.00 2.08
32 33 7.844779 AGTCTAAGACTTGAACCCTAATGGATA 59.155 37.037 0.00 0.00 40.28 2.59
33 34 6.674419 AGTCTAAGACTTGAACCCTAATGGAT 59.326 38.462 0.00 0.00 40.28 3.41
34 35 6.023603 AGTCTAAGACTTGAACCCTAATGGA 58.976 40.000 0.00 0.00 40.28 3.41
35 36 6.301169 AGTCTAAGACTTGAACCCTAATGG 57.699 41.667 0.00 0.00 40.28 3.16
48 49 2.037772 CACCAGTGCCAAGTCTAAGACT 59.962 50.000 0.00 0.00 45.64 3.24
49 50 2.417719 CACCAGTGCCAAGTCTAAGAC 58.582 52.381 0.00 0.00 0.00 3.01
50 51 2.839486 CACCAGTGCCAAGTCTAAGA 57.161 50.000 0.00 0.00 0.00 2.10
79 80 9.198837 GTCGGAAAGCCTGAAATAAATTAAAAA 57.801 29.630 0.00 0.00 0.00 1.94
80 81 8.361139 TGTCGGAAAGCCTGAAATAAATTAAAA 58.639 29.630 0.00 0.00 0.00 1.52
81 82 7.887381 TGTCGGAAAGCCTGAAATAAATTAAA 58.113 30.769 0.00 0.00 0.00 1.52
82 83 7.455641 TGTCGGAAAGCCTGAAATAAATTAA 57.544 32.000 0.00 0.00 0.00 1.40
83 84 7.455641 TTGTCGGAAAGCCTGAAATAAATTA 57.544 32.000 0.00 0.00 0.00 1.40
84 85 5.975693 TGTCGGAAAGCCTGAAATAAATT 57.024 34.783 0.00 0.00 0.00 1.82
85 86 5.975693 TTGTCGGAAAGCCTGAAATAAAT 57.024 34.783 0.00 0.00 0.00 1.40
86 87 5.975693 ATTGTCGGAAAGCCTGAAATAAA 57.024 34.783 0.00 0.00 0.00 1.40
87 88 7.338196 TGAATATTGTCGGAAAGCCTGAAATAA 59.662 33.333 0.00 0.00 0.00 1.40
88 89 6.826231 TGAATATTGTCGGAAAGCCTGAAATA 59.174 34.615 0.00 0.00 0.00 1.40
89 90 5.652014 TGAATATTGTCGGAAAGCCTGAAAT 59.348 36.000 0.00 0.00 0.00 2.17
90 91 5.007034 TGAATATTGTCGGAAAGCCTGAAA 58.993 37.500 0.00 0.00 0.00 2.69
91 92 4.584874 TGAATATTGTCGGAAAGCCTGAA 58.415 39.130 0.00 0.00 0.00 3.02
92 93 4.214986 TGAATATTGTCGGAAAGCCTGA 57.785 40.909 0.00 0.00 0.00 3.86
93 94 5.066375 TGAATGAATATTGTCGGAAAGCCTG 59.934 40.000 0.00 0.00 0.00 4.85
94 95 5.192927 TGAATGAATATTGTCGGAAAGCCT 58.807 37.500 0.00 0.00 0.00 4.58
95 96 5.066505 ACTGAATGAATATTGTCGGAAAGCC 59.933 40.000 0.00 0.00 0.00 4.35
96 97 5.967674 CACTGAATGAATATTGTCGGAAAGC 59.032 40.000 0.00 0.00 0.00 3.51
97 98 6.458751 CCCACTGAATGAATATTGTCGGAAAG 60.459 42.308 0.00 0.00 0.00 2.62
98 99 5.356751 CCCACTGAATGAATATTGTCGGAAA 59.643 40.000 0.00 0.00 0.00 3.13
99 100 4.881273 CCCACTGAATGAATATTGTCGGAA 59.119 41.667 0.00 0.00 0.00 4.30
100 101 4.163268 TCCCACTGAATGAATATTGTCGGA 59.837 41.667 0.00 0.00 0.00 4.55
101 102 4.450976 TCCCACTGAATGAATATTGTCGG 58.549 43.478 0.00 0.00 0.00 4.79
102 103 5.118990 ACTCCCACTGAATGAATATTGTCG 58.881 41.667 0.00 0.00 0.00 4.35
103 104 7.396540 AAACTCCCACTGAATGAATATTGTC 57.603 36.000 0.00 0.00 0.00 3.18
104 105 7.781324 AAAACTCCCACTGAATGAATATTGT 57.219 32.000 0.00 0.00 0.00 2.71
107 108 9.533831 AGTTAAAAACTCCCACTGAATGAATAT 57.466 29.630 0.00 0.00 37.02 1.28
108 109 8.934023 AGTTAAAAACTCCCACTGAATGAATA 57.066 30.769 0.00 0.00 37.02 1.75
109 110 7.839680 AGTTAAAAACTCCCACTGAATGAAT 57.160 32.000 0.00 0.00 37.02 2.57
110 111 8.792633 CATAGTTAAAAACTCCCACTGAATGAA 58.207 33.333 0.00 0.00 41.77 2.57
111 112 8.160765 TCATAGTTAAAAACTCCCACTGAATGA 58.839 33.333 0.00 0.00 41.77 2.57
112 113 8.335532 TCATAGTTAAAAACTCCCACTGAATG 57.664 34.615 0.00 0.00 41.77 2.67
113 114 8.934023 TTCATAGTTAAAAACTCCCACTGAAT 57.066 30.769 0.00 0.00 41.77 2.57
114 115 7.447238 CCTTCATAGTTAAAAACTCCCACTGAA 59.553 37.037 0.00 0.45 41.77 3.02
115 116 6.940298 CCTTCATAGTTAAAAACTCCCACTGA 59.060 38.462 0.00 0.00 41.77 3.41
116 117 6.349363 GCCTTCATAGTTAAAAACTCCCACTG 60.349 42.308 0.00 0.00 41.77 3.66
117 118 5.710567 GCCTTCATAGTTAAAAACTCCCACT 59.289 40.000 0.00 0.00 41.77 4.00
118 119 5.475564 TGCCTTCATAGTTAAAAACTCCCAC 59.524 40.000 0.00 0.00 41.77 4.61
119 120 5.636123 TGCCTTCATAGTTAAAAACTCCCA 58.364 37.500 0.00 0.00 41.77 4.37
120 121 6.208797 AGTTGCCTTCATAGTTAAAAACTCCC 59.791 38.462 0.00 0.00 41.77 4.30
121 122 7.084486 CAGTTGCCTTCATAGTTAAAAACTCC 58.916 38.462 0.00 0.00 41.77 3.85
122 123 7.591426 CACAGTTGCCTTCATAGTTAAAAACTC 59.409 37.037 0.00 0.00 41.77 3.01
123 124 7.425606 CACAGTTGCCTTCATAGTTAAAAACT 58.574 34.615 0.00 0.00 45.40 2.66
124 125 6.143919 GCACAGTTGCCTTCATAGTTAAAAAC 59.856 38.462 0.00 0.00 43.66 2.43
125 126 6.212955 GCACAGTTGCCTTCATAGTTAAAAA 58.787 36.000 0.00 0.00 43.66 1.94
126 127 5.768317 GCACAGTTGCCTTCATAGTTAAAA 58.232 37.500 0.00 0.00 43.66 1.52
127 128 5.371115 GCACAGTTGCCTTCATAGTTAAA 57.629 39.130 0.00 0.00 43.66 1.52
141 142 1.159713 TGACGAAGGCAGCACAGTTG 61.160 55.000 0.00 0.00 0.00 3.16
142 143 0.463654 TTGACGAAGGCAGCACAGTT 60.464 50.000 0.00 0.00 0.00 3.16
143 144 0.250467 ATTGACGAAGGCAGCACAGT 60.250 50.000 0.00 0.00 0.00 3.55
144 145 0.445436 GATTGACGAAGGCAGCACAG 59.555 55.000 0.00 0.00 0.00 3.66
145 146 0.035317 AGATTGACGAAGGCAGCACA 59.965 50.000 0.00 0.00 0.00 4.57
146 147 0.723981 GAGATTGACGAAGGCAGCAC 59.276 55.000 0.00 0.00 0.00 4.40
147 148 0.321346 TGAGATTGACGAAGGCAGCA 59.679 50.000 0.00 0.00 0.00 4.41
148 149 1.005340 CTGAGATTGACGAAGGCAGC 58.995 55.000 0.00 0.00 0.00 5.25
149 150 1.205655 TCCTGAGATTGACGAAGGCAG 59.794 52.381 0.00 0.00 0.00 4.85
150 151 1.266178 TCCTGAGATTGACGAAGGCA 58.734 50.000 0.00 0.00 0.00 4.75
151 152 2.159043 TCATCCTGAGATTGACGAAGGC 60.159 50.000 0.00 0.00 0.00 4.35
152 153 3.808466 TCATCCTGAGATTGACGAAGG 57.192 47.619 0.00 0.00 0.00 3.46
153 154 5.348179 GCATATCATCCTGAGATTGACGAAG 59.652 44.000 0.00 0.00 0.00 3.79
154 155 5.233225 GCATATCATCCTGAGATTGACGAA 58.767 41.667 0.00 0.00 0.00 3.85
155 156 4.322273 GGCATATCATCCTGAGATTGACGA 60.322 45.833 0.00 0.00 0.00 4.20
156 157 3.931468 GGCATATCATCCTGAGATTGACG 59.069 47.826 0.00 0.00 0.00 4.35
157 158 3.931468 CGGCATATCATCCTGAGATTGAC 59.069 47.826 0.00 0.00 0.00 3.18
158 159 3.055602 CCGGCATATCATCCTGAGATTGA 60.056 47.826 0.00 0.00 0.00 2.57
159 160 3.268330 CCGGCATATCATCCTGAGATTG 58.732 50.000 0.00 0.00 0.00 2.67
160 161 2.355513 GCCGGCATATCATCCTGAGATT 60.356 50.000 24.80 0.00 0.00 2.40
161 162 1.209019 GCCGGCATATCATCCTGAGAT 59.791 52.381 24.80 0.00 0.00 2.75
162 163 0.610174 GCCGGCATATCATCCTGAGA 59.390 55.000 24.80 0.00 0.00 3.27
163 164 0.612229 AGCCGGCATATCATCCTGAG 59.388 55.000 31.54 0.00 0.00 3.35
164 165 0.610174 GAGCCGGCATATCATCCTGA 59.390 55.000 31.54 0.00 0.00 3.86
165 166 0.322648 TGAGCCGGCATATCATCCTG 59.677 55.000 31.54 0.00 0.00 3.86
166 167 1.059098 TTGAGCCGGCATATCATCCT 58.941 50.000 31.54 3.33 0.00 3.24
167 168 2.012673 GATTGAGCCGGCATATCATCC 58.987 52.381 31.54 13.84 0.00 3.51
168 169 2.983229 AGATTGAGCCGGCATATCATC 58.017 47.619 31.54 20.52 0.00 2.92
169 170 3.430042 AAGATTGAGCCGGCATATCAT 57.570 42.857 31.54 17.14 0.00 2.45
170 171 2.936919 AAGATTGAGCCGGCATATCA 57.063 45.000 31.54 21.33 0.00 2.15
171 172 2.158449 CGAAAGATTGAGCCGGCATATC 59.842 50.000 31.54 25.17 0.00 1.63
172 173 2.146342 CGAAAGATTGAGCCGGCATAT 58.854 47.619 31.54 18.37 0.00 1.78
173 174 1.138069 TCGAAAGATTGAGCCGGCATA 59.862 47.619 31.54 14.63 33.31 3.14
174 175 0.107703 TCGAAAGATTGAGCCGGCAT 60.108 50.000 31.54 14.27 33.31 4.40
175 176 0.321210 TTCGAAAGATTGAGCCGGCA 60.321 50.000 31.54 8.70 41.60 5.69
176 177 0.375106 CTTCGAAAGATTGAGCCGGC 59.625 55.000 21.89 21.89 41.60 6.13
177 178 2.010145 TCTTCGAAAGATTGAGCCGG 57.990 50.000 0.00 0.00 41.60 6.13
178 179 4.363999 AGTATCTTCGAAAGATTGAGCCG 58.636 43.478 13.04 0.00 45.75 5.52
179 180 5.352284 TGAGTATCTTCGAAAGATTGAGCC 58.648 41.667 13.04 0.00 45.75 4.70
180 181 8.581057 TTATGAGTATCTTCGAAAGATTGAGC 57.419 34.615 13.04 0.14 45.75 4.26
181 182 9.958234 TCTTATGAGTATCTTCGAAAGATTGAG 57.042 33.333 13.04 4.60 45.75 3.02
182 183 9.958234 CTCTTATGAGTATCTTCGAAAGATTGA 57.042 33.333 13.04 1.68 46.77 2.57
199 200 1.920574 CGCACAACCGACTCTTATGAG 59.079 52.381 4.14 4.14 45.43 2.90
200 201 1.271379 ACGCACAACCGACTCTTATGA 59.729 47.619 0.00 0.00 0.00 2.15
201 202 1.390123 CACGCACAACCGACTCTTATG 59.610 52.381 0.00 0.00 0.00 1.90
202 203 1.710013 CACGCACAACCGACTCTTAT 58.290 50.000 0.00 0.00 0.00 1.73
203 204 0.942410 GCACGCACAACCGACTCTTA 60.942 55.000 0.00 0.00 0.00 2.10
204 205 2.244651 GCACGCACAACCGACTCTT 61.245 57.895 0.00 0.00 0.00 2.85
205 206 2.661866 GCACGCACAACCGACTCT 60.662 61.111 0.00 0.00 0.00 3.24
206 207 4.059459 CGCACGCACAACCGACTC 62.059 66.667 0.00 0.00 0.00 3.36
207 208 4.884257 ACGCACGCACAACCGACT 62.884 61.111 0.00 0.00 0.00 4.18
208 209 4.643385 CACGCACGCACAACCGAC 62.643 66.667 0.00 0.00 0.00 4.79
223 224 4.921547 TCTATCTCTATGAACGTGTGCAC 58.078 43.478 10.75 10.75 0.00 4.57
224 225 5.067805 ACATCTATCTCTATGAACGTGTGCA 59.932 40.000 0.00 0.00 0.00 4.57
225 226 5.400782 CACATCTATCTCTATGAACGTGTGC 59.599 44.000 0.00 0.00 0.00 4.57
226 227 6.416161 CACACATCTATCTCTATGAACGTGTG 59.584 42.308 0.00 0.00 39.45 3.82
227 228 6.499172 CACACATCTATCTCTATGAACGTGT 58.501 40.000 0.00 0.00 33.62 4.49
228 229 5.400782 GCACACATCTATCTCTATGAACGTG 59.599 44.000 0.00 0.00 0.00 4.49
229 230 5.524284 GCACACATCTATCTCTATGAACGT 58.476 41.667 0.00 0.00 0.00 3.99
230 231 4.614702 CGCACACATCTATCTCTATGAACG 59.385 45.833 0.00 0.00 0.00 3.95
231 232 4.384247 GCGCACACATCTATCTCTATGAAC 59.616 45.833 0.30 0.00 0.00 3.18
232 233 4.037923 TGCGCACACATCTATCTCTATGAA 59.962 41.667 5.66 0.00 0.00 2.57
233 234 3.569701 TGCGCACACATCTATCTCTATGA 59.430 43.478 5.66 0.00 0.00 2.15
234 235 3.905784 TGCGCACACATCTATCTCTATG 58.094 45.455 5.66 0.00 0.00 2.23
235 236 4.021632 ACATGCGCACACATCTATCTCTAT 60.022 41.667 14.90 0.00 0.00 1.98
236 237 3.319122 ACATGCGCACACATCTATCTCTA 59.681 43.478 14.90 0.00 0.00 2.43
237 238 2.102084 ACATGCGCACACATCTATCTCT 59.898 45.455 14.90 0.00 0.00 3.10
238 239 2.477825 ACATGCGCACACATCTATCTC 58.522 47.619 14.90 0.00 0.00 2.75
239 240 2.609427 ACATGCGCACACATCTATCT 57.391 45.000 14.90 0.00 0.00 1.98
240 241 3.989817 TCATACATGCGCACACATCTATC 59.010 43.478 14.90 0.00 0.00 2.08
241 242 3.992427 CTCATACATGCGCACACATCTAT 59.008 43.478 14.90 0.00 0.00 1.98
242 243 3.181476 ACTCATACATGCGCACACATCTA 60.181 43.478 14.90 0.00 0.00 1.98
243 244 2.207590 CTCATACATGCGCACACATCT 58.792 47.619 14.90 0.00 0.00 2.90
244 245 1.935873 ACTCATACATGCGCACACATC 59.064 47.619 14.90 0.00 0.00 3.06
245 246 1.667212 CACTCATACATGCGCACACAT 59.333 47.619 14.90 2.32 0.00 3.21
246 247 1.077915 CACTCATACATGCGCACACA 58.922 50.000 14.90 0.00 0.00 3.72
247 248 1.061131 GACACTCATACATGCGCACAC 59.939 52.381 14.90 0.00 0.00 3.82
248 249 1.066929 AGACACTCATACATGCGCACA 60.067 47.619 14.90 0.12 0.00 4.57
249 250 1.325640 CAGACACTCATACATGCGCAC 59.674 52.381 14.90 0.00 0.00 5.34
250 251 1.643880 CAGACACTCATACATGCGCA 58.356 50.000 14.96 14.96 0.00 6.09
251 252 0.302890 GCAGACACTCATACATGCGC 59.697 55.000 0.00 0.00 0.00 6.09
253 254 1.645034 ACGCAGACACTCATACATGC 58.355 50.000 0.00 0.00 0.00 4.06
254 255 3.433274 ACAAACGCAGACACTCATACATG 59.567 43.478 0.00 0.00 0.00 3.21
255 256 3.664107 ACAAACGCAGACACTCATACAT 58.336 40.909 0.00 0.00 0.00 2.29
256 257 3.106242 ACAAACGCAGACACTCATACA 57.894 42.857 0.00 0.00 0.00 2.29
257 258 5.347635 TCAATACAAACGCAGACACTCATAC 59.652 40.000 0.00 0.00 0.00 2.39
258 259 5.474825 TCAATACAAACGCAGACACTCATA 58.525 37.500 0.00 0.00 0.00 2.15
259 260 4.314961 TCAATACAAACGCAGACACTCAT 58.685 39.130 0.00 0.00 0.00 2.90
260 261 3.723260 TCAATACAAACGCAGACACTCA 58.277 40.909 0.00 0.00 0.00 3.41
261 262 3.741344 ACTCAATACAAACGCAGACACTC 59.259 43.478 0.00 0.00 0.00 3.51
262 263 3.728845 ACTCAATACAAACGCAGACACT 58.271 40.909 0.00 0.00 0.00 3.55
263 264 4.468095 AACTCAATACAAACGCAGACAC 57.532 40.909 0.00 0.00 0.00 3.67
264 265 5.534407 TCTAACTCAATACAAACGCAGACA 58.466 37.500 0.00 0.00 0.00 3.41
265 266 6.462073 TTCTAACTCAATACAAACGCAGAC 57.538 37.500 0.00 0.00 0.00 3.51
266 267 7.485418 TTTTCTAACTCAATACAAACGCAGA 57.515 32.000 0.00 0.00 0.00 4.26
291 292 8.508875 CGTACACAACTAATTTCCCAACTATTT 58.491 33.333 0.00 0.00 0.00 1.40
292 293 7.662669 ACGTACACAACTAATTTCCCAACTATT 59.337 33.333 0.00 0.00 0.00 1.73
293 294 7.163441 ACGTACACAACTAATTTCCCAACTAT 58.837 34.615 0.00 0.00 0.00 2.12
294 295 6.523840 ACGTACACAACTAATTTCCCAACTA 58.476 36.000 0.00 0.00 0.00 2.24
295 296 5.370679 ACGTACACAACTAATTTCCCAACT 58.629 37.500 0.00 0.00 0.00 3.16
296 297 5.678132 ACGTACACAACTAATTTCCCAAC 57.322 39.130 0.00 0.00 0.00 3.77
297 298 6.286758 TGTACGTACACAACTAATTTCCCAA 58.713 36.000 24.10 0.00 0.00 4.12
298 299 5.851720 TGTACGTACACAACTAATTTCCCA 58.148 37.500 24.10 0.00 0.00 4.37
312 313 4.799949 GCGGAATATTTCAGTGTACGTACA 59.200 41.667 24.10 24.10 0.00 2.90
313 314 4.799949 TGCGGAATATTTCAGTGTACGTAC 59.200 41.667 18.90 18.90 0.00 3.67
314 315 4.996344 TGCGGAATATTTCAGTGTACGTA 58.004 39.130 0.00 0.00 0.00 3.57
315 316 3.852286 TGCGGAATATTTCAGTGTACGT 58.148 40.909 0.00 0.00 0.00 3.57
316 317 4.850859 TTGCGGAATATTTCAGTGTACG 57.149 40.909 0.00 0.00 0.00 3.67
317 318 9.730420 ATTATTTTGCGGAATATTTCAGTGTAC 57.270 29.630 0.00 0.00 0.00 2.90
319 320 9.086336 CAATTATTTTGCGGAATATTTCAGTGT 57.914 29.630 0.00 0.00 0.00 3.55
320 321 8.542132 CCAATTATTTTGCGGAATATTTCAGTG 58.458 33.333 0.00 0.00 0.00 3.66
321 322 8.257306 ACCAATTATTTTGCGGAATATTTCAGT 58.743 29.630 0.00 0.00 0.00 3.41
322 323 8.542132 CACCAATTATTTTGCGGAATATTTCAG 58.458 33.333 0.00 0.00 0.00 3.02
323 324 8.037758 ACACCAATTATTTTGCGGAATATTTCA 58.962 29.630 0.00 0.00 0.00 2.69
324 325 8.419076 ACACCAATTATTTTGCGGAATATTTC 57.581 30.769 0.00 0.00 0.00 2.17
325 326 8.037758 TGACACCAATTATTTTGCGGAATATTT 58.962 29.630 0.00 0.00 0.00 1.40
326 327 7.491048 GTGACACCAATTATTTTGCGGAATATT 59.509 33.333 0.00 0.00 0.00 1.28
327 328 6.978080 GTGACACCAATTATTTTGCGGAATAT 59.022 34.615 0.00 0.00 0.00 1.28
328 329 6.326375 GTGACACCAATTATTTTGCGGAATA 58.674 36.000 0.00 0.00 0.00 1.75
329 330 5.167845 GTGACACCAATTATTTTGCGGAAT 58.832 37.500 0.00 0.00 0.00 3.01
330 331 4.551388 GTGACACCAATTATTTTGCGGAA 58.449 39.130 0.00 0.00 0.00 4.30
331 332 4.167554 GTGACACCAATTATTTTGCGGA 57.832 40.909 0.00 0.00 0.00 5.54
624 625 0.320946 CCGTGGTGGTAACGTGGAAT 60.321 55.000 0.00 0.00 39.38 3.01
625 626 1.069427 CCGTGGTGGTAACGTGGAA 59.931 57.895 0.00 0.00 39.38 3.53
626 627 2.735883 CCGTGGTGGTAACGTGGA 59.264 61.111 0.00 0.00 39.38 4.02
627 628 3.045492 GCCGTGGTGGTAACGTGG 61.045 66.667 0.00 0.00 41.21 4.94
628 629 2.280254 TGCCGTGGTGGTAACGTG 60.280 61.111 0.00 0.00 41.21 4.49
629 630 2.280321 GTGCCGTGGTGGTAACGT 60.280 61.111 0.00 0.00 41.21 3.99
630 631 3.045492 GGTGCCGTGGTGGTAACG 61.045 66.667 0.00 0.00 41.21 3.18
631 632 2.111460 TGGTGCCGTGGTGGTAAC 59.889 61.111 0.00 0.00 41.14 2.50
632 633 2.111460 GTGGTGCCGTGGTGGTAA 59.889 61.111 0.00 0.00 41.21 2.85
633 634 3.943691 GGTGGTGCCGTGGTGGTA 61.944 66.667 0.00 0.00 41.21 3.25
642 643 4.887190 ACAACGTGGGGTGGTGCC 62.887 66.667 0.00 0.00 29.22 5.01
643 644 3.284449 GACAACGTGGGGTGGTGC 61.284 66.667 0.00 0.00 31.08 5.01
673 674 1.068281 CGATCTGTGAGGTGGAGGATG 59.932 57.143 0.00 0.00 0.00 3.51
742 743 1.840635 GACCTGTTTAGCTGGGAGGAT 59.159 52.381 0.00 0.00 40.14 3.24
751 752 5.739161 CGAGCAAATAATTGACCTGTTTAGC 59.261 40.000 0.00 0.00 38.94 3.09
836 837 1.067142 TGTCGTGGACAGATGGCTTAC 60.067 52.381 0.00 0.00 37.67 2.34
916 917 5.565592 ACACCAAGTGCATGTATGTATTG 57.434 39.130 0.00 0.00 36.98 1.90
944 945 1.638467 GCGCAGATAAACCAGCTCG 59.362 57.895 0.30 0.00 0.00 5.03
970 971 1.133915 CGGAGCTTCTACTCTCCCTCT 60.134 57.143 3.01 0.00 44.61 3.69
1011 1012 1.304282 GCACACCACCATCTCCCAT 59.696 57.895 0.00 0.00 0.00 4.00
1236 2132 0.041535 TGAGGGCAATCTTTGGGCAT 59.958 50.000 0.00 0.00 0.00 4.40
1237 2133 0.899717 GTGAGGGCAATCTTTGGGCA 60.900 55.000 0.00 0.00 0.00 5.36
1238 2134 0.613012 AGTGAGGGCAATCTTTGGGC 60.613 55.000 0.00 0.00 0.00 5.36
1239 2135 1.928868 AAGTGAGGGCAATCTTTGGG 58.071 50.000 0.00 0.00 0.00 4.12
1240 2136 5.011023 ACTTAAAAGTGAGGGCAATCTTTGG 59.989 40.000 0.00 0.00 37.98 3.28
1394 2296 4.931661 TGATAAATACTCCCTCCGTCAC 57.068 45.455 0.00 0.00 0.00 3.67
1396 2298 5.532664 ACTTGATAAATACTCCCTCCGTC 57.467 43.478 0.00 0.00 0.00 4.79
1491 2397 9.645059 TGAAACTTTTGTCAATGTTTGTCATAA 57.355 25.926 16.75 0.00 39.28 1.90
1492 2398 9.645059 TTGAAACTTTTGTCAATGTTTGTCATA 57.355 25.926 16.75 4.62 39.28 2.15
1494 2400 7.655328 AGTTGAAACTTTTGTCAATGTTTGTCA 59.345 29.630 16.75 10.10 39.28 3.58
1495 2401 7.951565 CAGTTGAAACTTTTGTCAATGTTTGTC 59.048 33.333 16.75 8.35 39.28 3.18
1496 2402 7.571059 GCAGTTGAAACTTTTGTCAATGTTTGT 60.571 33.333 16.75 1.04 39.28 2.83
1497 2403 6.737750 GCAGTTGAAACTTTTGTCAATGTTTG 59.262 34.615 16.75 8.19 39.28 2.93
1498 2404 6.650390 AGCAGTTGAAACTTTTGTCAATGTTT 59.350 30.769 13.57 13.57 40.94 2.83
1499 2405 6.165577 AGCAGTTGAAACTTTTGTCAATGTT 58.834 32.000 0.00 0.00 37.08 2.71
1500 2406 5.723295 AGCAGTTGAAACTTTTGTCAATGT 58.277 33.333 0.00 0.00 37.08 2.71
1501 2407 6.471839 CAAGCAGTTGAAACTTTTGTCAATG 58.528 36.000 0.00 0.00 37.08 2.82
1502 2408 5.063817 GCAAGCAGTTGAAACTTTTGTCAAT 59.936 36.000 14.12 0.00 37.08 2.57
1503 2409 4.388469 GCAAGCAGTTGAAACTTTTGTCAA 59.612 37.500 14.12 0.00 37.08 3.18
1545 2451 1.154205 CCGCGCCTTCTAGGAATGTG 61.154 60.000 0.00 0.00 37.67 3.21
1569 2475 8.921670 GCATTTTCATAGTACCGATTTTGTTTT 58.078 29.630 0.00 0.00 0.00 2.43
1570 2476 8.303876 AGCATTTTCATAGTACCGATTTTGTTT 58.696 29.630 0.00 0.00 0.00 2.83
1573 2479 8.612619 ACTAGCATTTTCATAGTACCGATTTTG 58.387 33.333 0.00 0.00 0.00 2.44
1584 2490 8.746922 TGCTTTTGAAACTAGCATTTTCATAG 57.253 30.769 7.58 8.96 41.45 2.23
1598 2504 3.248363 GTGCTCCCAAATGCTTTTGAAAC 59.752 43.478 22.76 11.59 44.11 2.78
1603 2509 2.318908 TCAGTGCTCCCAAATGCTTTT 58.681 42.857 0.00 0.00 0.00 2.27
1675 2587 7.475771 GACAAACATTGGCAAAAGTTTCATA 57.524 32.000 23.00 0.00 35.58 2.15
1676 2588 6.362210 GACAAACATTGGCAAAAGTTTCAT 57.638 33.333 23.00 16.98 35.58 2.57
1725 2638 8.668510 ATGAGCTCGATGAACAGTAAAAATAT 57.331 30.769 9.64 0.00 0.00 1.28
1727 2640 6.992063 ATGAGCTCGATGAACAGTAAAAAT 57.008 33.333 9.64 0.00 0.00 1.82
1734 2647 4.517641 CTCAAATGAGCTCGATGAACAG 57.482 45.455 9.64 0.00 35.13 3.16
1966 2885 7.321717 TGAATGGTCCATTTTGGGAATTTAA 57.678 32.000 18.31 0.00 39.05 1.52
1967 2886 6.942163 TGAATGGTCCATTTTGGGAATTTA 57.058 33.333 18.31 0.00 39.05 1.40
1973 2892 4.772100 ACTAGTTGAATGGTCCATTTTGGG 59.228 41.667 18.31 9.35 38.32 4.12


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

AutoCloner maintained by Alex Coulton.