Multiple sequence alignment - TraesCS3B01G389400

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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 TraesCS3B01G389400 chr3B 100.000 2591 0 0 1 2591 612798731 612801321 0.000000e+00 4785.0
1 TraesCS3B01G389400 chr3B 98.985 197 2 0 1 197 194637025 194636829 1.140000e-93 353.0
2 TraesCS3B01G389400 chr3D 89.679 1618 64 42 458 2016 461950682 461952255 0.000000e+00 1967.0
3 TraesCS3B01G389400 chr3D 87.081 209 16 8 192 395 461950463 461950665 2.590000e-55 226.0
4 TraesCS3B01G389400 chr3A 87.057 1468 61 59 458 1876 604325074 604326461 0.000000e+00 1539.0
5 TraesCS3B01G389400 chr3A 97.525 202 4 1 1 201 644616607 644616808 6.860000e-91 344.0
6 TraesCS3B01G389400 chr3A 94.836 213 9 2 1 212 500983473 500983262 5.340000e-87 331.0
7 TraesCS3B01G389400 chr3A 93.662 142 9 0 1875 2016 604326623 604326764 2.020000e-51 213.0
8 TraesCS3B01G389400 chr2B 95.480 531 23 1 2056 2585 323087616 323087086 0.000000e+00 846.0
9 TraesCS3B01G389400 chr2B 89.744 234 20 3 2059 2291 749408418 749408188 1.950000e-76 296.0
10 TraesCS3B01G389400 chr5D 93.923 543 31 2 2050 2591 484028813 484029354 0.000000e+00 819.0
11 TraesCS3B01G389400 chr5D 86.585 82 9 2 1172 1252 525302710 525302790 3.550000e-14 89.8
12 TraesCS3B01G389400 chr7B 91.328 542 37 3 2050 2591 221832672 221833203 0.000000e+00 732.0
13 TraesCS3B01G389400 chr7D 90.909 539 48 1 2054 2591 500254486 500255024 0.000000e+00 723.0
14 TraesCS3B01G389400 chr4D 89.883 514 49 3 2079 2591 15777579 15777068 0.000000e+00 658.0
15 TraesCS3B01G389400 chr4D 89.041 73 8 0 1327 1399 351737385 351737457 9.870000e-15 91.6
16 TraesCS3B01G389400 chr2D 92.511 454 32 1 2057 2510 615052240 615051789 0.000000e+00 649.0
17 TraesCS3B01G389400 chr1B 88.007 542 59 2 2050 2591 368681655 368682190 1.010000e-178 636.0
18 TraesCS3B01G389400 chr1B 99.492 197 1 0 1 197 575885157 575885353 2.450000e-95 359.0
19 TraesCS3B01G389400 chr1B 80.357 224 20 15 1177 1400 513481425 513481226 5.780000e-32 148.0
20 TraesCS3B01G389400 chr1B 85.366 82 10 2 1173 1253 33857284 33857204 1.650000e-12 84.2
21 TraesCS3B01G389400 chr1A 88.082 537 61 3 2055 2591 313494028 313493495 3.640000e-178 634.0
22 TraesCS3B01G389400 chr1A 98.571 70 1 0 1331 1400 482964107 482964038 9.740000e-25 124.0
23 TraesCS3B01G389400 chr1A 86.585 82 9 2 1173 1253 22282864 22282784 3.550000e-14 89.8
24 TraesCS3B01G389400 chr1D 93.062 418 26 3 2176 2591 24194940 24195356 2.200000e-170 608.0
25 TraesCS3B01G389400 chr1D 98.571 70 1 0 1331 1400 383177970 383177901 9.740000e-25 124.0
26 TraesCS3B01G389400 chr1D 86.420 81 9 2 1174 1253 20061997 20062076 1.280000e-13 87.9
27 TraesCS3B01G389400 chr1D 86.250 80 9 2 1175 1253 20193515 20193593 4.590000e-13 86.1
28 TraesCS3B01G389400 chr5B 97.980 198 4 0 1 198 648357622 648357425 6.860000e-91 344.0
29 TraesCS3B01G389400 chr5B 75.591 254 36 19 1164 1399 659604768 659605013 4.560000e-18 102.0
30 TraesCS3B01G389400 chr5A 97.970 197 4 0 1 197 839970 840166 2.470000e-90 342.0
31 TraesCS3B01G389400 chr5A 76.891 238 32 15 1178 1399 651635666 651635896 2.110000e-21 113.0
32 TraesCS3B01G389400 chr5A 76.349 241 38 17 1168 1399 651755174 651755404 7.580000e-21 111.0
33 TraesCS3B01G389400 chr5A 76.349 241 31 21 1178 1399 651588716 651588949 3.530000e-19 106.0
34 TraesCS3B01G389400 chr4A 97.970 197 4 0 1 197 17724901 17725097 2.470000e-90 342.0
35 TraesCS3B01G389400 chr2A 96.585 205 6 1 1 204 84977725 84977521 3.190000e-89 339.0
36 TraesCS3B01G389400 chr7A 92.544 228 11 5 1 226 653023098 653023321 3.220000e-84 322.0
37 TraesCS3B01G389400 chr4B 89.041 73 8 0 1327 1399 434714186 434714258 9.870000e-15 91.6


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 TraesCS3B01G389400 chr3B 612798731 612801321 2590 False 4785.0 4785 100.0000 1 2591 1 chr3B.!!$F1 2590
1 TraesCS3B01G389400 chr3D 461950463 461952255 1792 False 1096.5 1967 88.3800 192 2016 2 chr3D.!!$F1 1824
2 TraesCS3B01G389400 chr3A 604325074 604326764 1690 False 876.0 1539 90.3595 458 2016 2 chr3A.!!$F2 1558
3 TraesCS3B01G389400 chr2B 323087086 323087616 530 True 846.0 846 95.4800 2056 2585 1 chr2B.!!$R1 529
4 TraesCS3B01G389400 chr5D 484028813 484029354 541 False 819.0 819 93.9230 2050 2591 1 chr5D.!!$F1 541
5 TraesCS3B01G389400 chr7B 221832672 221833203 531 False 732.0 732 91.3280 2050 2591 1 chr7B.!!$F1 541
6 TraesCS3B01G389400 chr7D 500254486 500255024 538 False 723.0 723 90.9090 2054 2591 1 chr7D.!!$F1 537
7 TraesCS3B01G389400 chr4D 15777068 15777579 511 True 658.0 658 89.8830 2079 2591 1 chr4D.!!$R1 512
8 TraesCS3B01G389400 chr1B 368681655 368682190 535 False 636.0 636 88.0070 2050 2591 1 chr1B.!!$F1 541
9 TraesCS3B01G389400 chr1A 313493495 313494028 533 True 634.0 634 88.0820 2055 2591 1 chr1A.!!$R2 536

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
117 118 0.037419 ATTTTTGCTTCCGCCGCAAT 60.037 45.0 5.33 0.0 45.67 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2294 0.108019 ACTGTCCCTCCCGTTGTTTC 59.892 55.0 0.0 0.0 0.0 2.78 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
25 26 8.251383 TCCAACTTTGACCATAAATTTAACCA 57.749 30.769 1.21 0.00 0.00 3.67
26 27 8.705594 TCCAACTTTGACCATAAATTTAACCAA 58.294 29.630 1.21 2.19 0.00 3.67
27 28 8.769891 CCAACTTTGACCATAAATTTAACCAAC 58.230 33.333 1.21 0.00 0.00 3.77
28 29 9.319143 CAACTTTGACCATAAATTTAACCAACA 57.681 29.630 1.21 0.00 0.00 3.33
29 30 9.892130 AACTTTGACCATAAATTTAACCAACAA 57.108 25.926 1.21 3.68 0.00 2.83
30 31 9.541143 ACTTTGACCATAAATTTAACCAACAAG 57.459 29.630 1.21 4.46 0.00 3.16
31 32 9.757227 CTTTGACCATAAATTTAACCAACAAGA 57.243 29.630 1.21 0.00 0.00 3.02
32 33 9.535878 TTTGACCATAAATTTAACCAACAAGAC 57.464 29.630 1.21 0.00 0.00 3.01
33 34 7.662897 TGACCATAAATTTAACCAACAAGACC 58.337 34.615 1.21 0.00 0.00 3.85
34 35 7.287927 TGACCATAAATTTAACCAACAAGACCA 59.712 33.333 1.21 0.00 0.00 4.02
35 36 8.024145 ACCATAAATTTAACCAACAAGACCAA 57.976 30.769 1.21 0.00 0.00 3.67
36 37 7.929245 ACCATAAATTTAACCAACAAGACCAAC 59.071 33.333 1.21 0.00 0.00 3.77
37 38 8.147704 CCATAAATTTAACCAACAAGACCAACT 58.852 33.333 1.21 0.00 0.00 3.16
38 39 8.977505 CATAAATTTAACCAACAAGACCAACTG 58.022 33.333 1.21 0.00 0.00 3.16
39 40 4.379339 TTTAACCAACAAGACCAACTGC 57.621 40.909 0.00 0.00 0.00 4.40
40 41 0.738389 AACCAACAAGACCAACTGCG 59.262 50.000 0.00 0.00 0.00 5.18
41 42 1.101049 ACCAACAAGACCAACTGCGG 61.101 55.000 0.00 0.00 0.00 5.69
42 43 1.008538 CAACAAGACCAACTGCGGC 60.009 57.895 0.00 0.00 0.00 6.53
43 44 2.542907 AACAAGACCAACTGCGGCG 61.543 57.895 0.51 0.51 0.00 6.46
44 45 3.726517 CAAGACCAACTGCGGCGG 61.727 66.667 9.78 7.39 0.00 6.13
49 50 4.697756 CCAACTGCGGCGGGAGAA 62.698 66.667 19.55 0.00 35.29 2.87
50 51 2.668212 CAACTGCGGCGGGAGAAA 60.668 61.111 19.55 0.00 35.29 2.52
51 52 2.112297 AACTGCGGCGGGAGAAAA 59.888 55.556 19.55 0.00 35.29 2.29
52 53 1.527380 AACTGCGGCGGGAGAAAAA 60.527 52.632 19.55 0.00 35.29 1.94
110 111 9.520204 AATTCACTGATATAATTTTTGCTTCCG 57.480 29.630 0.00 0.00 0.00 4.30
111 112 6.494842 TCACTGATATAATTTTTGCTTCCGC 58.505 36.000 0.00 0.00 0.00 5.54
112 113 5.687285 CACTGATATAATTTTTGCTTCCGCC 59.313 40.000 0.00 0.00 34.43 6.13
113 114 4.854399 TGATATAATTTTTGCTTCCGCCG 58.146 39.130 0.00 0.00 34.43 6.46
114 115 1.921243 ATAATTTTTGCTTCCGCCGC 58.079 45.000 0.00 0.00 34.43 6.53
115 116 0.598562 TAATTTTTGCTTCCGCCGCA 59.401 45.000 0.00 0.00 35.22 5.69
116 117 0.249657 AATTTTTGCTTCCGCCGCAA 60.250 45.000 0.00 0.00 44.83 4.85
117 118 0.037419 ATTTTTGCTTCCGCCGCAAT 60.037 45.000 5.33 0.00 45.67 3.56
118 119 0.665972 TTTTTGCTTCCGCCGCAATC 60.666 50.000 5.33 0.00 45.67 2.67
119 120 2.794627 TTTTGCTTCCGCCGCAATCG 62.795 55.000 5.33 0.00 45.67 3.34
130 131 3.436001 CGCAATCGGTCTTGGTAGT 57.564 52.632 0.00 0.00 0.00 2.73
131 132 1.722011 CGCAATCGGTCTTGGTAGTT 58.278 50.000 0.00 0.00 0.00 2.24
132 133 2.883574 CGCAATCGGTCTTGGTAGTTA 58.116 47.619 0.00 0.00 0.00 2.24
133 134 3.255725 CGCAATCGGTCTTGGTAGTTAA 58.744 45.455 0.00 0.00 0.00 2.01
134 135 3.680937 CGCAATCGGTCTTGGTAGTTAAA 59.319 43.478 0.00 0.00 0.00 1.52
135 136 4.331717 CGCAATCGGTCTTGGTAGTTAAAT 59.668 41.667 0.00 0.00 0.00 1.40
136 137 5.163794 CGCAATCGGTCTTGGTAGTTAAATT 60.164 40.000 0.00 0.00 0.00 1.82
137 138 6.617879 GCAATCGGTCTTGGTAGTTAAATTT 58.382 36.000 0.00 0.00 0.00 1.82
138 139 6.526674 GCAATCGGTCTTGGTAGTTAAATTTG 59.473 38.462 0.00 0.00 0.00 2.32
139 140 5.616488 TCGGTCTTGGTAGTTAAATTTGC 57.384 39.130 0.00 0.00 0.00 3.68
140 141 4.152759 TCGGTCTTGGTAGTTAAATTTGCG 59.847 41.667 0.00 0.00 0.00 4.85
141 142 4.670735 CGGTCTTGGTAGTTAAATTTGCGG 60.671 45.833 0.00 0.00 0.00 5.69
142 143 4.216902 GGTCTTGGTAGTTAAATTTGCGGT 59.783 41.667 0.00 0.00 0.00 5.68
143 144 5.388111 GTCTTGGTAGTTAAATTTGCGGTC 58.612 41.667 0.00 0.00 0.00 4.79
144 145 5.049267 GTCTTGGTAGTTAAATTTGCGGTCA 60.049 40.000 0.00 0.00 0.00 4.02
145 146 5.531659 TCTTGGTAGTTAAATTTGCGGTCAA 59.468 36.000 0.00 0.00 0.00 3.18
146 147 5.769484 TGGTAGTTAAATTTGCGGTCAAA 57.231 34.783 0.00 1.25 45.24 2.69
147 148 5.764131 TGGTAGTTAAATTTGCGGTCAAAG 58.236 37.500 0.00 0.00 44.47 2.77
148 149 5.299782 TGGTAGTTAAATTTGCGGTCAAAGT 59.700 36.000 0.00 0.00 44.47 2.66
150 151 6.143278 GGTAGTTAAATTTGCGGTCAAAGTTG 59.857 38.462 15.52 0.00 46.10 3.16
151 152 5.897050 AGTTAAATTTGCGGTCAAAGTTGA 58.103 33.333 15.52 8.60 46.10 3.18
152 153 6.334202 AGTTAAATTTGCGGTCAAAGTTGAA 58.666 32.000 15.52 7.62 46.10 2.69
153 154 6.475402 AGTTAAATTTGCGGTCAAAGTTGAAG 59.525 34.615 15.52 0.00 46.10 3.02
154 155 2.202295 TTTGCGGTCAAAGTTGAAGC 57.798 45.000 12.95 12.95 40.91 3.86
155 156 1.098869 TTGCGGTCAAAGTTGAAGCA 58.901 45.000 16.61 16.61 45.11 3.91
156 157 0.380378 TGCGGTCAAAGTTGAAGCAC 59.620 50.000 16.61 0.00 43.36 4.40
157 158 0.657368 GCGGTCAAAGTTGAAGCACG 60.657 55.000 14.26 9.65 40.52 5.34
158 159 0.934496 CGGTCAAAGTTGAAGCACGA 59.066 50.000 0.00 0.00 39.21 4.35
159 160 1.070577 CGGTCAAAGTTGAAGCACGAG 60.071 52.381 0.00 0.00 39.21 4.18
160 161 1.264288 GGTCAAAGTTGAAGCACGAGG 59.736 52.381 0.00 0.00 39.21 4.63
161 162 2.210116 GTCAAAGTTGAAGCACGAGGA 58.790 47.619 0.00 0.00 39.21 3.71
162 163 2.808543 GTCAAAGTTGAAGCACGAGGAT 59.191 45.455 0.00 0.00 39.21 3.24
163 164 3.994392 GTCAAAGTTGAAGCACGAGGATA 59.006 43.478 0.00 0.00 39.21 2.59
164 165 4.092091 GTCAAAGTTGAAGCACGAGGATAG 59.908 45.833 0.00 0.00 39.21 2.08
165 166 4.021456 TCAAAGTTGAAGCACGAGGATAGA 60.021 41.667 0.00 0.00 33.55 1.98
166 167 3.791973 AGTTGAAGCACGAGGATAGAG 57.208 47.619 0.00 0.00 0.00 2.43
167 168 2.428890 AGTTGAAGCACGAGGATAGAGG 59.571 50.000 0.00 0.00 0.00 3.69
168 169 2.427453 GTTGAAGCACGAGGATAGAGGA 59.573 50.000 0.00 0.00 0.00 3.71
169 170 2.735151 TGAAGCACGAGGATAGAGGAA 58.265 47.619 0.00 0.00 0.00 3.36
170 171 2.690497 TGAAGCACGAGGATAGAGGAAG 59.310 50.000 0.00 0.00 0.00 3.46
171 172 1.036707 AGCACGAGGATAGAGGAAGC 58.963 55.000 0.00 0.00 0.00 3.86
172 173 0.747255 GCACGAGGATAGAGGAAGCA 59.253 55.000 0.00 0.00 0.00 3.91
173 174 1.537135 GCACGAGGATAGAGGAAGCAC 60.537 57.143 0.00 0.00 0.00 4.40
174 175 2.028130 CACGAGGATAGAGGAAGCACT 58.972 52.381 0.00 0.00 0.00 4.40
175 176 3.215151 CACGAGGATAGAGGAAGCACTA 58.785 50.000 0.00 0.00 0.00 2.74
176 177 3.003897 CACGAGGATAGAGGAAGCACTAC 59.996 52.174 0.00 0.00 0.00 2.73
177 178 3.215151 CGAGGATAGAGGAAGCACTACA 58.785 50.000 0.00 0.00 0.00 2.74
178 179 3.823873 CGAGGATAGAGGAAGCACTACAT 59.176 47.826 0.00 0.00 0.00 2.29
179 180 4.279671 CGAGGATAGAGGAAGCACTACATT 59.720 45.833 0.00 0.00 0.00 2.71
180 181 5.537188 GAGGATAGAGGAAGCACTACATTG 58.463 45.833 0.00 0.00 0.00 2.82
181 182 4.965532 AGGATAGAGGAAGCACTACATTGT 59.034 41.667 0.00 0.00 0.00 2.71
182 183 5.053145 GGATAGAGGAAGCACTACATTGTG 58.947 45.833 0.00 0.00 40.62 3.33
183 184 3.340814 AGAGGAAGCACTACATTGTGG 57.659 47.619 0.00 0.00 38.31 4.17
184 185 2.906389 AGAGGAAGCACTACATTGTGGA 59.094 45.455 7.20 0.00 38.31 4.02
185 186 3.327757 AGAGGAAGCACTACATTGTGGAA 59.672 43.478 7.20 0.00 38.31 3.53
186 187 4.018960 AGAGGAAGCACTACATTGTGGAAT 60.019 41.667 7.20 0.00 38.31 3.01
187 188 4.012374 AGGAAGCACTACATTGTGGAATG 58.988 43.478 7.20 0.00 44.11 2.67
188 189 3.129287 GGAAGCACTACATTGTGGAATGG 59.871 47.826 7.20 0.00 43.00 3.16
189 190 3.719268 AGCACTACATTGTGGAATGGA 57.281 42.857 7.20 0.00 43.00 3.41
193 194 3.931907 CTACATTGTGGAATGGAGGGA 57.068 47.619 0.00 0.00 44.23 4.20
194 195 2.814805 ACATTGTGGAATGGAGGGAG 57.185 50.000 0.00 0.00 43.00 4.30
195 196 1.995542 ACATTGTGGAATGGAGGGAGT 59.004 47.619 0.00 0.00 43.00 3.85
196 197 3.189606 ACATTGTGGAATGGAGGGAGTA 58.810 45.455 0.00 0.00 43.00 2.59
197 198 3.054361 ACATTGTGGAATGGAGGGAGTAC 60.054 47.826 0.00 0.00 43.00 2.73
211 212 6.618610 TGGAGGGAGTACTACTAGTCAAGATA 59.381 42.308 4.77 0.00 0.00 1.98
231 233 3.770263 ATACACTACGTACGTGTGCAT 57.230 42.857 32.00 26.58 44.63 3.96
245 247 3.521560 GTGTGCATCGGAACAGATAGAA 58.478 45.455 0.00 0.00 31.55 2.10
247 249 4.033358 GTGTGCATCGGAACAGATAGAAAG 59.967 45.833 0.00 0.00 31.55 2.62
248 250 3.557595 GTGCATCGGAACAGATAGAAAGG 59.442 47.826 0.00 0.00 0.00 3.11
256 258 4.938226 GGAACAGATAGAAAGGGTCACAAG 59.062 45.833 0.00 0.00 0.00 3.16
257 259 5.513267 GGAACAGATAGAAAGGGTCACAAGT 60.513 44.000 0.00 0.00 0.00 3.16
263 265 2.076863 GAAAGGGTCACAAGTGGATCG 58.923 52.381 0.00 0.00 0.00 3.69
315 317 2.964389 GGAGAGCGCGCCATCTTC 60.964 66.667 30.33 20.33 33.67 2.87
316 318 2.105930 GAGAGCGCGCCATCTTCT 59.894 61.111 30.33 23.65 0.00 2.85
317 319 1.520342 GAGAGCGCGCCATCTTCTT 60.520 57.895 30.33 6.10 0.00 2.52
318 320 1.486644 GAGAGCGCGCCATCTTCTTC 61.487 60.000 30.33 16.31 0.00 2.87
329 331 5.447279 GCGCCATCTTCTTCTTCGAAAAATA 60.447 40.000 0.00 0.00 0.00 1.40
341 343 3.601435 TCGAAAAATATGGAGAACCGCA 58.399 40.909 0.00 0.00 39.42 5.69
361 363 2.629763 GTGGCGTCACACGAAACC 59.370 61.111 16.80 0.00 46.05 3.27
362 364 2.589442 TGGCGTCACACGAAACCC 60.589 61.111 0.00 0.00 46.05 4.11
366 368 1.666872 CGTCACACGAAACCCTCCC 60.667 63.158 0.00 0.00 46.05 4.30
367 369 1.752833 GTCACACGAAACCCTCCCT 59.247 57.895 0.00 0.00 0.00 4.20
368 370 0.971386 GTCACACGAAACCCTCCCTA 59.029 55.000 0.00 0.00 0.00 3.53
369 371 1.345415 GTCACACGAAACCCTCCCTAA 59.655 52.381 0.00 0.00 0.00 2.69
395 400 0.231279 CGTGAAAAACACCCGTCGAG 59.769 55.000 0.00 0.00 45.73 4.04
396 401 0.584876 GTGAAAAACACCCGTCGAGG 59.415 55.000 0.00 0.00 43.05 4.63
397 402 1.161563 TGAAAAACACCCGTCGAGGC 61.162 55.000 0.00 0.00 39.21 4.70
398 403 2.166584 GAAAAACACCCGTCGAGGCG 62.167 60.000 0.00 0.00 39.21 5.52
406 411 4.175489 CGTCGAGGCGTCGTCCAT 62.175 66.667 26.11 0.00 46.85 3.41
407 412 2.278013 GTCGAGGCGTCGTCCATC 60.278 66.667 26.11 10.65 46.85 3.51
408 413 2.748647 TCGAGGCGTCGTCCATCA 60.749 61.111 26.11 5.15 46.85 3.07
410 415 1.658717 CGAGGCGTCGTCCATCATC 60.659 63.158 20.10 0.00 41.57 2.92
411 416 1.736586 GAGGCGTCGTCCATCATCT 59.263 57.895 8.15 0.00 0.00 2.90
412 417 0.596083 GAGGCGTCGTCCATCATCTG 60.596 60.000 8.15 0.00 0.00 2.90
413 418 1.141881 GGCGTCGTCCATCATCTGT 59.858 57.895 0.00 0.00 0.00 3.41
414 419 0.460284 GGCGTCGTCCATCATCTGTT 60.460 55.000 0.00 0.00 0.00 3.16
415 420 0.924090 GCGTCGTCCATCATCTGTTC 59.076 55.000 0.00 0.00 0.00 3.18
416 421 1.560923 CGTCGTCCATCATCTGTTCC 58.439 55.000 0.00 0.00 0.00 3.62
417 422 1.135112 CGTCGTCCATCATCTGTTCCA 60.135 52.381 0.00 0.00 0.00 3.53
418 423 2.271800 GTCGTCCATCATCTGTTCCAC 58.728 52.381 0.00 0.00 0.00 4.02
419 424 1.899142 TCGTCCATCATCTGTTCCACA 59.101 47.619 0.00 0.00 0.00 4.17
420 425 2.301583 TCGTCCATCATCTGTTCCACAA 59.698 45.455 0.00 0.00 0.00 3.33
421 426 3.073678 CGTCCATCATCTGTTCCACAAA 58.926 45.455 0.00 0.00 0.00 2.83
422 427 3.501828 CGTCCATCATCTGTTCCACAAAA 59.498 43.478 0.00 0.00 0.00 2.44
423 428 4.613622 CGTCCATCATCTGTTCCACAAAAC 60.614 45.833 0.00 0.00 0.00 2.43
424 429 3.826157 TCCATCATCTGTTCCACAAAACC 59.174 43.478 0.00 0.00 0.00 3.27
425 430 3.573538 CCATCATCTGTTCCACAAAACCA 59.426 43.478 0.00 0.00 0.00 3.67
426 431 4.549458 CATCATCTGTTCCACAAAACCAC 58.451 43.478 0.00 0.00 0.00 4.16
427 432 2.616376 TCATCTGTTCCACAAAACCACG 59.384 45.455 0.00 0.00 0.00 4.94
428 433 1.384525 TCTGTTCCACAAAACCACGG 58.615 50.000 0.00 0.00 0.00 4.94
429 434 0.248866 CTGTTCCACAAAACCACGGC 60.249 55.000 0.00 0.00 0.00 5.68
430 435 1.066752 GTTCCACAAAACCACGGCC 59.933 57.895 0.00 0.00 0.00 6.13
431 436 2.482333 TTCCACAAAACCACGGCCG 61.482 57.895 26.86 26.86 0.00 6.13
432 437 4.639171 CCACAAAACCACGGCCGC 62.639 66.667 28.58 0.00 0.00 6.53
433 438 4.973360 CACAAAACCACGGCCGCG 62.973 66.667 28.58 17.55 0.00 6.46
444 449 4.557605 GGCCGCGGACGATACGAA 62.558 66.667 33.48 0.00 43.93 3.85
445 450 2.354305 GCCGCGGACGATACGAAT 60.354 61.111 33.48 0.00 43.93 3.34
446 451 1.081906 GCCGCGGACGATACGAATA 60.082 57.895 33.48 0.00 43.93 1.75
447 452 1.332882 GCCGCGGACGATACGAATAC 61.333 60.000 33.48 1.16 43.93 1.89
448 453 1.056464 CCGCGGACGATACGAATACG 61.056 60.000 24.07 0.00 43.93 3.06
449 454 0.111134 CGCGGACGATACGAATACGA 60.111 55.000 0.00 0.00 43.93 3.43
450 455 1.463034 CGCGGACGATACGAATACGAT 60.463 52.381 0.00 0.00 43.93 3.73
451 456 2.222574 CGCGGACGATACGAATACGATA 60.223 50.000 0.00 0.00 43.93 2.92
452 457 3.542875 CGCGGACGATACGAATACGATAT 60.543 47.826 0.00 0.00 43.93 1.63
453 458 3.717890 GCGGACGATACGAATACGATATG 59.282 47.826 0.00 0.00 42.66 1.78
454 459 4.493057 GCGGACGATACGAATACGATATGA 60.493 45.833 0.00 0.00 42.66 2.15
455 460 5.735324 CGGACGATACGAATACGATATGAT 58.265 41.667 0.00 0.00 42.66 2.45
456 461 5.839753 CGGACGATACGAATACGATATGATC 59.160 44.000 0.00 0.00 42.66 2.92
464 469 5.096169 CGAATACGATATGATCCAGTCACC 58.904 45.833 0.00 0.00 39.88 4.02
493 498 4.312231 GCAAGTCGCAACGCAGCA 62.312 61.111 0.00 0.00 41.79 4.41
499 504 4.332637 CGCAACGCAGCAAGCCTT 62.333 61.111 0.00 0.00 41.38 4.35
500 505 2.732094 GCAACGCAGCAAGCCTTG 60.732 61.111 0.00 0.00 40.71 3.61
501 506 2.049802 CAACGCAGCAAGCCTTGG 60.050 61.111 6.57 0.00 41.38 3.61
502 507 3.297620 AACGCAGCAAGCCTTGGG 61.298 61.111 6.57 0.00 41.38 4.12
518 523 1.347221 GGGCGATCGCTTTTACGTG 59.653 57.895 36.25 0.00 41.60 4.49
658 670 2.196382 CTTCTGGAACGACGAGGCGA 62.196 60.000 4.95 0.00 34.83 5.54
699 721 2.124320 CCTAACCATGTGCCCCGG 60.124 66.667 0.00 0.00 0.00 5.73
871 910 4.865905 TCTCCTTCTCTACAAGATCAGCT 58.134 43.478 0.00 0.00 32.82 4.24
944 983 0.881118 TGGAATTTCAGTTCGCTGCC 59.119 50.000 0.00 0.00 44.62 4.85
945 984 0.881118 GGAATTTCAGTTCGCTGCCA 59.119 50.000 0.00 0.00 44.62 4.92
957 996 1.589716 CGCTGCCAGGAAGAAAAGGG 61.590 60.000 0.00 0.00 0.00 3.95
958 997 1.253593 GCTGCCAGGAAGAAAAGGGG 61.254 60.000 0.00 0.00 0.00 4.79
959 998 0.405585 CTGCCAGGAAGAAAAGGGGA 59.594 55.000 0.00 0.00 0.00 4.81
960 999 1.006400 CTGCCAGGAAGAAAAGGGGAT 59.994 52.381 0.00 0.00 0.00 3.85
961 1000 2.242196 CTGCCAGGAAGAAAAGGGGATA 59.758 50.000 0.00 0.00 0.00 2.59
962 1001 2.242196 TGCCAGGAAGAAAAGGGGATAG 59.758 50.000 0.00 0.00 0.00 2.08
963 1002 2.937519 CCAGGAAGAAAAGGGGATAGC 58.062 52.381 0.00 0.00 0.00 2.97
964 1003 2.242196 CCAGGAAGAAAAGGGGATAGCA 59.758 50.000 0.00 0.00 0.00 3.49
965 1004 3.282885 CAGGAAGAAAAGGGGATAGCAC 58.717 50.000 0.00 0.00 0.00 4.40
966 1005 3.054065 CAGGAAGAAAAGGGGATAGCACT 60.054 47.826 0.00 0.00 0.00 4.40
967 1006 3.593780 AGGAAGAAAAGGGGATAGCACTT 59.406 43.478 0.00 0.00 0.00 3.16
968 1007 3.696548 GGAAGAAAAGGGGATAGCACTTG 59.303 47.826 0.00 0.00 0.00 3.16
969 1008 2.728007 AGAAAAGGGGATAGCACTTGC 58.272 47.619 0.00 0.00 42.49 4.01
970 1009 2.041620 AGAAAAGGGGATAGCACTTGCA 59.958 45.455 3.62 0.00 45.16 4.08
971 1010 2.134789 AAAGGGGATAGCACTTGCAG 57.865 50.000 3.62 0.00 45.16 4.41
972 1011 0.394899 AAGGGGATAGCACTTGCAGC 60.395 55.000 3.62 0.00 45.16 5.25
973 1012 1.225704 GGGGATAGCACTTGCAGCT 59.774 57.895 3.62 4.22 45.16 4.24
974 1013 1.099879 GGGGATAGCACTTGCAGCTG 61.100 60.000 10.11 10.11 43.33 4.24
981 1020 0.883833 GCACTTGCAGCTGGTTACAT 59.116 50.000 17.12 0.00 41.59 2.29
1293 1344 2.592623 TACTGCACGATCAGACCGCG 62.593 60.000 13.79 0.00 37.51 6.46
1297 1348 3.823330 ACGATCAGACCGCGGACC 61.823 66.667 35.90 22.69 0.00 4.46
1298 1349 3.822192 CGATCAGACCGCGGACCA 61.822 66.667 35.90 16.18 0.00 4.02
1299 1350 2.577059 GATCAGACCGCGGACCAA 59.423 61.111 35.90 17.30 0.00 3.67
1785 1853 6.881602 AGTAATTTTCAGAGAGGATGGTTGAC 59.118 38.462 0.00 0.00 0.00 3.18
1789 1857 4.705110 TCAGAGAGGATGGTTGACAAAA 57.295 40.909 0.00 0.00 0.00 2.44
1851 1925 1.134551 GCAGGCTCTCTTCCGAATTCT 60.135 52.381 3.52 0.00 0.00 2.40
1947 2190 7.928307 ACGGTGTCTAACTGAATTAGTACTA 57.072 36.000 0.00 0.00 41.13 1.82
2020 2268 8.475331 TGCACAGTATTCTTTAAACTACTAGC 57.525 34.615 0.00 12.13 0.00 3.42
2021 2269 8.092068 TGCACAGTATTCTTTAAACTACTAGCA 58.908 33.333 14.85 14.85 34.67 3.49
2022 2270 8.381387 GCACAGTATTCTTTAAACTACTAGCAC 58.619 37.037 0.00 0.00 30.77 4.40
2023 2271 9.419297 CACAGTATTCTTTAAACTACTAGCACA 57.581 33.333 0.00 0.00 0.00 4.57
2024 2272 9.991906 ACAGTATTCTTTAAACTACTAGCACAA 57.008 29.630 0.00 0.00 0.00 3.33
2027 2275 9.704098 GTATTCTTTAAACTACTAGCACAATGC 57.296 33.333 0.00 0.00 45.46 3.56
2028 2276 6.737254 TCTTTAAACTACTAGCACAATGCC 57.263 37.500 0.00 0.00 46.52 4.40
2029 2277 6.472887 TCTTTAAACTACTAGCACAATGCCT 58.527 36.000 0.00 0.00 46.52 4.75
2030 2278 7.617225 TCTTTAAACTACTAGCACAATGCCTA 58.383 34.615 0.00 0.00 46.52 3.93
2031 2279 8.265055 TCTTTAAACTACTAGCACAATGCCTAT 58.735 33.333 0.00 0.00 46.52 2.57
2032 2280 7.786178 TTAAACTACTAGCACAATGCCTATG 57.214 36.000 0.00 0.00 46.52 2.23
2033 2281 3.733337 ACTACTAGCACAATGCCTATGC 58.267 45.455 0.00 0.00 46.52 3.14
2034 2282 1.586422 ACTAGCACAATGCCTATGCG 58.414 50.000 0.00 0.00 46.52 4.73
2035 2283 1.134401 ACTAGCACAATGCCTATGCGT 60.134 47.619 0.00 0.00 46.52 5.24
2036 2284 1.942657 CTAGCACAATGCCTATGCGTT 59.057 47.619 0.00 0.00 46.52 4.84
2041 2289 3.719699 AATGCCTATGCGTTGCAAC 57.280 47.368 19.89 19.89 44.90 4.17
2054 2302 1.843753 GTTGCAACGGAAGAAACAACG 59.156 47.619 14.90 0.00 33.56 4.10
2081 2329 2.475487 GACAGTTGTCTCGCTGTAAACC 59.525 50.000 5.04 0.00 44.89 3.27
2138 2387 3.447944 AGTCAACGACTTAATCCCCTCTC 59.552 47.826 0.00 0.00 40.28 3.20
2150 2399 2.907892 TCCCCTCTCTCATCACAAAGT 58.092 47.619 0.00 0.00 0.00 2.66
2153 2402 4.026744 CCCCTCTCTCATCACAAAGTCTA 58.973 47.826 0.00 0.00 0.00 2.59
2159 2408 7.492020 CCTCTCTCATCACAAAGTCTATTGAAG 59.508 40.741 0.00 0.00 34.38 3.02
2273 2522 4.335647 CCAGAGCAGCCAACCGGT 62.336 66.667 0.00 0.00 33.28 5.28
2319 2569 9.823647 TGTTTTGAGGCTAAATTGTTTGATTTA 57.176 25.926 0.00 0.00 31.96 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.251383 TGGTTAAATTTATGGTCAAAGTTGGA 57.749 30.769 0.00 0.00 29.44 3.53
2 3 9.319143 TGTTGGTTAAATTTATGGTCAAAGTTG 57.681 29.630 0.00 0.00 29.44 3.16
4 5 9.541143 CTTGTTGGTTAAATTTATGGTCAAAGT 57.459 29.630 0.00 0.00 0.00 2.66
5 6 9.757227 TCTTGTTGGTTAAATTTATGGTCAAAG 57.243 29.630 0.00 1.33 0.00 2.77
6 7 9.535878 GTCTTGTTGGTTAAATTTATGGTCAAA 57.464 29.630 0.00 0.00 0.00 2.69
7 8 8.145122 GGTCTTGTTGGTTAAATTTATGGTCAA 58.855 33.333 0.00 0.00 0.00 3.18
8 9 7.287927 TGGTCTTGTTGGTTAAATTTATGGTCA 59.712 33.333 0.00 0.00 0.00 4.02
10 11 7.604657 TGGTCTTGTTGGTTAAATTTATGGT 57.395 32.000 0.00 0.00 0.00 3.55
11 12 8.147704 AGTTGGTCTTGTTGGTTAAATTTATGG 58.852 33.333 0.00 0.00 0.00 2.74
12 13 8.977505 CAGTTGGTCTTGTTGGTTAAATTTATG 58.022 33.333 0.00 0.00 0.00 1.90
13 14 7.655732 GCAGTTGGTCTTGTTGGTTAAATTTAT 59.344 33.333 0.00 0.00 0.00 1.40
14 15 6.981559 GCAGTTGGTCTTGTTGGTTAAATTTA 59.018 34.615 0.00 0.00 0.00 1.40
15 16 5.815222 GCAGTTGGTCTTGTTGGTTAAATTT 59.185 36.000 0.00 0.00 0.00 1.82
16 17 5.356426 GCAGTTGGTCTTGTTGGTTAAATT 58.644 37.500 0.00 0.00 0.00 1.82
17 18 4.499019 CGCAGTTGGTCTTGTTGGTTAAAT 60.499 41.667 0.00 0.00 0.00 1.40
18 19 3.181495 CGCAGTTGGTCTTGTTGGTTAAA 60.181 43.478 0.00 0.00 0.00 1.52
19 20 2.356382 CGCAGTTGGTCTTGTTGGTTAA 59.644 45.455 0.00 0.00 0.00 2.01
20 21 1.944024 CGCAGTTGGTCTTGTTGGTTA 59.056 47.619 0.00 0.00 0.00 2.85
21 22 0.738389 CGCAGTTGGTCTTGTTGGTT 59.262 50.000 0.00 0.00 0.00 3.67
22 23 1.101049 CCGCAGTTGGTCTTGTTGGT 61.101 55.000 0.00 0.00 0.00 3.67
23 24 1.654220 CCGCAGTTGGTCTTGTTGG 59.346 57.895 0.00 0.00 0.00 3.77
24 25 1.008538 GCCGCAGTTGGTCTTGTTG 60.009 57.895 0.00 0.00 0.00 3.33
25 26 2.542907 CGCCGCAGTTGGTCTTGTT 61.543 57.895 0.00 0.00 0.00 2.83
26 27 2.972505 CGCCGCAGTTGGTCTTGT 60.973 61.111 0.00 0.00 0.00 3.16
27 28 3.726517 CCGCCGCAGTTGGTCTTG 61.727 66.667 0.00 0.00 0.00 3.02
32 33 4.697756 TTCTCCCGCCGCAGTTGG 62.698 66.667 0.00 0.00 0.00 3.77
33 34 1.791103 TTTTTCTCCCGCCGCAGTTG 61.791 55.000 0.00 0.00 0.00 3.16
34 35 1.527380 TTTTTCTCCCGCCGCAGTT 60.527 52.632 0.00 0.00 0.00 3.16
35 36 2.112297 TTTTTCTCCCGCCGCAGT 59.888 55.556 0.00 0.00 0.00 4.40
84 85 9.520204 CGGAAGCAAAAATTATATCAGTGAATT 57.480 29.630 0.00 0.00 0.00 2.17
112 113 1.722011 AACTACCAAGACCGATTGCG 58.278 50.000 0.00 0.00 37.24 4.85
113 114 5.813080 ATTTAACTACCAAGACCGATTGC 57.187 39.130 0.00 0.00 0.00 3.56
114 115 6.526674 GCAAATTTAACTACCAAGACCGATTG 59.473 38.462 0.00 0.00 0.00 2.67
115 116 6.617879 GCAAATTTAACTACCAAGACCGATT 58.382 36.000 0.00 0.00 0.00 3.34
116 117 5.163794 CGCAAATTTAACTACCAAGACCGAT 60.164 40.000 0.00 0.00 0.00 4.18
117 118 4.152759 CGCAAATTTAACTACCAAGACCGA 59.847 41.667 0.00 0.00 0.00 4.69
118 119 4.399978 CGCAAATTTAACTACCAAGACCG 58.600 43.478 0.00 0.00 0.00 4.79
119 120 4.216902 ACCGCAAATTTAACTACCAAGACC 59.783 41.667 0.00 0.00 0.00 3.85
120 121 5.049267 TGACCGCAAATTTAACTACCAAGAC 60.049 40.000 0.00 0.00 0.00 3.01
121 122 5.064558 TGACCGCAAATTTAACTACCAAGA 58.935 37.500 0.00 0.00 0.00 3.02
122 123 5.365403 TGACCGCAAATTTAACTACCAAG 57.635 39.130 0.00 0.00 0.00 3.61
123 124 5.769484 TTGACCGCAAATTTAACTACCAA 57.231 34.783 0.00 0.00 0.00 3.67
124 125 5.299782 ACTTTGACCGCAAATTTAACTACCA 59.700 36.000 0.00 0.00 42.66 3.25
125 126 5.765176 ACTTTGACCGCAAATTTAACTACC 58.235 37.500 0.00 0.00 42.66 3.18
126 127 6.913673 TCAACTTTGACCGCAAATTTAACTAC 59.086 34.615 0.00 0.00 42.66 2.73
127 128 7.028926 TCAACTTTGACCGCAAATTTAACTA 57.971 32.000 0.00 0.00 42.66 2.24
128 129 5.897050 TCAACTTTGACCGCAAATTTAACT 58.103 33.333 0.00 0.00 42.66 2.24
129 130 6.576551 TTCAACTTTGACCGCAAATTTAAC 57.423 33.333 0.00 0.00 42.66 2.01
130 131 5.233263 GCTTCAACTTTGACCGCAAATTTAA 59.767 36.000 0.00 0.00 42.66 1.52
131 132 4.742659 GCTTCAACTTTGACCGCAAATTTA 59.257 37.500 0.00 0.00 42.66 1.40
132 133 3.555547 GCTTCAACTTTGACCGCAAATTT 59.444 39.130 7.29 0.00 42.66 1.82
133 134 3.123050 GCTTCAACTTTGACCGCAAATT 58.877 40.909 7.29 0.00 42.66 1.82
134 135 2.100584 TGCTTCAACTTTGACCGCAAAT 59.899 40.909 10.94 0.00 42.66 2.32
135 136 1.474478 TGCTTCAACTTTGACCGCAAA 59.526 42.857 10.94 0.00 39.43 3.68
136 137 1.098869 TGCTTCAACTTTGACCGCAA 58.901 45.000 10.94 0.00 39.43 4.85
137 138 0.380378 GTGCTTCAACTTTGACCGCA 59.620 50.000 9.80 9.80 39.81 5.69
138 139 0.657368 CGTGCTTCAACTTTGACCGC 60.657 55.000 5.78 5.78 36.83 5.68
139 140 0.934496 TCGTGCTTCAACTTTGACCG 59.066 50.000 0.00 0.00 36.83 4.79
140 141 1.264288 CCTCGTGCTTCAACTTTGACC 59.736 52.381 0.00 0.00 36.83 4.02
141 142 2.210116 TCCTCGTGCTTCAACTTTGAC 58.790 47.619 0.00 0.00 36.83 3.18
142 143 2.613026 TCCTCGTGCTTCAACTTTGA 57.387 45.000 0.00 0.00 34.92 2.69
143 144 4.245660 TCTATCCTCGTGCTTCAACTTTG 58.754 43.478 0.00 0.00 0.00 2.77
144 145 4.499183 CTCTATCCTCGTGCTTCAACTTT 58.501 43.478 0.00 0.00 0.00 2.66
145 146 3.118956 CCTCTATCCTCGTGCTTCAACTT 60.119 47.826 0.00 0.00 0.00 2.66
146 147 2.428890 CCTCTATCCTCGTGCTTCAACT 59.571 50.000 0.00 0.00 0.00 3.16
147 148 2.427453 TCCTCTATCCTCGTGCTTCAAC 59.573 50.000 0.00 0.00 0.00 3.18
148 149 2.735151 TCCTCTATCCTCGTGCTTCAA 58.265 47.619 0.00 0.00 0.00 2.69
149 150 2.437085 TCCTCTATCCTCGTGCTTCA 57.563 50.000 0.00 0.00 0.00 3.02
150 151 2.544903 GCTTCCTCTATCCTCGTGCTTC 60.545 54.545 0.00 0.00 0.00 3.86
151 152 1.410882 GCTTCCTCTATCCTCGTGCTT 59.589 52.381 0.00 0.00 0.00 3.91
152 153 1.036707 GCTTCCTCTATCCTCGTGCT 58.963 55.000 0.00 0.00 0.00 4.40
153 154 0.747255 TGCTTCCTCTATCCTCGTGC 59.253 55.000 0.00 0.00 0.00 5.34
154 155 2.028130 AGTGCTTCCTCTATCCTCGTG 58.972 52.381 0.00 0.00 0.00 4.35
155 156 2.445682 AGTGCTTCCTCTATCCTCGT 57.554 50.000 0.00 0.00 0.00 4.18
156 157 3.215151 TGTAGTGCTTCCTCTATCCTCG 58.785 50.000 0.00 0.00 0.00 4.63
157 158 5.069781 ACAATGTAGTGCTTCCTCTATCCTC 59.930 44.000 0.00 0.00 0.00 3.71
158 159 4.965532 ACAATGTAGTGCTTCCTCTATCCT 59.034 41.667 0.00 0.00 0.00 3.24
159 160 5.053145 CACAATGTAGTGCTTCCTCTATCC 58.947 45.833 0.00 0.00 32.04 2.59
160 161 5.053145 CCACAATGTAGTGCTTCCTCTATC 58.947 45.833 0.00 0.00 38.18 2.08
161 162 4.716784 TCCACAATGTAGTGCTTCCTCTAT 59.283 41.667 0.00 0.00 38.18 1.98
162 163 4.093743 TCCACAATGTAGTGCTTCCTCTA 58.906 43.478 0.00 0.00 38.18 2.43
163 164 2.906389 TCCACAATGTAGTGCTTCCTCT 59.094 45.455 0.00 0.00 38.18 3.69
164 165 3.334583 TCCACAATGTAGTGCTTCCTC 57.665 47.619 0.00 0.00 38.18 3.71
165 166 3.788227 TTCCACAATGTAGTGCTTCCT 57.212 42.857 0.00 0.00 38.18 3.36
166 167 3.129287 CCATTCCACAATGTAGTGCTTCC 59.871 47.826 0.00 0.00 38.22 3.46
167 168 4.009675 TCCATTCCACAATGTAGTGCTTC 58.990 43.478 0.00 0.00 38.22 3.86
168 169 4.012374 CTCCATTCCACAATGTAGTGCTT 58.988 43.478 0.00 0.00 38.22 3.91
169 170 3.614092 CTCCATTCCACAATGTAGTGCT 58.386 45.455 0.00 0.00 38.22 4.40
170 171 2.684881 CCTCCATTCCACAATGTAGTGC 59.315 50.000 0.00 0.00 38.22 4.40
171 172 3.054434 TCCCTCCATTCCACAATGTAGTG 60.054 47.826 0.00 0.00 38.22 2.74
172 173 3.189606 TCCCTCCATTCCACAATGTAGT 58.810 45.455 0.00 0.00 38.22 2.73
173 174 3.200825 ACTCCCTCCATTCCACAATGTAG 59.799 47.826 0.00 0.00 38.22 2.74
174 175 3.189606 ACTCCCTCCATTCCACAATGTA 58.810 45.455 0.00 0.00 38.22 2.29
175 176 1.995542 ACTCCCTCCATTCCACAATGT 59.004 47.619 0.00 0.00 38.22 2.71
176 177 2.814805 ACTCCCTCCATTCCACAATG 57.185 50.000 0.00 0.00 39.45 2.82
177 178 3.464828 AGTACTCCCTCCATTCCACAAT 58.535 45.455 0.00 0.00 0.00 2.71
178 179 2.915869 AGTACTCCCTCCATTCCACAA 58.084 47.619 0.00 0.00 0.00 3.33
179 180 2.642171 AGTACTCCCTCCATTCCACA 57.358 50.000 0.00 0.00 0.00 4.17
180 181 3.644335 AGTAGTACTCCCTCCATTCCAC 58.356 50.000 0.00 0.00 0.00 4.02
181 182 4.481280 ACTAGTAGTACTCCCTCCATTCCA 59.519 45.833 5.96 0.00 0.00 3.53
182 183 5.064314 ACTAGTAGTACTCCCTCCATTCC 57.936 47.826 5.96 0.00 0.00 3.01
183 184 5.692928 TGACTAGTAGTACTCCCTCCATTC 58.307 45.833 5.96 0.00 0.00 2.67
184 185 5.728937 TGACTAGTAGTACTCCCTCCATT 57.271 43.478 5.96 0.00 0.00 3.16
185 186 5.432390 TCTTGACTAGTAGTACTCCCTCCAT 59.568 44.000 5.96 0.00 0.00 3.41
186 187 4.786994 TCTTGACTAGTAGTACTCCCTCCA 59.213 45.833 5.96 0.00 0.00 3.86
187 188 5.370875 TCTTGACTAGTAGTACTCCCTCC 57.629 47.826 5.96 0.00 0.00 4.30
188 189 9.657419 GTATATCTTGACTAGTAGTACTCCCTC 57.343 40.741 5.96 0.83 0.00 4.30
189 190 9.168553 TGTATATCTTGACTAGTAGTACTCCCT 57.831 37.037 5.96 0.00 0.00 4.20
190 191 9.218440 GTGTATATCTTGACTAGTAGTACTCCC 57.782 40.741 5.96 0.00 0.00 4.30
231 233 3.194968 GTGACCCTTTCTATCTGTTCCGA 59.805 47.826 0.00 0.00 0.00 4.55
245 247 1.002087 GTCGATCCACTTGTGACCCTT 59.998 52.381 1.89 0.00 0.00 3.95
247 249 0.736325 CGTCGATCCACTTGTGACCC 60.736 60.000 1.89 0.00 0.00 4.46
248 250 0.242825 TCGTCGATCCACTTGTGACC 59.757 55.000 1.89 0.00 0.00 4.02
256 258 2.349297 ACTTGTTCTCGTCGATCCAC 57.651 50.000 0.00 0.00 0.00 4.02
257 259 3.668757 CGTTACTTGTTCTCGTCGATCCA 60.669 47.826 0.00 0.00 0.00 3.41
263 265 6.467047 TCGATTATTCGTTACTTGTTCTCGTC 59.533 38.462 6.89 0.00 45.65 4.20
298 300 2.914777 AAGAAGATGGCGCGCTCTCC 62.915 60.000 32.29 15.26 0.00 3.71
315 317 6.478588 CGGTTCTCCATATTTTTCGAAGAAG 58.521 40.000 7.25 0.00 45.90 2.85
316 318 5.163794 GCGGTTCTCCATATTTTTCGAAGAA 60.164 40.000 3.34 3.34 45.90 2.52
317 319 4.331717 GCGGTTCTCCATATTTTTCGAAGA 59.668 41.667 0.00 0.00 0.00 2.87
318 320 4.094294 TGCGGTTCTCCATATTTTTCGAAG 59.906 41.667 0.00 0.00 0.00 3.79
329 331 2.434884 CACGCTGCGGTTCTCCAT 60.435 61.111 26.95 0.00 0.00 3.41
361 363 3.887621 TTCACGAGTGAATTAGGGAGG 57.112 47.619 13.96 0.00 43.90 4.30
395 400 0.460284 AACAGATGATGGACGACGCC 60.460 55.000 0.00 0.00 0.00 5.68
396 401 0.924090 GAACAGATGATGGACGACGC 59.076 55.000 0.00 0.00 0.00 5.19
397 402 1.135112 TGGAACAGATGATGGACGACG 60.135 52.381 0.00 0.00 0.00 5.12
398 403 2.271800 GTGGAACAGATGATGGACGAC 58.728 52.381 0.00 0.00 41.80 4.34
412 417 1.066752 GGCCGTGGTTTTGTGGAAC 59.933 57.895 0.00 0.00 37.35 3.62
413 418 2.482333 CGGCCGTGGTTTTGTGGAA 61.482 57.895 19.50 0.00 0.00 3.53
414 419 2.902846 CGGCCGTGGTTTTGTGGA 60.903 61.111 19.50 0.00 0.00 4.02
415 420 4.639171 GCGGCCGTGGTTTTGTGG 62.639 66.667 28.70 0.00 0.00 4.17
416 421 4.973360 CGCGGCCGTGGTTTTGTG 62.973 66.667 30.86 0.00 0.00 3.33
427 432 2.462255 TATTCGTATCGTCCGCGGCC 62.462 60.000 23.51 8.79 38.89 6.13
428 433 1.081906 TATTCGTATCGTCCGCGGC 60.082 57.895 23.51 15.21 38.89 6.53
429 434 1.056464 CGTATTCGTATCGTCCGCGG 61.056 60.000 22.12 22.12 38.89 6.46
430 435 0.111134 TCGTATTCGTATCGTCCGCG 60.111 55.000 0.00 0.00 38.33 6.46
431 436 2.238245 ATCGTATTCGTATCGTCCGC 57.762 50.000 0.00 0.00 38.33 5.54
432 437 5.134978 TCATATCGTATTCGTATCGTCCG 57.865 43.478 0.00 0.00 38.33 4.79
433 438 6.134730 GGATCATATCGTATTCGTATCGTCC 58.865 44.000 0.00 0.00 38.33 4.79
434 439 6.712549 TGGATCATATCGTATTCGTATCGTC 58.287 40.000 0.00 0.00 38.33 4.20
435 440 6.315642 ACTGGATCATATCGTATTCGTATCGT 59.684 38.462 0.00 0.00 38.33 3.73
436 441 6.716438 ACTGGATCATATCGTATTCGTATCG 58.284 40.000 0.00 0.00 38.33 2.92
437 442 7.640630 GTGACTGGATCATATCGTATTCGTATC 59.359 40.741 0.00 0.00 40.28 2.24
438 443 7.415318 GGTGACTGGATCATATCGTATTCGTAT 60.415 40.741 0.00 0.00 40.28 3.06
439 444 6.128090 GGTGACTGGATCATATCGTATTCGTA 60.128 42.308 0.00 0.00 40.28 3.43
440 445 5.335740 GGTGACTGGATCATATCGTATTCGT 60.336 44.000 0.00 0.00 40.28 3.85
441 446 5.096169 GGTGACTGGATCATATCGTATTCG 58.904 45.833 0.00 0.00 40.28 3.34
442 447 6.274157 AGGTGACTGGATCATATCGTATTC 57.726 41.667 0.00 0.00 40.28 1.75
443 448 6.127980 CGTAGGTGACTGGATCATATCGTATT 60.128 42.308 0.00 0.00 43.88 1.89
444 449 5.354513 CGTAGGTGACTGGATCATATCGTAT 59.645 44.000 0.00 0.00 43.88 3.06
445 450 4.694037 CGTAGGTGACTGGATCATATCGTA 59.306 45.833 0.00 0.00 43.88 3.43
446 451 3.502595 CGTAGGTGACTGGATCATATCGT 59.497 47.826 0.00 0.00 43.88 3.73
447 452 3.670895 GCGTAGGTGACTGGATCATATCG 60.671 52.174 0.00 0.00 43.88 2.92
448 453 3.367498 GGCGTAGGTGACTGGATCATATC 60.367 52.174 0.00 0.00 43.88 1.63
449 454 2.563179 GGCGTAGGTGACTGGATCATAT 59.437 50.000 0.00 0.00 43.88 1.78
450 455 1.961394 GGCGTAGGTGACTGGATCATA 59.039 52.381 0.00 0.00 43.88 2.15
451 456 0.753262 GGCGTAGGTGACTGGATCAT 59.247 55.000 0.00 0.00 43.88 2.45
452 457 1.663379 CGGCGTAGGTGACTGGATCA 61.663 60.000 0.00 0.00 43.88 2.92
453 458 1.065928 CGGCGTAGGTGACTGGATC 59.934 63.158 0.00 0.00 43.88 3.36
454 459 3.077519 GCGGCGTAGGTGACTGGAT 62.078 63.158 9.37 0.00 43.88 3.41
455 460 3.755628 GCGGCGTAGGTGACTGGA 61.756 66.667 9.37 0.00 43.88 3.86
456 461 4.814294 GGCGGCGTAGGTGACTGG 62.814 72.222 9.37 0.00 43.88 4.00
482 487 4.332637 AAGGCTTGCTGCGTTGCG 62.333 61.111 0.00 0.00 46.40 4.85
499 504 1.079681 ACGTAAAAGCGATCGCCCA 60.080 52.632 34.89 15.77 43.17 5.36
500 505 1.347221 CACGTAAAAGCGATCGCCC 59.653 57.895 34.89 17.08 43.17 6.13
501 506 1.296649 GCACGTAAAAGCGATCGCC 60.297 57.895 34.89 18.86 43.17 5.54
502 507 4.247361 GCACGTAAAAGCGATCGC 57.753 55.556 32.15 32.15 42.33 4.58
594 604 3.243336 GGCGATGGTTAGCTACTAATCG 58.757 50.000 19.45 19.45 41.75 3.34
658 670 6.238456 GGCAATAAAAAGTTTGCTTGCTTTCT 60.238 34.615 20.39 0.00 45.81 2.52
774 800 1.876156 GTGGAGCCACTCAAACTCAAG 59.124 52.381 12.30 0.00 43.12 3.02
832 871 3.118738 AGGAGAGTTGTTCACGTCAAAGT 60.119 43.478 0.00 0.00 0.00 2.66
871 910 2.053865 CCGGTAGGAGTTGCGGGTA 61.054 63.158 0.00 0.00 41.02 3.69
944 983 3.054065 AGTGCTATCCCCTTTTCTTCCTG 60.054 47.826 0.00 0.00 0.00 3.86
945 984 3.193782 AGTGCTATCCCCTTTTCTTCCT 58.806 45.455 0.00 0.00 0.00 3.36
957 996 0.393537 ACCAGCTGCAAGTGCTATCC 60.394 55.000 8.66 0.00 42.66 2.59
958 997 1.457346 AACCAGCTGCAAGTGCTATC 58.543 50.000 8.66 0.00 42.66 2.08
959 998 2.290260 TGTAACCAGCTGCAAGTGCTAT 60.290 45.455 8.66 0.00 42.66 2.97
960 999 1.071542 TGTAACCAGCTGCAAGTGCTA 59.928 47.619 8.66 0.00 42.66 3.49
961 1000 0.179020 TGTAACCAGCTGCAAGTGCT 60.179 50.000 8.66 0.00 42.66 4.40
962 1001 0.883833 ATGTAACCAGCTGCAAGTGC 59.116 50.000 8.66 0.00 42.50 4.40
963 1002 3.599343 TCTATGTAACCAGCTGCAAGTG 58.401 45.455 8.66 0.00 35.30 3.16
964 1003 3.981071 TCTATGTAACCAGCTGCAAGT 57.019 42.857 8.66 0.00 35.30 3.16
965 1004 3.492383 CGATCTATGTAACCAGCTGCAAG 59.508 47.826 8.66 0.00 0.00 4.01
966 1005 3.132111 TCGATCTATGTAACCAGCTGCAA 59.868 43.478 8.66 0.00 0.00 4.08
967 1006 2.693074 TCGATCTATGTAACCAGCTGCA 59.307 45.455 8.66 0.38 0.00 4.41
968 1007 3.371102 TCGATCTATGTAACCAGCTGC 57.629 47.619 8.66 0.00 0.00 5.25
969 1008 5.384063 AGATCGATCTATGTAACCAGCTG 57.616 43.478 26.27 6.78 34.85 4.24
970 1009 4.155099 CGAGATCGATCTATGTAACCAGCT 59.845 45.833 27.36 1.04 43.02 4.24
971 1010 4.154375 TCGAGATCGATCTATGTAACCAGC 59.846 45.833 27.36 10.21 44.22 4.85
972 1011 5.864628 TCGAGATCGATCTATGTAACCAG 57.135 43.478 27.36 10.42 44.22 4.00
1275 1326 2.125912 GCGGTCTGATCGTGCAGT 60.126 61.111 12.41 0.00 37.20 4.40
1491 1548 2.582978 GGCGGGTAGTTCAGGTCC 59.417 66.667 0.00 0.00 0.00 4.46
1530 1587 2.975799 GCCGACGTTTCTTGCCCA 60.976 61.111 0.00 0.00 0.00 5.36
1785 1853 6.920758 TGTCAAGGATTACGTTCCAAATTTTG 59.079 34.615 8.93 1.99 38.32 2.44
1789 1857 5.710099 ACATGTCAAGGATTACGTTCCAAAT 59.290 36.000 8.93 0.00 38.32 2.32
1907 2150 3.175929 CACCGTTTGTGTCTTTGGAAAC 58.824 45.455 0.00 0.00 40.26 2.78
1947 2190 8.450964 CCAATTTTACTCAATCATCACGTAGTT 58.549 33.333 0.00 0.00 41.61 2.24
2016 2264 1.586422 ACGCATAGGCATTGTGCTAG 58.414 50.000 0.00 0.00 44.28 3.42
2017 2265 1.670295 CAACGCATAGGCATTGTGCTA 59.330 47.619 0.00 0.00 44.28 3.49
2018 2266 0.452987 CAACGCATAGGCATTGTGCT 59.547 50.000 0.00 0.00 44.28 4.40
2019 2267 1.141591 GCAACGCATAGGCATTGTGC 61.142 55.000 10.04 4.13 44.58 4.57
2020 2268 0.170784 TGCAACGCATAGGCATTGTG 59.829 50.000 10.04 0.00 44.58 3.33
2021 2269 0.887247 TTGCAACGCATAGGCATTGT 59.113 45.000 10.04 0.00 44.58 2.71
2022 2270 1.270971 GTTGCAACGCATAGGCATTG 58.729 50.000 14.90 3.46 45.48 2.82
2023 2271 0.179166 CGTTGCAACGCATAGGCATT 60.179 50.000 35.89 0.00 46.06 3.56
2024 2272 1.429021 CGTTGCAACGCATAGGCAT 59.571 52.632 35.89 0.00 46.06 4.40
2025 2273 2.866750 CGTTGCAACGCATAGGCA 59.133 55.556 35.89 0.00 46.06 4.75
2034 2282 1.843753 CGTTGTTTCTTCCGTTGCAAC 59.156 47.619 19.89 19.89 34.61 4.17
2035 2283 1.202200 CCGTTGTTTCTTCCGTTGCAA 60.202 47.619 0.00 0.00 0.00 4.08
2036 2284 0.378962 CCGTTGTTTCTTCCGTTGCA 59.621 50.000 0.00 0.00 0.00 4.08
2037 2285 0.317519 CCCGTTGTTTCTTCCGTTGC 60.318 55.000 0.00 0.00 0.00 4.17
2038 2286 1.263217 CTCCCGTTGTTTCTTCCGTTG 59.737 52.381 0.00 0.00 0.00 4.10
2039 2287 1.589803 CTCCCGTTGTTTCTTCCGTT 58.410 50.000 0.00 0.00 0.00 4.44
2040 2288 0.250166 CCTCCCGTTGTTTCTTCCGT 60.250 55.000 0.00 0.00 0.00 4.69
2041 2289 0.953960 CCCTCCCGTTGTTTCTTCCG 60.954 60.000 0.00 0.00 0.00 4.30
2042 2290 0.399075 TCCCTCCCGTTGTTTCTTCC 59.601 55.000 0.00 0.00 0.00 3.46
2043 2291 1.202722 TGTCCCTCCCGTTGTTTCTTC 60.203 52.381 0.00 0.00 0.00 2.87
2044 2292 0.841289 TGTCCCTCCCGTTGTTTCTT 59.159 50.000 0.00 0.00 0.00 2.52
2045 2293 0.396811 CTGTCCCTCCCGTTGTTTCT 59.603 55.000 0.00 0.00 0.00 2.52
2046 2294 0.108019 ACTGTCCCTCCCGTTGTTTC 59.892 55.000 0.00 0.00 0.00 2.78
2047 2295 0.549469 AACTGTCCCTCCCGTTGTTT 59.451 50.000 0.00 0.00 0.00 2.83
2048 2296 0.179029 CAACTGTCCCTCCCGTTGTT 60.179 55.000 0.00 0.00 33.82 2.83
2052 2300 1.152312 AGACAACTGTCCCTCCCGT 60.152 57.895 6.23 0.00 45.85 5.28
2054 2302 1.592223 CGAGACAACTGTCCCTCCC 59.408 63.158 6.23 0.00 45.85 4.30
2138 2387 6.148315 TGTGCTTCAATAGACTTTGTGATGAG 59.852 38.462 0.00 0.00 0.00 2.90
2153 2402 7.148239 GGCTTAACTACTATGTTGTGCTTCAAT 60.148 37.037 0.00 0.00 38.38 2.57
2159 2408 3.242316 GCGGCTTAACTACTATGTTGTGC 60.242 47.826 0.00 0.00 0.00 4.57
2273 2522 9.364989 CAAAACAACAAAATTTCCTGACTAGAA 57.635 29.630 0.00 0.00 0.00 2.10
2319 2569 3.940852 TGATGATGTGCAAGCTACGAAAT 59.059 39.130 0.00 0.00 0.00 2.17
2453 2703 1.061424 TGGCTCCATGGATCTAGGGAA 60.061 52.381 16.63 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.