Multiple sequence alignment - TraesCS3B01G346200

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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 TraesCS3B01G346200 chr3B 100.000 2963 0 0 1 2963 555736279 555739241 0.000000e+00 5472.0
1 TraesCS3B01G346200 chr3B 98.180 2472 45 0 492 2963 555925545 555928016 0.000000e+00 4316.0
2 TraesCS3B01G346200 chr3B 95.122 205 10 0 1 205 167653820 167654024 1.020000e-84 324.0
3 TraesCS3B01G346200 chr3B 95.122 205 10 0 1 205 253228337 253228133 1.020000e-84 324.0
4 TraesCS3B01G346200 chr3B 95.122 205 9 1 1 205 555729232 555729435 3.680000e-84 322.0
5 TraesCS3B01G346200 chr3B 94.231 208 12 0 1 208 253037694 253037487 4.770000e-83 318.0
6 TraesCS3B01G346200 chr3B 93.427 213 14 0 2 214 83098885 83099097 1.710000e-82 316.0
7 TraesCS3B01G346200 chr3B 92.202 218 17 0 1 218 479601757 479601974 2.870000e-80 309.0
8 TraesCS3B01G346200 chr3B 95.652 92 4 0 206 297 826191086 826191177 6.620000e-32 148.0
9 TraesCS3B01G346200 chr3B 90.123 81 0 2 2427 2503 555738669 555738745 6.760000e-17 99.0
10 TraesCS3B01G346200 chr3B 90.123 81 0 2 2391 2467 555738705 555738781 6.760000e-17 99.0
11 TraesCS3B01G346200 chr3B 90.123 81 0 2 2427 2503 555927444 555927520 6.760000e-17 99.0
12 TraesCS3B01G346200 chr3B 88.889 81 1 3 2391 2467 555927480 555927556 3.140000e-15 93.5
13 TraesCS3B01G346200 chr3B 100.000 37 0 0 2467 2503 555738669 555738705 5.300000e-08 69.4
14 TraesCS3B01G346200 chr3B 100.000 37 0 0 2391 2427 555738745 555738781 5.300000e-08 69.4
15 TraesCS3B01G346200 chr3B 100.000 37 0 0 2467 2503 555927444 555927480 5.300000e-08 69.4
16 TraesCS3B01G346200 chr3A 97.179 1347 26 5 682 2022 562571473 562570133 0.000000e+00 2266.0
17 TraesCS3B01G346200 chr3A 95.515 379 17 0 2585 2963 562570109 562569731 9.080000e-170 606.0
18 TraesCS3B01G346200 chr3A 89.362 235 12 7 206 437 562572885 562572661 1.740000e-72 283.0
19 TraesCS3B01G346200 chr3A 77.489 231 43 6 1412 1642 103018684 103018905 2.400000e-26 130.0
20 TraesCS3B01G346200 chr2B 84.026 914 128 12 910 1814 79704470 79703566 0.000000e+00 863.0
21 TraesCS3B01G346200 chr2B 83.011 930 125 21 905 1814 79702775 79701859 0.000000e+00 811.0
22 TraesCS3B01G346200 chr2B 94.762 210 10 1 1 210 790265295 790265503 2.850000e-85 326.0
23 TraesCS3B01G346200 chr2B 94.634 205 11 0 1 205 790258185 790258389 4.770000e-83 318.0
24 TraesCS3B01G346200 chr2B 82.320 362 33 14 561 894 79704877 79704519 4.830000e-73 285.0
25 TraesCS3B01G346200 chr2B 96.739 92 3 0 206 297 222121953 222122044 1.420000e-33 154.0
26 TraesCS3B01G346200 chr2A 80.926 1101 161 23 910 1962 52568402 52567303 0.000000e+00 824.0
27 TraesCS3B01G346200 chr2A 82.778 360 34 16 561 898 52568803 52568450 2.230000e-76 296.0
28 TraesCS3B01G346200 chr7B 93.897 213 10 3 1 212 8345097 8344887 4.770000e-83 318.0
29 TraesCS3B01G346200 chrUn 89.894 188 14 4 301 488 290757922 290757740 1.370000e-58 237.0
30 TraesCS3B01G346200 chrUn 89.894 188 14 4 301 488 319226666 319226848 1.370000e-58 237.0
31 TraesCS3B01G346200 chr6A 90.000 150 11 1 334 483 191232667 191232522 1.080000e-44 191.0
32 TraesCS3B01G346200 chr6A 95.652 92 4 0 206 297 591340691 591340782 6.620000e-32 148.0
33 TraesCS3B01G346200 chr6A 97.647 85 2 0 214 298 78485646 78485730 2.380000e-31 147.0
34 TraesCS3B01G346200 chr4D 85.263 190 21 5 301 487 478747550 478747365 3.900000e-44 189.0
35 TraesCS3B01G346200 chr3D 82.775 209 28 6 300 508 578897370 578897170 2.350000e-41 180.0
36 TraesCS3B01G346200 chr6D 95.652 92 4 0 206 297 331252295 331252386 6.620000e-32 148.0
37 TraesCS3B01G346200 chr5D 95.652 92 4 0 206 297 438062229 438062320 6.620000e-32 148.0
38 TraesCS3B01G346200 chr5D 94.624 93 5 0 206 298 367421492 367421400 8.560000e-31 145.0
39 TraesCS3B01G346200 chr1B 95.652 92 4 0 206 297 143086648 143086739 6.620000e-32 148.0
40 TraesCS3B01G346200 chr4A 88.764 89 8 1 292 380 615005175 615005261 1.120000e-19 108.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G346200 chr3B 555736279 555739241 2962 False 1161.760000 5472 96.049200 1 2963 5 chr3B.!!$F6 2962
1 TraesCS3B01G346200 chr3B 555925545 555928016 2471 False 1144.475000 4316 94.298000 492 2963 4 chr3B.!!$F7 2471
2 TraesCS3B01G346200 chr3A 562569731 562572885 3154 True 1051.666667 2266 94.018667 206 2963 3 chr3A.!!$R1 2757
3 TraesCS3B01G346200 chr2B 79701859 79704877 3018 True 653.000000 863 83.119000 561 1814 3 chr2B.!!$R1 1253
4 TraesCS3B01G346200 chr2A 52567303 52568803 1500 True 560.000000 824 81.852000 561 1962 2 chr2A.!!$R1 1401

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
49 50 0.034477 AACGGGGAAAATGCTCGGAT 60.034 50.0 0.0 0.0 0.00 4.18 F
181 182 0.035439 AATAACTGGCGGACACCTGG 60.035 55.0 0.0 0.0 33.19 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 2697 1.070786 GGCTGACAACTTCGGTGGA 59.929 57.895 0.0 0.0 32.41 4.02 R
2115 3853 3.153369 TGATTGCTAACTGGGAAAGCA 57.847 42.857 0.0 0.0 44.15 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
20 21 2.474816 GACATAGGAGTGTCGGATTGC 58.525 52.381 0.00 0.00 39.12 3.56
21 22 1.831106 ACATAGGAGTGTCGGATTGCA 59.169 47.619 0.00 0.00 0.00 4.08
22 23 2.236146 ACATAGGAGTGTCGGATTGCAA 59.764 45.455 0.00 0.00 0.00 4.08
23 24 3.270027 CATAGGAGTGTCGGATTGCAAA 58.730 45.455 1.71 0.00 0.00 3.68
24 25 2.270352 AGGAGTGTCGGATTGCAAAA 57.730 45.000 1.71 0.00 0.00 2.44
25 26 1.880027 AGGAGTGTCGGATTGCAAAAC 59.120 47.619 1.71 0.26 0.00 2.43
26 27 1.399727 GGAGTGTCGGATTGCAAAACG 60.400 52.381 16.99 16.99 0.00 3.60
27 28 0.591170 AGTGTCGGATTGCAAAACGG 59.409 50.000 21.03 14.34 32.27 4.44
28 29 0.589223 GTGTCGGATTGCAAAACGGA 59.411 50.000 21.03 15.98 32.27 4.69
29 30 1.002251 GTGTCGGATTGCAAAACGGAA 60.002 47.619 21.03 10.45 30.36 4.30
30 31 1.676529 TGTCGGATTGCAAAACGGAAA 59.323 42.857 21.03 12.55 30.36 3.13
31 32 2.099263 TGTCGGATTGCAAAACGGAAAA 59.901 40.909 21.03 10.02 30.36 2.29
32 33 2.469886 GTCGGATTGCAAAACGGAAAAC 59.530 45.455 21.03 11.30 30.36 2.43
43 44 3.116073 CGGAAAACGGGGAAAATGC 57.884 52.632 0.00 0.00 39.42 3.56
44 45 0.601057 CGGAAAACGGGGAAAATGCT 59.399 50.000 0.00 0.00 39.42 3.79
45 46 1.402325 CGGAAAACGGGGAAAATGCTC 60.402 52.381 0.00 0.00 39.42 4.26
46 47 1.402325 GGAAAACGGGGAAAATGCTCG 60.402 52.381 0.00 0.00 0.00 5.03
47 48 0.601057 AAAACGGGGAAAATGCTCGG 59.399 50.000 0.00 0.00 0.00 4.63
48 49 0.250989 AAACGGGGAAAATGCTCGGA 60.251 50.000 0.00 0.00 0.00 4.55
49 50 0.034477 AACGGGGAAAATGCTCGGAT 60.034 50.000 0.00 0.00 0.00 4.18
50 51 0.748005 ACGGGGAAAATGCTCGGATG 60.748 55.000 0.00 0.00 0.00 3.51
51 52 1.735973 GGGGAAAATGCTCGGATGC 59.264 57.895 0.00 0.00 0.00 3.91
59 60 2.089017 TGCTCGGATGCATGAAACG 58.911 52.632 2.46 3.47 38.12 3.60
60 61 0.390998 TGCTCGGATGCATGAAACGA 60.391 50.000 2.46 8.03 38.12 3.85
61 62 0.726827 GCTCGGATGCATGAAACGAA 59.273 50.000 2.46 0.00 32.80 3.85
62 63 1.529826 GCTCGGATGCATGAAACGAAC 60.530 52.381 2.46 0.61 32.80 3.95
63 64 1.731709 CTCGGATGCATGAAACGAACA 59.268 47.619 2.46 0.00 32.80 3.18
64 65 1.463056 TCGGATGCATGAAACGAACAC 59.537 47.619 2.46 0.00 0.00 3.32
65 66 1.786575 CGGATGCATGAAACGAACACG 60.787 52.381 2.46 0.00 0.00 4.49
66 67 1.196808 GGATGCATGAAACGAACACGT 59.803 47.619 2.46 0.00 42.17 4.49
67 68 2.413796 GGATGCATGAAACGAACACGTA 59.586 45.455 2.46 0.00 39.39 3.57
68 69 3.063452 GGATGCATGAAACGAACACGTAT 59.937 43.478 2.46 0.00 39.39 3.06
69 70 3.447752 TGCATGAAACGAACACGTATG 57.552 42.857 0.00 0.00 39.39 2.39
70 71 2.166007 GCATGAAACGAACACGTATGC 58.834 47.619 11.24 11.24 40.02 3.14
71 72 2.412195 GCATGAAACGAACACGTATGCA 60.412 45.455 17.76 0.00 43.15 3.96
72 73 3.804688 CATGAAACGAACACGTATGCAA 58.195 40.909 0.00 0.00 39.39 4.08
73 74 3.946308 TGAAACGAACACGTATGCAAA 57.054 38.095 0.00 0.00 39.39 3.68
74 75 4.274421 TGAAACGAACACGTATGCAAAA 57.726 36.364 0.00 0.00 39.39 2.44
75 76 4.849883 TGAAACGAACACGTATGCAAAAT 58.150 34.783 0.00 0.00 39.39 1.82
76 77 4.672862 TGAAACGAACACGTATGCAAAATG 59.327 37.500 0.00 0.00 39.39 2.32
77 78 4.475763 AACGAACACGTATGCAAAATGA 57.524 36.364 0.00 0.00 39.39 2.57
78 79 4.475763 ACGAACACGTATGCAAAATGAA 57.524 36.364 0.00 0.00 38.51 2.57
79 80 4.849883 ACGAACACGTATGCAAAATGAAA 58.150 34.783 0.00 0.00 38.51 2.69
80 81 5.457140 ACGAACACGTATGCAAAATGAAAT 58.543 33.333 0.00 0.00 38.51 2.17
81 82 5.341993 ACGAACACGTATGCAAAATGAAATG 59.658 36.000 0.00 0.00 38.51 2.32
82 83 5.514059 AACACGTATGCAAAATGAAATGC 57.486 34.783 0.00 0.00 42.86 3.56
92 93 7.062906 TGCAAAATGAAATGCACATGATAAC 57.937 32.000 0.00 0.00 46.87 1.89
93 94 6.649557 TGCAAAATGAAATGCACATGATAACA 59.350 30.769 0.00 0.00 46.87 2.41
94 95 7.334671 TGCAAAATGAAATGCACATGATAACAT 59.665 29.630 0.00 0.00 46.87 2.71
95 96 7.638295 GCAAAATGAAATGCACATGATAACATG 59.362 33.333 11.14 11.14 44.17 3.21
120 121 5.977489 ATGAAATGCATATGAGGACATGG 57.023 39.130 6.97 0.00 37.87 3.66
121 122 3.570975 TGAAATGCATATGAGGACATGGC 59.429 43.478 6.97 0.00 37.87 4.40
122 123 2.963599 ATGCATATGAGGACATGGCA 57.036 45.000 6.97 0.00 45.02 4.92
123 124 2.732844 TGCATATGAGGACATGGCAA 57.267 45.000 6.97 0.00 41.46 4.52
124 125 3.015675 TGCATATGAGGACATGGCAAA 57.984 42.857 6.97 0.00 41.46 3.68
125 126 2.953648 TGCATATGAGGACATGGCAAAG 59.046 45.455 6.97 0.00 41.46 2.77
126 127 2.954318 GCATATGAGGACATGGCAAAGT 59.046 45.455 6.97 0.00 37.74 2.66
127 128 3.243301 GCATATGAGGACATGGCAAAGTG 60.243 47.826 6.97 0.00 37.74 3.16
128 129 1.180029 ATGAGGACATGGCAAAGTGC 58.820 50.000 0.00 6.81 44.08 4.40
129 130 2.290832 TATGAGGACATGGCAAAGTGCA 60.291 45.455 15.17 5.58 40.35 4.57
130 131 3.813598 TATGAGGACATGGCAAAGTGCAA 60.814 43.478 15.17 5.59 40.35 4.08
131 132 5.876929 TATGAGGACATGGCAAAGTGCAAC 61.877 45.833 15.17 9.99 40.35 4.17
146 147 2.605030 TGCAACACACAAGCAAAAGAC 58.395 42.857 0.00 0.00 34.97 3.01
147 148 2.029560 TGCAACACACAAGCAAAAGACA 60.030 40.909 0.00 0.00 34.97 3.41
148 149 3.189285 GCAACACACAAGCAAAAGACAT 58.811 40.909 0.00 0.00 0.00 3.06
149 150 3.000523 GCAACACACAAGCAAAAGACATG 59.999 43.478 0.00 0.00 0.00 3.21
150 151 3.441496 ACACACAAGCAAAAGACATGG 57.559 42.857 0.00 0.00 0.00 3.66
151 152 2.129607 CACACAAGCAAAAGACATGGC 58.870 47.619 0.00 0.00 0.00 4.40
152 153 1.755959 ACACAAGCAAAAGACATGGCA 59.244 42.857 0.00 0.00 0.00 4.92
153 154 2.168106 ACACAAGCAAAAGACATGGCAA 59.832 40.909 0.00 0.00 0.00 4.52
154 155 2.540931 CACAAGCAAAAGACATGGCAAC 59.459 45.455 0.00 0.00 0.00 4.17
155 156 1.788308 CAAGCAAAAGACATGGCAACG 59.212 47.619 0.00 0.00 42.51 4.10
156 157 1.317613 AGCAAAAGACATGGCAACGA 58.682 45.000 0.00 0.00 42.51 3.85
157 158 1.001378 AGCAAAAGACATGGCAACGAC 60.001 47.619 0.00 0.00 42.51 4.34
158 159 1.673760 CAAAAGACATGGCAACGACG 58.326 50.000 0.00 0.00 42.51 5.12
159 160 0.591170 AAAAGACATGGCAACGACGG 59.409 50.000 0.00 0.00 42.51 4.79
160 161 1.852067 AAAGACATGGCAACGACGGC 61.852 55.000 0.00 0.00 42.51 5.68
161 162 4.147322 GACATGGCAACGACGGCG 62.147 66.667 10.39 10.39 44.79 6.46
162 163 4.673298 ACATGGCAACGACGGCGA 62.673 61.111 22.49 0.00 41.64 5.54
163 164 3.418913 CATGGCAACGACGGCGAA 61.419 61.111 22.49 0.00 41.64 4.70
164 165 2.435938 ATGGCAACGACGGCGAAT 60.436 55.556 22.49 1.56 41.64 3.34
165 166 1.153529 ATGGCAACGACGGCGAATA 60.154 52.632 22.49 0.00 41.64 1.75
166 167 0.741574 ATGGCAACGACGGCGAATAA 60.742 50.000 22.49 0.00 41.64 1.40
167 168 1.059838 GGCAACGACGGCGAATAAC 59.940 57.895 22.49 0.67 41.64 1.89
168 169 1.356527 GGCAACGACGGCGAATAACT 61.357 55.000 22.49 0.00 41.64 2.24
169 170 0.247145 GCAACGACGGCGAATAACTG 60.247 55.000 22.49 5.42 41.64 3.16
170 171 0.368907 CAACGACGGCGAATAACTGG 59.631 55.000 22.49 0.00 41.64 4.00
171 172 1.356527 AACGACGGCGAATAACTGGC 61.357 55.000 22.49 0.00 41.64 4.85
175 176 3.406559 GGCGAATAACTGGCGGAC 58.593 61.111 0.00 0.00 0.00 4.79
176 177 1.448893 GGCGAATAACTGGCGGACA 60.449 57.895 0.00 0.00 0.00 4.02
177 178 1.702491 GGCGAATAACTGGCGGACAC 61.702 60.000 0.00 0.00 0.00 3.67
178 179 1.702491 GCGAATAACTGGCGGACACC 61.702 60.000 0.00 0.00 0.00 4.16
179 180 0.108329 CGAATAACTGGCGGACACCT 60.108 55.000 0.00 0.00 0.00 4.00
180 181 1.369625 GAATAACTGGCGGACACCTG 58.630 55.000 0.00 0.00 34.95 4.00
181 182 0.035439 AATAACTGGCGGACACCTGG 60.035 55.000 0.00 0.00 33.19 4.45
182 183 2.536997 ATAACTGGCGGACACCTGGC 62.537 60.000 0.00 0.00 43.87 4.85
190 191 4.980805 GACACCTGGCGCAACGGA 62.981 66.667 10.83 0.00 0.00 4.69
191 192 4.329545 ACACCTGGCGCAACGGAT 62.330 61.111 10.83 0.00 0.00 4.18
192 193 3.499737 CACCTGGCGCAACGGATC 61.500 66.667 10.83 0.00 0.00 3.36
193 194 4.778143 ACCTGGCGCAACGGATCC 62.778 66.667 10.83 0.00 0.00 3.36
194 195 4.776322 CCTGGCGCAACGGATCCA 62.776 66.667 13.41 0.00 0.00 3.41
195 196 3.197790 CTGGCGCAACGGATCCAG 61.198 66.667 13.41 7.30 39.95 3.86
196 197 4.776322 TGGCGCAACGGATCCAGG 62.776 66.667 13.41 0.91 0.00 4.45
200 201 4.778143 GCAACGGATCCAGGGCGT 62.778 66.667 13.41 0.00 0.00 5.68
201 202 2.046314 CAACGGATCCAGGGCGTT 60.046 61.111 13.41 6.72 0.00 4.84
202 203 1.219664 CAACGGATCCAGGGCGTTA 59.780 57.895 13.41 0.00 0.00 3.18
203 204 1.087771 CAACGGATCCAGGGCGTTAC 61.088 60.000 13.41 0.00 0.00 2.50
204 205 1.546589 AACGGATCCAGGGCGTTACA 61.547 55.000 13.41 0.00 0.00 2.41
205 206 1.335132 ACGGATCCAGGGCGTTACAT 61.335 55.000 13.41 0.00 0.00 2.29
206 207 0.600255 CGGATCCAGGGCGTTACATC 60.600 60.000 13.41 0.00 0.00 3.06
207 208 0.468226 GGATCCAGGGCGTTACATCA 59.532 55.000 6.95 0.00 0.00 3.07
208 209 1.072331 GGATCCAGGGCGTTACATCAT 59.928 52.381 6.95 0.00 0.00 2.45
209 210 2.146342 GATCCAGGGCGTTACATCATG 58.854 52.381 0.00 0.00 0.00 3.07
210 211 1.199615 TCCAGGGCGTTACATCATGA 58.800 50.000 0.00 0.00 0.00 3.07
211 212 1.768275 TCCAGGGCGTTACATCATGAT 59.232 47.619 1.18 1.18 0.00 2.45
212 213 2.172505 TCCAGGGCGTTACATCATGATT 59.827 45.455 5.16 0.66 0.00 2.57
229 230 5.458452 TCATGATTCTTTGTGTTTGCGTTTC 59.542 36.000 0.00 0.00 0.00 2.78
236 237 0.913876 GTGTTTGCGTTTCAGTGTGC 59.086 50.000 0.00 0.00 0.00 4.57
267 268 6.042781 AGGGTCAACTACTTTGTACTGATTCA 59.957 38.462 0.00 0.00 36.49 2.57
400 404 1.213094 CGCCGTGTTTCTTCGACTGT 61.213 55.000 0.00 0.00 0.00 3.55
406 410 3.543460 CGTGTTTCTTCGACTGTTGTTCC 60.543 47.826 0.00 0.00 0.00 3.62
483 487 2.729156 GCAACAAGCGTTCAATAGGAGC 60.729 50.000 0.00 0.00 31.13 4.70
484 488 2.744202 CAACAAGCGTTCAATAGGAGCT 59.256 45.455 0.00 0.00 40.20 4.09
486 490 1.936547 CAAGCGTTCAATAGGAGCTCC 59.063 52.381 26.22 26.22 37.15 4.70
488 492 0.178068 GCGTTCAATAGGAGCTCCCA 59.822 55.000 29.54 17.52 37.41 4.37
489 493 1.406887 GCGTTCAATAGGAGCTCCCAA 60.407 52.381 29.54 18.33 37.41 4.12
490 494 2.746472 GCGTTCAATAGGAGCTCCCAAT 60.746 50.000 29.54 19.82 37.41 3.16
571 575 0.539438 TTCTTTGGGCCGTTCTGCAT 60.539 50.000 0.00 0.00 0.00 3.96
1035 2049 3.470709 TCTCACTGAAACCAAGCTCTTG 58.529 45.455 2.74 2.74 40.13 3.02
1358 2386 3.274288 CCTACAAACAAGCCTCCATCTC 58.726 50.000 0.00 0.00 0.00 2.75
1377 2405 1.281925 CCTCCTATGCCCTGGTTGGT 61.282 60.000 0.00 0.00 0.00 3.67
1421 2449 4.814294 GGGCGTCGGCACCTACTG 62.814 72.222 21.23 0.00 42.47 2.74
1611 2642 1.741770 GCCGGAGCACACTCGAATT 60.742 57.895 5.05 0.00 44.48 2.17
1932 3014 2.475155 TCCAGATCTTGCAGGAGTCAT 58.525 47.619 4.35 0.00 0.00 3.06
1935 3017 2.169978 CAGATCTTGCAGGAGTCATGGA 59.830 50.000 6.95 0.00 0.00 3.41
2093 3831 5.237127 TGTTGAGGCTTCATTTGCGATATAG 59.763 40.000 0.00 0.00 32.27 1.31
2115 3853 5.251764 AGTCATGCTGCTCTTTTGTATCTT 58.748 37.500 0.00 0.00 0.00 2.40
2214 3952 3.205784 GAGCAAATCCAGCCTGTATCT 57.794 47.619 0.00 0.00 0.00 1.98
2223 3961 3.711190 TCCAGCCTGTATCTAGATTTGCA 59.289 43.478 11.25 7.27 0.00 4.08
2568 4306 0.823356 AACTGCACAAATCCGGCTGT 60.823 50.000 0.00 0.00 40.70 4.40
2608 4346 1.451927 GGATGGCGCCTCATTCACA 60.452 57.895 29.70 4.25 0.00 3.58
2640 4378 1.855360 GCTATGAACACTCGCACTAGC 59.145 52.381 0.00 0.00 37.42 3.42
2667 4487 7.488322 TCTGAAACCAACAAAGAGGTTATTTG 58.512 34.615 0.00 0.00 46.92 2.32
2719 4539 9.880064 GAGAACTATTGTTAGTTTTCCAACTTC 57.120 33.333 5.54 0.00 46.32 3.01
2889 4709 9.671279 TGCAAATATGTTCTTCAGATCTCTTAA 57.329 29.630 0.00 0.00 0.00 1.85
2957 4777 2.588925 AGGCCTTCCTTACCCATACT 57.411 50.000 0.00 0.00 40.66 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.159099 TGCAATCCGACACTCCTATGTC 60.159 50.000 0.00 0.00 44.68 3.06
1 2 1.831106 TGCAATCCGACACTCCTATGT 59.169 47.619 0.00 0.00 34.78 2.29
2 3 2.602257 TGCAATCCGACACTCCTATG 57.398 50.000 0.00 0.00 0.00 2.23
3 4 3.627395 TTTGCAATCCGACACTCCTAT 57.373 42.857 0.00 0.00 0.00 2.57
4 5 3.071479 GTTTTGCAATCCGACACTCCTA 58.929 45.455 0.00 0.00 0.00 2.94
5 6 1.880027 GTTTTGCAATCCGACACTCCT 59.120 47.619 0.00 0.00 0.00 3.69
6 7 1.399727 CGTTTTGCAATCCGACACTCC 60.400 52.381 11.58 0.00 0.00 3.85
7 8 1.399727 CCGTTTTGCAATCCGACACTC 60.400 52.381 16.97 0.00 0.00 3.51
8 9 0.591170 CCGTTTTGCAATCCGACACT 59.409 50.000 16.97 0.00 0.00 3.55
9 10 0.589223 TCCGTTTTGCAATCCGACAC 59.411 50.000 16.97 0.95 0.00 3.67
10 11 1.309950 TTCCGTTTTGCAATCCGACA 58.690 45.000 16.97 3.67 0.00 4.35
11 12 2.409152 TTTCCGTTTTGCAATCCGAC 57.591 45.000 16.97 6.34 0.00 4.79
12 13 2.733517 GTTTTCCGTTTTGCAATCCGA 58.266 42.857 16.97 4.93 0.00 4.55
13 14 1.450161 CGTTTTCCGTTTTGCAATCCG 59.550 47.619 0.00 5.58 0.00 4.18
14 15 1.790043 CCGTTTTCCGTTTTGCAATCC 59.210 47.619 0.00 0.00 33.66 3.01
15 16 1.790043 CCCGTTTTCCGTTTTGCAATC 59.210 47.619 0.00 0.00 33.66 2.67
16 17 1.539280 CCCCGTTTTCCGTTTTGCAAT 60.539 47.619 0.00 0.00 33.66 3.56
17 18 0.179108 CCCCGTTTTCCGTTTTGCAA 60.179 50.000 0.00 0.00 33.66 4.08
18 19 1.035932 TCCCCGTTTTCCGTTTTGCA 61.036 50.000 0.00 0.00 33.66 4.08
19 20 0.102663 TTCCCCGTTTTCCGTTTTGC 59.897 50.000 0.00 0.00 33.66 3.68
20 21 2.580966 TTTCCCCGTTTTCCGTTTTG 57.419 45.000 0.00 0.00 33.66 2.44
21 22 3.459145 CATTTTCCCCGTTTTCCGTTTT 58.541 40.909 0.00 0.00 33.66 2.43
22 23 2.803852 GCATTTTCCCCGTTTTCCGTTT 60.804 45.455 0.00 0.00 33.66 3.60
23 24 1.269883 GCATTTTCCCCGTTTTCCGTT 60.270 47.619 0.00 0.00 33.66 4.44
24 25 0.315886 GCATTTTCCCCGTTTTCCGT 59.684 50.000 0.00 0.00 33.66 4.69
25 26 0.601057 AGCATTTTCCCCGTTTTCCG 59.399 50.000 0.00 0.00 0.00 4.30
26 27 1.402325 CGAGCATTTTCCCCGTTTTCC 60.402 52.381 0.00 0.00 0.00 3.13
27 28 1.402325 CCGAGCATTTTCCCCGTTTTC 60.402 52.381 0.00 0.00 0.00 2.29
28 29 0.601057 CCGAGCATTTTCCCCGTTTT 59.399 50.000 0.00 0.00 0.00 2.43
29 30 0.250989 TCCGAGCATTTTCCCCGTTT 60.251 50.000 0.00 0.00 0.00 3.60
30 31 0.034477 ATCCGAGCATTTTCCCCGTT 60.034 50.000 0.00 0.00 0.00 4.44
31 32 0.748005 CATCCGAGCATTTTCCCCGT 60.748 55.000 0.00 0.00 0.00 5.28
32 33 2.024918 CATCCGAGCATTTTCCCCG 58.975 57.895 0.00 0.00 0.00 5.73
33 34 1.037030 TGCATCCGAGCATTTTCCCC 61.037 55.000 0.00 0.00 40.11 4.81
34 35 2.492418 TGCATCCGAGCATTTTCCC 58.508 52.632 0.00 0.00 40.11 3.97
42 43 0.726827 TTCGTTTCATGCATCCGAGC 59.273 50.000 0.00 0.00 0.00 5.03
43 44 1.731709 TGTTCGTTTCATGCATCCGAG 59.268 47.619 0.00 0.00 0.00 4.63
44 45 1.463056 GTGTTCGTTTCATGCATCCGA 59.537 47.619 0.00 0.00 0.00 4.55
45 46 1.786575 CGTGTTCGTTTCATGCATCCG 60.787 52.381 0.00 0.00 0.00 4.18
46 47 1.882198 CGTGTTCGTTTCATGCATCC 58.118 50.000 0.00 0.00 0.00 3.51
56 57 9.386110 GCATTTCATTTTGCATACGTGTTCGTT 62.386 37.037 0.00 0.00 43.07 3.85
57 58 8.017529 GCATTTCATTTTGCATACGTGTTCGT 62.018 38.462 0.00 0.00 44.23 3.85
58 59 5.718290 GCATTTCATTTTGCATACGTGTTCG 60.718 40.000 0.00 0.00 38.72 3.95
59 60 5.118357 TGCATTTCATTTTGCATACGTGTTC 59.882 36.000 0.00 0.00 43.54 3.18
60 61 4.987285 TGCATTTCATTTTGCATACGTGTT 59.013 33.333 0.00 0.00 43.54 3.32
61 62 4.554292 TGCATTTCATTTTGCATACGTGT 58.446 34.783 0.00 0.00 43.54 4.49
68 69 6.649557 TGTTATCATGTGCATTTCATTTTGCA 59.350 30.769 0.00 0.00 46.03 4.08
69 70 7.062906 TGTTATCATGTGCATTTCATTTTGC 57.937 32.000 0.00 0.00 39.33 3.68
82 83 9.855021 ATGCATTTCATATCATGTTATCATGTG 57.145 29.630 12.41 5.43 41.56 3.21
89 90 9.962809 TCCTCATATGCATTTCATATCATGTTA 57.037 29.630 3.54 0.00 44.40 2.41
90 91 8.737175 GTCCTCATATGCATTTCATATCATGTT 58.263 33.333 3.54 0.00 44.40 2.71
91 92 7.886446 TGTCCTCATATGCATTTCATATCATGT 59.114 33.333 3.54 0.00 44.40 3.21
92 93 8.276252 TGTCCTCATATGCATTTCATATCATG 57.724 34.615 3.54 0.00 44.40 3.07
93 94 8.903820 CATGTCCTCATATGCATTTCATATCAT 58.096 33.333 3.54 0.81 44.40 2.45
94 95 7.338449 CCATGTCCTCATATGCATTTCATATCA 59.662 37.037 3.54 0.00 44.40 2.15
95 96 7.681304 GCCATGTCCTCATATGCATTTCATATC 60.681 40.741 3.54 0.00 44.40 1.63
96 97 6.096423 GCCATGTCCTCATATGCATTTCATAT 59.904 38.462 3.54 0.00 46.49 1.78
97 98 5.416639 GCCATGTCCTCATATGCATTTCATA 59.583 40.000 3.54 0.00 41.52 2.15
98 99 4.219944 GCCATGTCCTCATATGCATTTCAT 59.780 41.667 3.54 0.00 39.17 2.57
99 100 3.570975 GCCATGTCCTCATATGCATTTCA 59.429 43.478 3.54 0.00 33.81 2.69
100 101 3.570975 TGCCATGTCCTCATATGCATTTC 59.429 43.478 3.54 0.00 36.65 2.17
101 102 3.568443 TGCCATGTCCTCATATGCATTT 58.432 40.909 3.54 0.00 36.65 2.32
102 103 3.232720 TGCCATGTCCTCATATGCATT 57.767 42.857 3.54 0.00 36.65 3.56
103 104 2.963599 TGCCATGTCCTCATATGCAT 57.036 45.000 3.79 3.79 36.65 3.96
104 105 2.732844 TTGCCATGTCCTCATATGCA 57.267 45.000 0.00 0.00 38.40 3.96
105 106 2.954318 ACTTTGCCATGTCCTCATATGC 59.046 45.455 0.00 0.00 34.04 3.14
106 107 3.243301 GCACTTTGCCATGTCCTCATATG 60.243 47.826 0.00 0.00 37.42 1.78
107 108 2.954318 GCACTTTGCCATGTCCTCATAT 59.046 45.455 0.00 0.00 37.42 1.78
108 109 2.290832 TGCACTTTGCCATGTCCTCATA 60.291 45.455 0.00 0.00 44.23 2.15
109 110 1.180029 GCACTTTGCCATGTCCTCAT 58.820 50.000 0.00 0.00 37.42 2.90
110 111 0.178995 TGCACTTTGCCATGTCCTCA 60.179 50.000 0.00 0.00 44.23 3.86
111 112 0.961019 TTGCACTTTGCCATGTCCTC 59.039 50.000 0.00 0.00 44.23 3.71
112 113 0.675633 GTTGCACTTTGCCATGTCCT 59.324 50.000 0.00 0.00 44.23 3.85
113 114 0.388659 TGTTGCACTTTGCCATGTCC 59.611 50.000 0.00 0.00 44.23 4.02
114 115 1.202394 TGTGTTGCACTTTGCCATGTC 60.202 47.619 0.00 0.00 44.23 3.06
115 116 0.822811 TGTGTTGCACTTTGCCATGT 59.177 45.000 0.00 0.00 44.23 3.21
116 117 1.210870 GTGTGTTGCACTTTGCCATG 58.789 50.000 0.00 0.00 44.23 3.66
117 118 3.665544 GTGTGTTGCACTTTGCCAT 57.334 47.368 0.00 0.00 44.23 4.40
126 127 2.029560 TGTCTTTTGCTTGTGTGTTGCA 60.030 40.909 0.00 0.00 34.69 4.08
127 128 2.605030 TGTCTTTTGCTTGTGTGTTGC 58.395 42.857 0.00 0.00 0.00 4.17
128 129 3.552699 CCATGTCTTTTGCTTGTGTGTTG 59.447 43.478 0.00 0.00 0.00 3.33
129 130 3.784338 CCATGTCTTTTGCTTGTGTGTT 58.216 40.909 0.00 0.00 0.00 3.32
130 131 2.481795 GCCATGTCTTTTGCTTGTGTGT 60.482 45.455 0.00 0.00 0.00 3.72
131 132 2.129607 GCCATGTCTTTTGCTTGTGTG 58.870 47.619 0.00 0.00 0.00 3.82
132 133 1.755959 TGCCATGTCTTTTGCTTGTGT 59.244 42.857 0.00 0.00 0.00 3.72
133 134 2.512485 TGCCATGTCTTTTGCTTGTG 57.488 45.000 0.00 0.00 0.00 3.33
134 135 2.799207 CGTTGCCATGTCTTTTGCTTGT 60.799 45.455 0.00 0.00 0.00 3.16
135 136 1.788308 CGTTGCCATGTCTTTTGCTTG 59.212 47.619 0.00 0.00 0.00 4.01
136 137 1.680735 TCGTTGCCATGTCTTTTGCTT 59.319 42.857 0.00 0.00 0.00 3.91
137 138 1.001378 GTCGTTGCCATGTCTTTTGCT 60.001 47.619 0.00 0.00 0.00 3.91
138 139 1.408422 GTCGTTGCCATGTCTTTTGC 58.592 50.000 0.00 0.00 0.00 3.68
139 140 1.662876 CCGTCGTTGCCATGTCTTTTG 60.663 52.381 0.00 0.00 0.00 2.44
140 141 0.591170 CCGTCGTTGCCATGTCTTTT 59.409 50.000 0.00 0.00 0.00 2.27
141 142 1.852067 GCCGTCGTTGCCATGTCTTT 61.852 55.000 0.00 0.00 0.00 2.52
142 143 2.325082 GCCGTCGTTGCCATGTCTT 61.325 57.895 0.00 0.00 0.00 3.01
143 144 2.742372 GCCGTCGTTGCCATGTCT 60.742 61.111 0.00 0.00 0.00 3.41
144 145 4.147322 CGCCGTCGTTGCCATGTC 62.147 66.667 0.00 0.00 0.00 3.06
145 146 4.673298 TCGCCGTCGTTGCCATGT 62.673 61.111 0.00 0.00 36.96 3.21
146 147 1.425267 TATTCGCCGTCGTTGCCATG 61.425 55.000 0.00 0.00 36.96 3.66
147 148 0.741574 TTATTCGCCGTCGTTGCCAT 60.742 50.000 0.00 0.00 36.96 4.40
148 149 1.374378 TTATTCGCCGTCGTTGCCA 60.374 52.632 0.00 0.00 36.96 4.92
149 150 1.059838 GTTATTCGCCGTCGTTGCC 59.940 57.895 0.00 0.00 36.96 4.52
150 151 0.247145 CAGTTATTCGCCGTCGTTGC 60.247 55.000 0.00 0.00 36.96 4.17
151 152 0.368907 CCAGTTATTCGCCGTCGTTG 59.631 55.000 0.00 0.00 36.96 4.10
152 153 1.356527 GCCAGTTATTCGCCGTCGTT 61.357 55.000 0.00 0.00 36.96 3.85
153 154 1.808390 GCCAGTTATTCGCCGTCGT 60.808 57.895 0.00 0.00 36.96 4.34
154 155 2.856346 CGCCAGTTATTCGCCGTCG 61.856 63.158 0.00 0.00 0.00 5.12
155 156 2.522638 CCGCCAGTTATTCGCCGTC 61.523 63.158 0.00 0.00 0.00 4.79
156 157 2.510691 CCGCCAGTTATTCGCCGT 60.511 61.111 0.00 0.00 0.00 5.68
157 158 2.202824 TCCGCCAGTTATTCGCCG 60.203 61.111 0.00 0.00 0.00 6.46
158 159 1.448893 TGTCCGCCAGTTATTCGCC 60.449 57.895 0.00 0.00 0.00 5.54
159 160 1.702491 GGTGTCCGCCAGTTATTCGC 61.702 60.000 0.00 0.00 0.00 4.70
160 161 0.108329 AGGTGTCCGCCAGTTATTCG 60.108 55.000 0.00 0.00 0.00 3.34
161 162 1.369625 CAGGTGTCCGCCAGTTATTC 58.630 55.000 0.00 0.00 0.00 1.75
162 163 0.035439 CCAGGTGTCCGCCAGTTATT 60.035 55.000 0.00 0.00 0.00 1.40
163 164 1.602237 CCAGGTGTCCGCCAGTTAT 59.398 57.895 0.00 0.00 0.00 1.89
164 165 3.065306 CCAGGTGTCCGCCAGTTA 58.935 61.111 0.00 0.00 0.00 2.24
165 166 4.643387 GCCAGGTGTCCGCCAGTT 62.643 66.667 0.00 0.00 0.00 3.16
173 174 4.980805 TCCGTTGCGCCAGGTGTC 62.981 66.667 4.18 0.00 0.00 3.67
174 175 4.329545 ATCCGTTGCGCCAGGTGT 62.330 61.111 4.18 0.00 0.00 4.16
175 176 3.499737 GATCCGTTGCGCCAGGTG 61.500 66.667 4.18 0.00 0.00 4.00
176 177 4.778143 GGATCCGTTGCGCCAGGT 62.778 66.667 4.18 0.00 0.00 4.00
177 178 4.776322 TGGATCCGTTGCGCCAGG 62.776 66.667 4.18 5.65 0.00 4.45
178 179 3.197790 CTGGATCCGTTGCGCCAG 61.198 66.667 4.18 0.00 41.62 4.85
179 180 4.776322 CCTGGATCCGTTGCGCCA 62.776 66.667 4.18 0.00 0.00 5.69
183 184 2.862674 TAACGCCCTGGATCCGTTGC 62.863 60.000 21.40 11.67 43.93 4.17
184 185 1.087771 GTAACGCCCTGGATCCGTTG 61.088 60.000 21.40 4.93 43.93 4.10
185 186 1.219935 GTAACGCCCTGGATCCGTT 59.780 57.895 18.45 18.45 45.72 4.44
186 187 1.335132 ATGTAACGCCCTGGATCCGT 61.335 55.000 7.39 0.00 36.68 4.69
187 188 0.600255 GATGTAACGCCCTGGATCCG 60.600 60.000 7.39 1.76 0.00 4.18
188 189 0.468226 TGATGTAACGCCCTGGATCC 59.532 55.000 4.20 4.20 0.00 3.36
189 190 2.146342 CATGATGTAACGCCCTGGATC 58.854 52.381 0.00 0.00 0.00 3.36
190 191 1.768275 TCATGATGTAACGCCCTGGAT 59.232 47.619 0.00 0.00 0.00 3.41
191 192 1.199615 TCATGATGTAACGCCCTGGA 58.800 50.000 0.00 0.00 0.00 3.86
192 193 2.260844 ATCATGATGTAACGCCCTGG 57.739 50.000 7.59 0.00 0.00 4.45
193 194 3.470709 AGAATCATGATGTAACGCCCTG 58.529 45.455 9.46 0.00 0.00 4.45
194 195 3.845781 AGAATCATGATGTAACGCCCT 57.154 42.857 9.46 0.00 0.00 5.19
195 196 4.096382 ACAAAGAATCATGATGTAACGCCC 59.904 41.667 9.46 0.00 0.00 6.13
196 197 5.030295 CACAAAGAATCATGATGTAACGCC 58.970 41.667 9.46 0.00 0.00 5.68
197 198 5.631026 ACACAAAGAATCATGATGTAACGC 58.369 37.500 9.46 0.00 0.00 4.84
198 199 7.409661 GCAAACACAAAGAATCATGATGTAACG 60.410 37.037 9.46 1.18 0.00 3.18
199 200 7.409661 CGCAAACACAAAGAATCATGATGTAAC 60.410 37.037 9.46 1.95 0.00 2.50
200 201 6.581919 CGCAAACACAAAGAATCATGATGTAA 59.418 34.615 9.46 0.00 0.00 2.41
201 202 6.085573 CGCAAACACAAAGAATCATGATGTA 58.914 36.000 9.46 0.00 0.00 2.29
202 203 4.919168 CGCAAACACAAAGAATCATGATGT 59.081 37.500 9.46 0.40 0.00 3.06
203 204 4.919168 ACGCAAACACAAAGAATCATGATG 59.081 37.500 9.46 0.00 0.00 3.07
204 205 5.125100 ACGCAAACACAAAGAATCATGAT 57.875 34.783 1.18 1.18 0.00 2.45
205 206 4.566545 ACGCAAACACAAAGAATCATGA 57.433 36.364 0.00 0.00 0.00 3.07
206 207 5.231779 TGAAACGCAAACACAAAGAATCATG 59.768 36.000 0.00 0.00 0.00 3.07
207 208 5.347342 TGAAACGCAAACACAAAGAATCAT 58.653 33.333 0.00 0.00 0.00 2.45
208 209 4.738124 TGAAACGCAAACACAAAGAATCA 58.262 34.783 0.00 0.00 0.00 2.57
209 210 4.798387 ACTGAAACGCAAACACAAAGAATC 59.202 37.500 0.00 0.00 0.00 2.52
210 211 4.562394 CACTGAAACGCAAACACAAAGAAT 59.438 37.500 0.00 0.00 0.00 2.40
211 212 3.917380 CACTGAAACGCAAACACAAAGAA 59.083 39.130 0.00 0.00 0.00 2.52
212 213 3.057876 ACACTGAAACGCAAACACAAAGA 60.058 39.130 0.00 0.00 0.00 2.52
229 230 2.254546 TGACCCTTACAAGCACACTG 57.745 50.000 0.00 0.00 0.00 3.66
236 237 7.170998 CAGTACAAAGTAGTTGACCCTTACAAG 59.829 40.741 0.00 0.00 39.87 3.16
298 302 5.010617 GGCTTTTGTAAGAATCAAACCCTGA 59.989 40.000 0.00 0.00 35.05 3.86
302 306 6.084326 TGAGGCTTTTGTAAGAATCAAACC 57.916 37.500 0.00 0.00 35.05 3.27
345 349 2.754995 GCCCAAGCTAGCGAACAGC 61.755 63.158 9.55 6.56 40.64 4.40
346 350 3.490890 GCCCAAGCTAGCGAACAG 58.509 61.111 9.55 0.00 35.50 3.16
385 389 3.621715 AGGAACAACAGTCGAAGAAACAC 59.378 43.478 0.00 0.00 39.69 3.32
386 390 3.869065 AGGAACAACAGTCGAAGAAACA 58.131 40.909 0.00 0.00 39.69 2.83
387 391 4.877323 AAGGAACAACAGTCGAAGAAAC 57.123 40.909 0.00 0.00 39.69 2.78
388 392 5.667466 ACTAAGGAACAACAGTCGAAGAAA 58.333 37.500 0.00 0.00 39.69 2.52
389 393 5.272283 ACTAAGGAACAACAGTCGAAGAA 57.728 39.130 0.00 0.00 39.69 2.52
390 394 4.931661 ACTAAGGAACAACAGTCGAAGA 57.068 40.909 0.00 0.00 0.00 2.87
391 395 5.277345 CCAAACTAAGGAACAACAGTCGAAG 60.277 44.000 0.00 0.00 0.00 3.79
400 404 2.593026 CCAGCCCAAACTAAGGAACAA 58.407 47.619 0.00 0.00 0.00 2.83
444 448 3.670377 GTCCAACAGGGCGCCAAC 61.670 66.667 30.85 12.35 36.21 3.77
473 477 2.630098 CGAGATTGGGAGCTCCTATTGA 59.370 50.000 31.36 12.20 34.84 2.57
476 480 0.972883 GCGAGATTGGGAGCTCCTAT 59.027 55.000 31.36 23.62 34.84 2.57
477 481 1.115930 GGCGAGATTGGGAGCTCCTA 61.116 60.000 31.36 24.44 34.84 2.94
483 487 2.812619 GGGGAGGCGAGATTGGGAG 61.813 68.421 0.00 0.00 0.00 4.30
484 488 2.768344 GGGGAGGCGAGATTGGGA 60.768 66.667 0.00 0.00 0.00 4.37
486 490 2.770048 AGGGGGAGGCGAGATTGG 60.770 66.667 0.00 0.00 0.00 3.16
488 492 2.446802 GGAGGGGGAGGCGAGATT 60.447 66.667 0.00 0.00 0.00 2.40
489 493 4.565850 GGGAGGGGGAGGCGAGAT 62.566 72.222 0.00 0.00 0.00 2.75
571 575 3.282745 GAAGCAGACGGCCGACTGA 62.283 63.158 46.07 0.00 46.50 3.41
962 1976 1.021390 CCGAGTCTTGGCGCATTTCT 61.021 55.000 10.83 0.00 0.00 2.52
965 1979 0.739813 GTACCGAGTCTTGGCGCATT 60.740 55.000 10.83 0.00 0.00 3.56
1054 2068 2.983433 CATCGAAGCGGAAGATGCT 58.017 52.632 0.00 0.00 46.68 3.79
1358 2386 1.281925 ACCAACCAGGGCATAGGAGG 61.282 60.000 0.00 0.00 43.89 4.30
1419 2447 1.789078 AAGCCAGCGTGTCAAAGCAG 61.789 55.000 4.63 0.00 32.60 4.24
1420 2448 1.823470 AAGCCAGCGTGTCAAAGCA 60.823 52.632 4.63 0.00 32.60 3.91
1421 2449 1.370900 CAAGCCAGCGTGTCAAAGC 60.371 57.895 0.00 0.00 0.00 3.51
1515 2546 2.568612 CGCTCAGAGACGCCAAGA 59.431 61.111 0.00 0.00 0.00 3.02
1611 2642 1.490490 GGCATGTCAGTATCCTCCCAA 59.510 52.381 0.00 0.00 0.00 4.12
1660 2697 1.070786 GGCTGACAACTTCGGTGGA 59.929 57.895 0.00 0.00 32.41 4.02
2061 3143 6.404623 GCAAATGAAGCCTCAACATACATACA 60.405 38.462 0.00 0.00 34.49 2.29
2093 3831 5.330295 CAAGATACAAAAGAGCAGCATGAC 58.670 41.667 0.00 0.00 39.69 3.06
2115 3853 3.153369 TGATTGCTAACTGGGAAAGCA 57.847 42.857 0.00 0.00 44.15 3.91
2304 4042 7.653713 CACCATATACAAGCTCTTCTTCGTTAT 59.346 37.037 0.00 0.00 31.27 1.89
2608 4346 5.363101 AGTGTTCATAGCACGAATGATGAT 58.637 37.500 0.00 0.00 41.36 2.45
2640 4378 5.582689 AACCTCTTTGTTGGTTTCAGAAG 57.417 39.130 0.00 0.00 43.27 2.85
2667 4487 5.779529 AATCATTAGAATGTGGTGGCATC 57.220 39.130 0.00 0.00 37.65 3.91
2843 4663 7.575414 TTGCATAGAAGTGTTGTTTTCCTTA 57.425 32.000 0.00 0.00 0.00 2.69
2889 4709 6.483405 AGAGAAAGAAATCAGGAGCTCAAAT 58.517 36.000 17.19 2.35 0.00 2.32
2929 4749 0.466124 AAGGAAGGCCTATCTGCGAC 59.534 55.000 5.16 0.00 46.28 5.19


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

AutoCloner maintained by Alex Coulton.