Multiple sequence alignment - TraesCS5D01G329900

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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 TraesCS5D01G329900 chr5D 100.000 2747 0 0 1 2747 421591065 421593811 0.000000e+00 5073.0
1 TraesCS5D01G329900 chr5D 91.634 1016 57 12 736 1728 421573476 421574486 0.000000e+00 1380.0
2 TraesCS5D01G329900 chr5D 93.270 951 33 10 800 1723 421676162 421675216 0.000000e+00 1373.0
3 TraesCS5D01G329900 chr5D 86.317 972 87 18 795 1723 421671691 421670723 0.000000e+00 1016.0
4 TraesCS5D01G329900 chr5D 81.611 571 73 17 2022 2572 421670507 421669949 6.980000e-121 444.0
5 TraesCS5D01G329900 chr5D 84.468 470 38 14 1716 2156 421574533 421574996 5.430000e-117 431.0
6 TraesCS5D01G329900 chr5D 88.889 162 11 4 1856 2015 421674898 421674742 2.790000e-45 193.0
7 TraesCS5D01G329900 chr5D 85.294 136 11 5 1722 1853 421675158 421675028 6.170000e-27 132.0
8 TraesCS5D01G329900 chr5A 91.304 1012 67 14 736 1728 535157062 535158071 0.000000e+00 1362.0
9 TraesCS5D01G329900 chr5A 91.322 968 60 17 769 1726 535277844 535276891 0.000000e+00 1301.0
10 TraesCS5D01G329900 chr5A 90.842 950 66 16 790 1728 535183313 535184252 0.000000e+00 1253.0
11 TraesCS5D01G329900 chr5A 86.869 990 81 25 780 1726 535243509 535242526 0.000000e+00 1062.0
12 TraesCS5D01G329900 chr5A 92.079 505 28 6 228 731 535182083 535182576 0.000000e+00 701.0
13 TraesCS5D01G329900 chr5A 82.686 566 65 14 2022 2572 535242332 535241785 3.200000e-129 472.0
14 TraesCS5D01G329900 chr5A 86.686 338 36 7 1716 2050 535158118 535158449 1.550000e-97 366.0
15 TraesCS5D01G329900 chr5A 85.093 322 21 10 1716 2015 535184302 535184618 1.240000e-78 303.0
16 TraesCS5D01G329900 chr5A 80.317 315 31 15 1725 2015 535276833 535276526 2.770000e-50 209.0
17 TraesCS5D01G329900 chr5A 89.222 167 16 2 3 167 535160288 535160454 9.970000e-50 207.0
18 TraesCS5D01G329900 chr5A 100.000 41 0 0 165 205 535160509 535160549 2.930000e-10 76.8
19 TraesCS5D01G329900 chr5B 88.072 939 75 15 739 1641 508161265 508160328 0.000000e+00 1079.0
20 TraesCS5D01G329900 chr5B 90.754 822 53 4 928 1728 507932001 507932820 0.000000e+00 1075.0
21 TraesCS5D01G329900 chr5B 84.350 984 76 34 780 1723 508150726 508149781 0.000000e+00 893.0
22 TraesCS5D01G329900 chr5B 86.882 526 37 14 2236 2747 507933464 507933971 6.640000e-156 560.0
23 TraesCS5D01G329900 chr5B 82.445 319 21 17 1722 2015 508155072 508154764 2.110000e-61 246.0
24 TraesCS5D01G329900 chr5B 82.673 202 27 3 530 731 507897694 507897887 3.640000e-39 172.0
25 TraesCS5D01G329900 chr5B 86.555 119 10 3 2122 2240 507933272 507933384 2.870000e-25 126.0
26 TraesCS5D01G329900 chr5B 100.000 30 0 0 873 902 507931962 507931991 3.820000e-04 56.5


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 TraesCS5D01G329900 chr5D 421591065 421593811 2746 False 5073.000000 5073 100.00000 1 2747 1 chr5D.!!$F1 2746
1 TraesCS5D01G329900 chr5D 421573476 421574996 1520 False 905.500000 1380 88.05100 736 2156 2 chr5D.!!$F2 1420
2 TraesCS5D01G329900 chr5D 421669949 421676162 6213 True 631.600000 1373 87.07620 795 2572 5 chr5D.!!$R1 1777
3 TraesCS5D01G329900 chr5A 535241785 535243509 1724 True 767.000000 1062 84.77750 780 2572 2 chr5A.!!$R1 1792
4 TraesCS5D01G329900 chr5A 535276526 535277844 1318 True 755.000000 1301 85.81950 769 2015 2 chr5A.!!$R2 1246
5 TraesCS5D01G329900 chr5A 535182083 535184618 2535 False 752.333333 1253 89.33800 228 2015 3 chr5A.!!$F2 1787
6 TraesCS5D01G329900 chr5A 535157062 535160549 3487 False 502.950000 1362 91.80300 3 2050 4 chr5A.!!$F1 2047
7 TraesCS5D01G329900 chr5B 508160328 508161265 937 True 1079.000000 1079 88.07200 739 1641 1 chr5B.!!$R3 902
8 TraesCS5D01G329900 chr5B 508149781 508150726 945 True 893.000000 893 84.35000 780 1723 1 chr5B.!!$R1 943
9 TraesCS5D01G329900 chr5B 507931962 507933971 2009 False 454.375000 1075 91.04775 873 2747 4 chr5B.!!$F2 1874

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
926 1632 0.458543 TCTTTCGTCGGCTGCTGATC 60.459 55.0 15.18 7.61 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1922 7329 0.035317 TTTGAGCCATCGTGTGAGCT 59.965 50.0 0.0 0.0 37.15 4.09 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
51 52 9.967346 TTCATTGTATTTTTATTCCGTTTGTCA 57.033 25.926 0.00 0.00 0.00 3.58
52 53 9.967346 TCATTGTATTTTTATTCCGTTTGTCAA 57.033 25.926 0.00 0.00 0.00 3.18
79 80 9.875691 AAAATTAAACTTCCCAGAATTATCAGC 57.124 29.630 0.00 0.00 0.00 4.26
80 81 8.593945 AATTAAACTTCCCAGAATTATCAGCA 57.406 30.769 0.00 0.00 0.00 4.41
81 82 8.593945 ATTAAACTTCCCAGAATTATCAGCAA 57.406 30.769 0.00 0.00 0.00 3.91
82 83 6.521151 AAACTTCCCAGAATTATCAGCAAG 57.479 37.500 0.00 0.00 0.00 4.01
83 84 4.530875 ACTTCCCAGAATTATCAGCAAGG 58.469 43.478 0.00 0.00 0.00 3.61
84 85 4.018050 ACTTCCCAGAATTATCAGCAAGGT 60.018 41.667 0.00 0.00 0.00 3.50
85 86 5.191722 ACTTCCCAGAATTATCAGCAAGGTA 59.808 40.000 0.00 0.00 0.00 3.08
86 87 5.296151 TCCCAGAATTATCAGCAAGGTAG 57.704 43.478 0.00 0.00 0.00 3.18
87 88 4.721776 TCCCAGAATTATCAGCAAGGTAGT 59.278 41.667 0.00 0.00 0.00 2.73
88 89 4.818546 CCCAGAATTATCAGCAAGGTAGTG 59.181 45.833 0.00 0.00 0.00 2.74
89 90 4.274459 CCAGAATTATCAGCAAGGTAGTGC 59.726 45.833 0.00 0.00 45.28 4.40
98 99 3.923017 GCAAGGTAGTGCTCATTTGTT 57.077 42.857 0.00 0.00 41.51 2.83
99 100 4.243007 GCAAGGTAGTGCTCATTTGTTT 57.757 40.909 0.00 0.00 41.51 2.83
100 101 5.371115 GCAAGGTAGTGCTCATTTGTTTA 57.629 39.130 0.00 0.00 41.51 2.01
101 102 5.393962 GCAAGGTAGTGCTCATTTGTTTAG 58.606 41.667 0.00 0.00 41.51 1.85
102 103 5.181245 GCAAGGTAGTGCTCATTTGTTTAGA 59.819 40.000 0.00 0.00 41.51 2.10
103 104 6.293955 GCAAGGTAGTGCTCATTTGTTTAGAA 60.294 38.462 0.00 0.00 41.51 2.10
104 105 7.575720 GCAAGGTAGTGCTCATTTGTTTAGAAT 60.576 37.037 0.00 0.00 41.51 2.40
105 106 8.299570 CAAGGTAGTGCTCATTTGTTTAGAATT 58.700 33.333 0.00 0.00 0.00 2.17
106 107 8.409358 AGGTAGTGCTCATTTGTTTAGAATTT 57.591 30.769 0.00 0.00 0.00 1.82
107 108 8.860088 AGGTAGTGCTCATTTGTTTAGAATTTT 58.140 29.630 0.00 0.00 0.00 1.82
108 109 8.915654 GGTAGTGCTCATTTGTTTAGAATTTTG 58.084 33.333 0.00 0.00 0.00 2.44
109 110 9.463443 GTAGTGCTCATTTGTTTAGAATTTTGT 57.537 29.630 0.00 0.00 0.00 2.83
110 111 8.579682 AGTGCTCATTTGTTTAGAATTTTGTC 57.420 30.769 0.00 0.00 0.00 3.18
111 112 8.196771 AGTGCTCATTTGTTTAGAATTTTGTCA 58.803 29.630 0.00 0.00 0.00 3.58
112 113 8.816144 GTGCTCATTTGTTTAGAATTTTGTCAA 58.184 29.630 0.00 0.00 0.00 3.18
113 114 9.545105 TGCTCATTTGTTTAGAATTTTGTCAAT 57.455 25.926 0.00 0.00 0.00 2.57
140 141 9.460019 TTTTTCTGAGATTTTTCATTTTTGGGT 57.540 25.926 0.00 0.00 0.00 4.51
141 142 8.661352 TTTCTGAGATTTTTCATTTTTGGGTC 57.339 30.769 0.00 0.00 0.00 4.46
142 143 7.601705 TCTGAGATTTTTCATTTTTGGGTCT 57.398 32.000 0.00 0.00 0.00 3.85
143 144 8.704849 TCTGAGATTTTTCATTTTTGGGTCTA 57.295 30.769 0.00 0.00 0.00 2.59
144 145 9.312904 TCTGAGATTTTTCATTTTTGGGTCTAT 57.687 29.630 0.00 0.00 0.00 1.98
145 146 9.933723 CTGAGATTTTTCATTTTTGGGTCTATT 57.066 29.630 0.00 0.00 0.00 1.73
151 152 9.467796 TTTTTCATTTTTGGGTCTATTTTTGGT 57.532 25.926 0.00 0.00 0.00 3.67
152 153 8.443953 TTTCATTTTTGGGTCTATTTTTGGTG 57.556 30.769 0.00 0.00 0.00 4.17
153 154 7.366847 TCATTTTTGGGTCTATTTTTGGTGA 57.633 32.000 0.00 0.00 0.00 4.02
154 155 7.972301 TCATTTTTGGGTCTATTTTTGGTGAT 58.028 30.769 0.00 0.00 0.00 3.06
155 156 7.877097 TCATTTTTGGGTCTATTTTTGGTGATG 59.123 33.333 0.00 0.00 0.00 3.07
156 157 6.739331 TTTTGGGTCTATTTTTGGTGATGT 57.261 33.333 0.00 0.00 0.00 3.06
157 158 5.720371 TTGGGTCTATTTTTGGTGATGTG 57.280 39.130 0.00 0.00 0.00 3.21
158 159 4.085733 TGGGTCTATTTTTGGTGATGTGG 58.914 43.478 0.00 0.00 0.00 4.17
159 160 3.119137 GGGTCTATTTTTGGTGATGTGGC 60.119 47.826 0.00 0.00 0.00 5.01
160 161 3.763897 GGTCTATTTTTGGTGATGTGGCT 59.236 43.478 0.00 0.00 0.00 4.75
161 162 4.947388 GGTCTATTTTTGGTGATGTGGCTA 59.053 41.667 0.00 0.00 0.00 3.93
162 163 5.163652 GGTCTATTTTTGGTGATGTGGCTAC 60.164 44.000 0.00 0.00 0.00 3.58
163 164 5.648092 GTCTATTTTTGGTGATGTGGCTACT 59.352 40.000 0.64 0.00 0.00 2.57
164 165 4.789012 ATTTTTGGTGATGTGGCTACTG 57.211 40.909 0.64 0.00 0.00 2.74
165 166 3.500448 TTTTGGTGATGTGGCTACTGA 57.500 42.857 0.64 0.00 0.00 3.41
166 167 2.472695 TTGGTGATGTGGCTACTGAC 57.527 50.000 0.64 0.00 0.00 3.51
167 168 1.347062 TGGTGATGTGGCTACTGACA 58.653 50.000 0.64 0.00 0.00 3.58
176 177 3.483808 TGGCTACTGACACAATGTTGA 57.516 42.857 0.00 0.00 0.00 3.18
177 178 3.814625 TGGCTACTGACACAATGTTGAA 58.185 40.909 0.00 0.00 0.00 2.69
178 179 4.203226 TGGCTACTGACACAATGTTGAAA 58.797 39.130 0.00 0.00 0.00 2.69
179 180 4.275689 TGGCTACTGACACAATGTTGAAAG 59.724 41.667 0.00 0.00 0.00 2.62
180 181 4.275936 GGCTACTGACACAATGTTGAAAGT 59.724 41.667 0.00 0.96 0.00 2.66
181 182 5.221048 GGCTACTGACACAATGTTGAAAGTT 60.221 40.000 0.00 0.00 0.00 2.66
182 183 5.682862 GCTACTGACACAATGTTGAAAGTTG 59.317 40.000 0.00 0.00 0.00 3.16
183 184 5.643379 ACTGACACAATGTTGAAAGTTGT 57.357 34.783 0.00 0.00 36.57 3.32
184 185 5.640732 ACTGACACAATGTTGAAAGTTGTC 58.359 37.500 0.00 3.60 34.09 3.18
185 186 4.992688 TGACACAATGTTGAAAGTTGTCC 58.007 39.130 0.00 0.00 34.09 4.02
186 187 4.027572 ACACAATGTTGAAAGTTGTCCG 57.972 40.909 0.00 0.00 34.09 4.79
187 188 3.181491 ACACAATGTTGAAAGTTGTCCGG 60.181 43.478 0.00 0.00 34.09 5.14
188 189 3.020984 ACAATGTTGAAAGTTGTCCGGT 58.979 40.909 0.00 0.00 30.78 5.28
189 190 3.445805 ACAATGTTGAAAGTTGTCCGGTT 59.554 39.130 0.00 0.00 30.78 4.44
190 191 4.081917 ACAATGTTGAAAGTTGTCCGGTTT 60.082 37.500 0.00 0.00 30.78 3.27
191 192 4.729227 ATGTTGAAAGTTGTCCGGTTTT 57.271 36.364 0.00 0.00 0.00 2.43
192 193 5.838531 ATGTTGAAAGTTGTCCGGTTTTA 57.161 34.783 0.00 0.00 0.00 1.52
193 194 5.640189 TGTTGAAAGTTGTCCGGTTTTAA 57.360 34.783 0.00 0.00 0.00 1.52
194 195 5.642686 TGTTGAAAGTTGTCCGGTTTTAAG 58.357 37.500 0.00 0.00 0.00 1.85
195 196 5.415077 TGTTGAAAGTTGTCCGGTTTTAAGA 59.585 36.000 0.00 0.00 0.00 2.10
196 197 5.744666 TGAAAGTTGTCCGGTTTTAAGAG 57.255 39.130 0.00 0.00 0.00 2.85
197 198 5.187687 TGAAAGTTGTCCGGTTTTAAGAGT 58.812 37.500 0.00 0.00 0.00 3.24
198 199 5.648960 TGAAAGTTGTCCGGTTTTAAGAGTT 59.351 36.000 0.00 0.00 0.00 3.01
199 200 6.151480 TGAAAGTTGTCCGGTTTTAAGAGTTT 59.849 34.615 0.00 0.00 0.00 2.66
200 201 7.336427 TGAAAGTTGTCCGGTTTTAAGAGTTTA 59.664 33.333 0.00 0.00 0.00 2.01
201 202 6.856135 AGTTGTCCGGTTTTAAGAGTTTAG 57.144 37.500 0.00 0.00 0.00 1.85
202 203 5.761726 AGTTGTCCGGTTTTAAGAGTTTAGG 59.238 40.000 0.00 0.00 0.00 2.69
203 204 4.644498 TGTCCGGTTTTAAGAGTTTAGGG 58.356 43.478 0.00 0.00 0.00 3.53
204 205 4.102996 TGTCCGGTTTTAAGAGTTTAGGGT 59.897 41.667 0.00 0.00 0.00 4.34
205 206 4.692625 GTCCGGTTTTAAGAGTTTAGGGTC 59.307 45.833 0.00 0.00 0.00 4.46
206 207 3.681417 CCGGTTTTAAGAGTTTAGGGTCG 59.319 47.826 0.00 0.00 0.00 4.79
207 208 4.309933 CGGTTTTAAGAGTTTAGGGTCGT 58.690 43.478 0.00 0.00 0.00 4.34
208 209 5.469479 CGGTTTTAAGAGTTTAGGGTCGTA 58.531 41.667 0.00 0.00 0.00 3.43
209 210 5.925969 CGGTTTTAAGAGTTTAGGGTCGTAA 59.074 40.000 0.00 0.00 0.00 3.18
210 211 6.591448 CGGTTTTAAGAGTTTAGGGTCGTAAT 59.409 38.462 0.00 0.00 0.00 1.89
211 212 7.412237 CGGTTTTAAGAGTTTAGGGTCGTAATG 60.412 40.741 0.00 0.00 0.00 1.90
212 213 7.388776 GGTTTTAAGAGTTTAGGGTCGTAATGT 59.611 37.037 0.00 0.00 0.00 2.71
213 214 9.423061 GTTTTAAGAGTTTAGGGTCGTAATGTA 57.577 33.333 0.00 0.00 0.00 2.29
214 215 9.643693 TTTTAAGAGTTTAGGGTCGTAATGTAG 57.356 33.333 0.00 0.00 0.00 2.74
215 216 8.579850 TTAAGAGTTTAGGGTCGTAATGTAGA 57.420 34.615 0.00 0.00 0.00 2.59
216 217 6.448207 AGAGTTTAGGGTCGTAATGTAGAC 57.552 41.667 0.00 0.00 36.70 2.59
217 218 5.065731 AGAGTTTAGGGTCGTAATGTAGACG 59.934 44.000 0.00 0.00 41.69 4.18
218 219 4.096984 AGTTTAGGGTCGTAATGTAGACGG 59.903 45.833 0.00 0.00 40.70 4.79
219 220 2.134789 AGGGTCGTAATGTAGACGGT 57.865 50.000 0.00 0.00 40.70 4.83
220 221 3.281727 AGGGTCGTAATGTAGACGGTA 57.718 47.619 0.00 0.00 40.70 4.02
221 222 3.825328 AGGGTCGTAATGTAGACGGTAT 58.175 45.455 0.00 0.00 40.70 2.73
222 223 4.210331 AGGGTCGTAATGTAGACGGTATT 58.790 43.478 0.00 0.00 40.70 1.89
223 224 4.037208 AGGGTCGTAATGTAGACGGTATTG 59.963 45.833 0.00 0.00 40.70 1.90
224 225 4.036734 GGGTCGTAATGTAGACGGTATTGA 59.963 45.833 0.00 0.00 40.70 2.57
225 226 5.450412 GGGTCGTAATGTAGACGGTATTGAA 60.450 44.000 0.00 0.00 40.70 2.69
226 227 5.456822 GGTCGTAATGTAGACGGTATTGAAC 59.543 44.000 0.00 0.00 40.70 3.18
247 248 3.689649 ACTTCGGAGTTGAAATATGCACC 59.310 43.478 0.00 0.00 29.87 5.01
253 254 5.106157 CGGAGTTGAAATATGCACCTCTTTT 60.106 40.000 0.00 0.00 0.00 2.27
255 256 6.151817 GGAGTTGAAATATGCACCTCTTTTCT 59.848 38.462 0.00 0.00 0.00 2.52
284 285 5.660629 TTACACGATTCAACATTGTTCGT 57.339 34.783 14.92 14.92 43.33 3.85
303 304 3.865164 TCGTTCGATCCAGATTCAACATG 59.135 43.478 0.00 0.00 0.00 3.21
307 308 4.588899 TCGATCCAGATTCAACATGGTTT 58.411 39.130 0.00 0.00 35.51 3.27
342 343 2.107950 AATGGCGCACAAGTTAGCTA 57.892 45.000 10.83 0.00 0.00 3.32
346 347 1.404315 GGCGCACAAGTTAGCTAGAGT 60.404 52.381 10.83 0.00 0.00 3.24
369 370 8.243289 AGTTTCTTGTGTTTCAAATTTGTCAG 57.757 30.769 17.47 5.24 35.48 3.51
374 375 9.050601 TCTTGTGTTTCAAATTTGTCAGTTTTT 57.949 25.926 17.47 0.00 35.48 1.94
386 387 1.962807 TCAGTTTTTGGGGCTGTGATG 59.037 47.619 0.00 0.00 0.00 3.07
409 410 5.298777 TGCACCTGCTTTTATTTTGCAAAAT 59.701 32.000 33.26 33.26 42.66 1.82
410 411 5.626132 GCACCTGCTTTTATTTTGCAAAATG 59.374 36.000 36.30 24.63 37.34 2.32
415 417 9.332301 CCTGCTTTTATTTTGCAAAATGTATTG 57.668 29.630 36.30 24.81 38.90 1.90
444 446 1.537202 CAAGAGGCTTTTCCCGTCAAG 59.463 52.381 0.00 0.00 34.51 3.02
457 459 5.952526 TCCCGTCAAGTTTCTTTTATTCC 57.047 39.130 0.00 0.00 0.00 3.01
470 472 9.020813 GTTTCTTTTATTCCCTCGCAATTATTC 57.979 33.333 0.00 0.00 0.00 1.75
476 478 1.197721 CCCTCGCAATTATTCCGCATC 59.802 52.381 0.00 0.00 0.00 3.91
481 483 0.950836 CAATTATTCCGCATCCCGCA 59.049 50.000 0.00 0.00 42.60 5.69
599 601 0.676782 GTAGGTTGGTTGATGCCGCT 60.677 55.000 0.00 0.00 0.00 5.52
646 648 4.047059 GCCAACGGACGTCCTCGA 62.047 66.667 30.92 0.00 40.62 4.04
749 751 1.227263 CTAGCTACGTTGGCGCCAT 60.227 57.895 33.25 19.10 42.83 4.40
925 1631 0.459237 CTCTTTCGTCGGCTGCTGAT 60.459 55.000 15.18 0.00 0.00 2.90
926 1632 0.458543 TCTTTCGTCGGCTGCTGATC 60.459 55.000 15.18 7.61 0.00 2.92
927 1633 1.746727 CTTTCGTCGGCTGCTGATCG 61.747 60.000 15.18 18.23 0.00 3.69
928 1634 2.207788 TTTCGTCGGCTGCTGATCGA 62.208 55.000 22.83 22.83 0.00 3.59
952 1683 3.123620 CTGCTCCTTCCTGCACGC 61.124 66.667 0.00 0.00 35.20 5.34
995 1749 2.683933 ATCTCCCAAGTCGCCGGT 60.684 61.111 1.90 0.00 0.00 5.28
1056 1854 4.090588 GTCCCGGCCGTTCATCCA 62.091 66.667 26.12 0.00 0.00 3.41
1098 1896 1.298667 GCGAGAAAACCTGGGGCTA 59.701 57.895 0.00 0.00 0.00 3.93
1101 1899 2.510613 CGAGAAAACCTGGGGCTAAAA 58.489 47.619 0.00 0.00 0.00 1.52
1123 1921 2.520982 CGGATCCCTACGAGCCCA 60.521 66.667 6.06 0.00 44.86 5.36
1130 1928 2.202570 CTACGAGCCCAACGTCGG 60.203 66.667 0.00 0.00 43.62 4.79
1163 1961 1.308216 CCAAGGAGAGGGACCCCAT 60.308 63.158 7.00 0.00 38.92 4.00
1254 2052 2.581354 GTGCTCTGGATGGACGCT 59.419 61.111 0.00 0.00 0.00 5.07
1574 6871 1.269621 ACACTTCACGAGGTTCTTCGG 60.270 52.381 8.95 0.00 44.57 4.30
1590 6887 0.895530 TCGGGCGAGAAGATGAGTTT 59.104 50.000 0.00 0.00 0.00 2.66
1624 6921 1.664965 GCGCTTCGTCTGGTCAACT 60.665 57.895 0.00 0.00 0.00 3.16
1755 7115 4.307032 AGCTGCTTCCTAGGAAAAATCA 57.693 40.909 24.31 17.14 33.34 2.57
1756 7116 4.864726 AGCTGCTTCCTAGGAAAAATCAT 58.135 39.130 24.31 7.23 33.34 2.45
1819 7189 1.328680 CTGTGTATGTGATGCGCCTTC 59.671 52.381 4.18 2.11 0.00 3.46
1821 7191 0.809636 TGTATGTGATGCGCCTTCGG 60.810 55.000 4.18 0.00 35.95 4.30
1849 7220 8.795842 ATGTCGTTATTTGTAAACCCTAATCA 57.204 30.769 0.00 0.00 0.00 2.57
1852 7223 8.179615 GTCGTTATTTGTAAACCCTAATCAAGG 58.820 37.037 0.00 0.00 46.09 3.61
1888 7281 6.987386 TCATGGATGAACAAAAACCGTATTT 58.013 32.000 0.00 0.00 33.08 1.40
1889 7282 7.437748 TCATGGATGAACAAAAACCGTATTTT 58.562 30.769 0.00 0.00 33.08 1.82
2007 7419 6.570378 GCGATATGGGTCCCAAATTTTGATAG 60.570 42.308 16.55 2.15 36.95 2.08
2026 7438 7.855784 TGATAGGTGTAAGATATCACATGGT 57.144 36.000 5.32 0.00 36.43 3.55
2089 7833 4.214437 GAGTTGCGTATTAATCAGCATGC 58.786 43.478 10.51 10.51 39.50 4.06
2090 7834 3.003689 AGTTGCGTATTAATCAGCATGCC 59.996 43.478 15.66 0.00 39.50 4.40
2152 8895 6.603201 TGGTATGGGTGAATTTCTGAATCTTC 59.397 38.462 0.00 0.00 0.00 2.87
2183 8926 9.661563 TGTATATAAGTTAGTTTTGGACACCAG 57.338 33.333 0.00 0.00 33.81 4.00
2184 8927 9.662947 GTATATAAGTTAGTTTTGGACACCAGT 57.337 33.333 0.00 0.00 33.81 4.00
2212 8956 8.902040 TGATAATCTAACATCTCGATCGATTG 57.098 34.615 19.78 20.23 0.00 2.67
2213 8957 7.486232 TGATAATCTAACATCTCGATCGATTGC 59.514 37.037 19.78 4.54 0.00 3.56
2215 8959 2.209838 AACATCTCGATCGATTGCGT 57.790 45.000 19.78 10.71 38.98 5.24
2216 8960 3.349488 AACATCTCGATCGATTGCGTA 57.651 42.857 19.78 0.75 38.98 4.42
2217 8961 2.651701 ACATCTCGATCGATTGCGTAC 58.348 47.619 19.78 0.00 38.98 3.67
2278 9263 3.904965 TGGATATCAATTACACCGGCCTA 59.095 43.478 0.00 0.00 0.00 3.93
2289 9274 0.323360 ACCGGCCTATGCAACAACAT 60.323 50.000 0.00 0.00 40.13 2.71
2314 9299 9.950496 ATAATGTTGAGAACAAGTCTAGACATT 57.050 29.630 24.44 14.94 45.14 2.71
2336 9321 4.624336 AAGTATGCACACAACAACGAAA 57.376 36.364 0.00 0.00 0.00 3.46
2338 9323 4.597079 AGTATGCACACAACAACGAAAAG 58.403 39.130 0.00 0.00 0.00 2.27
2339 9324 3.773860 ATGCACACAACAACGAAAAGA 57.226 38.095 0.00 0.00 0.00 2.52
2405 9402 2.118683 CAATCAACGGCACACAACAAG 58.881 47.619 0.00 0.00 0.00 3.16
2419 9416 1.750778 CAACAAGGAGCAACAACACCT 59.249 47.619 0.00 0.00 31.23 4.00
2420 9417 1.392589 ACAAGGAGCAACAACACCTG 58.607 50.000 0.00 0.00 30.33 4.00
2421 9418 1.064758 ACAAGGAGCAACAACACCTGA 60.065 47.619 0.00 0.00 30.33 3.86
2422 9419 2.233271 CAAGGAGCAACAACACCTGAT 58.767 47.619 0.00 0.00 30.33 2.90
2423 9420 3.181445 ACAAGGAGCAACAACACCTGATA 60.181 43.478 0.00 0.00 30.33 2.15
2442 9439 7.127339 ACCTGATATAACACTACCCTTGACAAT 59.873 37.037 0.00 0.00 0.00 2.71
2446 9443 9.257651 GATATAACACTACCCTTGACAATACAC 57.742 37.037 0.00 0.00 0.00 2.90
2500 9497 1.374252 CCAGGAAGGGAACGACACG 60.374 63.158 0.00 0.00 0.00 4.49
2505 9502 1.282930 GAAGGGAACGACACGCAGAC 61.283 60.000 0.00 0.00 0.00 3.51
2512 9509 3.406361 GACACGCAGACGCCACAG 61.406 66.667 0.00 0.00 45.53 3.66
2516 9513 4.700365 CGCAGACGCCACAGTCGA 62.700 66.667 0.00 0.00 45.26 4.20
2522 9519 2.579787 CGCCACAGTCGACGGATC 60.580 66.667 22.71 9.17 0.00 3.36
2557 9554 6.455360 AAAAGCAAATCAAGAGTCTTCACA 57.545 33.333 1.26 0.00 0.00 3.58
2594 9593 2.352960 CGAGTAATCTCCAAGCAAAGCC 59.647 50.000 0.00 0.00 37.40 4.35
2646 9712 6.668541 ATCGTACATTCTTTGTTCATGAGG 57.331 37.500 0.00 0.00 39.87 3.86
2683 9749 3.136009 TGCATGCAGGAGAATAGGATG 57.864 47.619 18.46 0.00 34.68 3.51
2685 9751 3.117776 TGCATGCAGGAGAATAGGATGTT 60.118 43.478 18.46 0.00 34.16 2.71
2687 9753 4.711399 CATGCAGGAGAATAGGATGTTCA 58.289 43.478 0.00 0.00 0.00 3.18
2688 9754 5.314529 CATGCAGGAGAATAGGATGTTCAT 58.685 41.667 0.00 0.00 0.00 2.57
2689 9755 4.965814 TGCAGGAGAATAGGATGTTCATC 58.034 43.478 4.41 4.41 0.00 2.92
2690 9756 4.409901 TGCAGGAGAATAGGATGTTCATCA 59.590 41.667 13.64 0.00 0.00 3.07
2704 9770 7.013083 AGGATGTTCATCATTCATCAACTAAGC 59.987 37.037 13.64 0.00 39.47 3.09
2723 9789 6.992715 ACTAAGCGCAAATCCTAACTCATATT 59.007 34.615 11.47 0.00 0.00 1.28
2734 9800 7.067496 TCCTAACTCATATTCCAAGCCTAAG 57.933 40.000 0.00 0.00 0.00 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 9.967346 TGACAAACGGAATAAAAATACAATGAA 57.033 25.926 0.00 0.00 0.00 2.57
26 27 9.967346 TTGACAAACGGAATAAAAATACAATGA 57.033 25.926 0.00 0.00 0.00 2.57
53 54 9.875691 GCTGATAATTCTGGGAAGTTTAATTTT 57.124 29.630 0.00 0.00 0.00 1.82
54 55 9.034800 TGCTGATAATTCTGGGAAGTTTAATTT 57.965 29.630 0.00 0.00 0.00 1.82
55 56 8.593945 TGCTGATAATTCTGGGAAGTTTAATT 57.406 30.769 0.00 0.00 0.00 1.40
56 57 8.593945 TTGCTGATAATTCTGGGAAGTTTAAT 57.406 30.769 0.00 0.00 0.00 1.40
57 58 7.122650 CCTTGCTGATAATTCTGGGAAGTTTAA 59.877 37.037 0.00 0.00 0.00 1.52
58 59 6.603201 CCTTGCTGATAATTCTGGGAAGTTTA 59.397 38.462 0.00 0.00 0.00 2.01
59 60 5.420104 CCTTGCTGATAATTCTGGGAAGTTT 59.580 40.000 0.00 0.00 0.00 2.66
60 61 4.952335 CCTTGCTGATAATTCTGGGAAGTT 59.048 41.667 0.00 0.00 0.00 2.66
61 62 4.018050 ACCTTGCTGATAATTCTGGGAAGT 60.018 41.667 0.00 0.00 0.00 3.01
62 63 4.530875 ACCTTGCTGATAATTCTGGGAAG 58.469 43.478 0.00 0.00 0.00 3.46
63 64 4.591321 ACCTTGCTGATAATTCTGGGAA 57.409 40.909 0.00 0.00 0.00 3.97
64 65 4.721776 ACTACCTTGCTGATAATTCTGGGA 59.278 41.667 0.00 0.00 0.00 4.37
65 66 4.818546 CACTACCTTGCTGATAATTCTGGG 59.181 45.833 0.00 0.00 0.00 4.45
66 67 4.274459 GCACTACCTTGCTGATAATTCTGG 59.726 45.833 0.00 0.00 39.59 3.86
67 68 5.415415 GCACTACCTTGCTGATAATTCTG 57.585 43.478 0.00 0.00 39.59 3.02
78 79 3.923017 AACAAATGAGCACTACCTTGC 57.077 42.857 0.00 0.00 43.34 4.01
79 80 6.801539 TCTAAACAAATGAGCACTACCTTG 57.198 37.500 0.00 0.00 0.00 3.61
80 81 8.409358 AATTCTAAACAAATGAGCACTACCTT 57.591 30.769 0.00 0.00 0.00 3.50
81 82 8.409358 AAATTCTAAACAAATGAGCACTACCT 57.591 30.769 0.00 0.00 0.00 3.08
82 83 8.915654 CAAAATTCTAAACAAATGAGCACTACC 58.084 33.333 0.00 0.00 0.00 3.18
83 84 9.463443 ACAAAATTCTAAACAAATGAGCACTAC 57.537 29.630 0.00 0.00 0.00 2.73
84 85 9.677567 GACAAAATTCTAAACAAATGAGCACTA 57.322 29.630 0.00 0.00 0.00 2.74
85 86 8.196771 TGACAAAATTCTAAACAAATGAGCACT 58.803 29.630 0.00 0.00 0.00 4.40
86 87 8.351495 TGACAAAATTCTAAACAAATGAGCAC 57.649 30.769 0.00 0.00 0.00 4.40
87 88 8.939201 TTGACAAAATTCTAAACAAATGAGCA 57.061 26.923 0.00 0.00 0.00 4.26
114 115 9.460019 ACCCAAAAATGAAAAATCTCAGAAAAA 57.540 25.926 0.00 0.00 0.00 1.94
115 116 9.108284 GACCCAAAAATGAAAAATCTCAGAAAA 57.892 29.630 0.00 0.00 0.00 2.29
116 117 8.485392 AGACCCAAAAATGAAAAATCTCAGAAA 58.515 29.630 0.00 0.00 0.00 2.52
117 118 8.021898 AGACCCAAAAATGAAAAATCTCAGAA 57.978 30.769 0.00 0.00 0.00 3.02
118 119 7.601705 AGACCCAAAAATGAAAAATCTCAGA 57.398 32.000 0.00 0.00 0.00 3.27
119 120 9.933723 AATAGACCCAAAAATGAAAAATCTCAG 57.066 29.630 0.00 0.00 0.00 3.35
125 126 9.467796 ACCAAAAATAGACCCAAAAATGAAAAA 57.532 25.926 0.00 0.00 0.00 1.94
126 127 8.897752 CACCAAAAATAGACCCAAAAATGAAAA 58.102 29.630 0.00 0.00 0.00 2.29
127 128 8.267894 TCACCAAAAATAGACCCAAAAATGAAA 58.732 29.630 0.00 0.00 0.00 2.69
128 129 7.796054 TCACCAAAAATAGACCCAAAAATGAA 58.204 30.769 0.00 0.00 0.00 2.57
129 130 7.366847 TCACCAAAAATAGACCCAAAAATGA 57.633 32.000 0.00 0.00 0.00 2.57
130 131 7.661027 ACATCACCAAAAATAGACCCAAAAATG 59.339 33.333 0.00 0.00 0.00 2.32
131 132 7.661027 CACATCACCAAAAATAGACCCAAAAAT 59.339 33.333 0.00 0.00 0.00 1.82
132 133 6.989169 CACATCACCAAAAATAGACCCAAAAA 59.011 34.615 0.00 0.00 0.00 1.94
133 134 6.463614 CCACATCACCAAAAATAGACCCAAAA 60.464 38.462 0.00 0.00 0.00 2.44
134 135 5.011533 CCACATCACCAAAAATAGACCCAAA 59.988 40.000 0.00 0.00 0.00 3.28
135 136 4.526262 CCACATCACCAAAAATAGACCCAA 59.474 41.667 0.00 0.00 0.00 4.12
136 137 4.085733 CCACATCACCAAAAATAGACCCA 58.914 43.478 0.00 0.00 0.00 4.51
137 138 3.119137 GCCACATCACCAAAAATAGACCC 60.119 47.826 0.00 0.00 0.00 4.46
138 139 3.763897 AGCCACATCACCAAAAATAGACC 59.236 43.478 0.00 0.00 0.00 3.85
139 140 5.648092 AGTAGCCACATCACCAAAAATAGAC 59.352 40.000 0.00 0.00 0.00 2.59
140 141 5.647658 CAGTAGCCACATCACCAAAAATAGA 59.352 40.000 0.00 0.00 0.00 1.98
141 142 5.647658 TCAGTAGCCACATCACCAAAAATAG 59.352 40.000 0.00 0.00 0.00 1.73
142 143 5.414454 GTCAGTAGCCACATCACCAAAAATA 59.586 40.000 0.00 0.00 0.00 1.40
143 144 4.218417 GTCAGTAGCCACATCACCAAAAAT 59.782 41.667 0.00 0.00 0.00 1.82
144 145 3.568007 GTCAGTAGCCACATCACCAAAAA 59.432 43.478 0.00 0.00 0.00 1.94
145 146 3.146066 GTCAGTAGCCACATCACCAAAA 58.854 45.455 0.00 0.00 0.00 2.44
146 147 2.105649 TGTCAGTAGCCACATCACCAAA 59.894 45.455 0.00 0.00 0.00 3.28
147 148 1.696884 TGTCAGTAGCCACATCACCAA 59.303 47.619 0.00 0.00 0.00 3.67
148 149 1.001974 GTGTCAGTAGCCACATCACCA 59.998 52.381 0.00 0.00 0.00 4.17
149 150 1.001974 TGTGTCAGTAGCCACATCACC 59.998 52.381 0.00 0.00 36.70 4.02
150 151 2.455674 TGTGTCAGTAGCCACATCAC 57.544 50.000 0.00 0.00 36.70 3.06
151 152 3.244526 ACATTGTGTCAGTAGCCACATCA 60.245 43.478 0.00 0.00 40.94 3.07
152 153 3.338249 ACATTGTGTCAGTAGCCACATC 58.662 45.455 0.00 0.00 40.94 3.06
153 154 3.423539 ACATTGTGTCAGTAGCCACAT 57.576 42.857 0.00 0.00 40.94 3.21
154 155 2.877786 CAACATTGTGTCAGTAGCCACA 59.122 45.455 0.00 0.00 39.68 4.17
155 156 3.138304 TCAACATTGTGTCAGTAGCCAC 58.862 45.455 0.00 0.00 0.00 5.01
156 157 3.483808 TCAACATTGTGTCAGTAGCCA 57.516 42.857 0.00 0.00 0.00 4.75
157 158 4.275936 ACTTTCAACATTGTGTCAGTAGCC 59.724 41.667 0.00 0.00 0.00 3.93
158 159 5.424121 ACTTTCAACATTGTGTCAGTAGC 57.576 39.130 0.00 0.00 0.00 3.58
159 160 6.785191 ACAACTTTCAACATTGTGTCAGTAG 58.215 36.000 0.00 0.00 35.28 2.57
160 161 6.183360 GGACAACTTTCAACATTGTGTCAGTA 60.183 38.462 11.93 0.00 36.70 2.74
161 162 5.393027 GGACAACTTTCAACATTGTGTCAGT 60.393 40.000 11.93 0.00 36.70 3.41
162 163 5.036737 GGACAACTTTCAACATTGTGTCAG 58.963 41.667 11.93 0.00 36.70 3.51
163 164 4.438065 CGGACAACTTTCAACATTGTGTCA 60.438 41.667 11.93 0.00 36.70 3.58
164 165 4.035017 CGGACAACTTTCAACATTGTGTC 58.965 43.478 0.00 4.53 36.70 3.67
165 166 3.181491 CCGGACAACTTTCAACATTGTGT 60.181 43.478 0.00 0.00 36.70 3.72
166 167 3.181491 ACCGGACAACTTTCAACATTGTG 60.181 43.478 9.46 0.00 36.70 3.33
167 168 3.020984 ACCGGACAACTTTCAACATTGT 58.979 40.909 9.46 0.00 39.23 2.71
168 169 3.708563 ACCGGACAACTTTCAACATTG 57.291 42.857 9.46 0.00 0.00 2.82
169 170 4.729227 AAACCGGACAACTTTCAACATT 57.271 36.364 9.46 0.00 0.00 2.71
170 171 4.729227 AAAACCGGACAACTTTCAACAT 57.271 36.364 9.46 0.00 0.00 2.71
171 172 5.415077 TCTTAAAACCGGACAACTTTCAACA 59.585 36.000 9.46 0.00 0.00 3.33
172 173 5.882553 TCTTAAAACCGGACAACTTTCAAC 58.117 37.500 9.46 0.00 0.00 3.18
173 174 5.648960 ACTCTTAAAACCGGACAACTTTCAA 59.351 36.000 9.46 0.00 0.00 2.69
174 175 5.187687 ACTCTTAAAACCGGACAACTTTCA 58.812 37.500 9.46 0.00 0.00 2.69
175 176 5.746307 ACTCTTAAAACCGGACAACTTTC 57.254 39.130 9.46 0.00 0.00 2.62
176 177 6.519679 AAACTCTTAAAACCGGACAACTTT 57.480 33.333 9.46 0.00 0.00 2.66
177 178 6.261603 CCTAAACTCTTAAAACCGGACAACTT 59.738 38.462 9.46 0.00 0.00 2.66
178 179 5.761726 CCTAAACTCTTAAAACCGGACAACT 59.238 40.000 9.46 0.00 0.00 3.16
179 180 5.049198 CCCTAAACTCTTAAAACCGGACAAC 60.049 44.000 9.46 0.00 0.00 3.32
180 181 5.065235 CCCTAAACTCTTAAAACCGGACAA 58.935 41.667 9.46 0.00 0.00 3.18
181 182 4.102996 ACCCTAAACTCTTAAAACCGGACA 59.897 41.667 9.46 0.00 0.00 4.02
182 183 4.645535 ACCCTAAACTCTTAAAACCGGAC 58.354 43.478 9.46 0.00 0.00 4.79
183 184 4.561326 CGACCCTAAACTCTTAAAACCGGA 60.561 45.833 9.46 0.00 0.00 5.14
184 185 3.681417 CGACCCTAAACTCTTAAAACCGG 59.319 47.826 0.00 0.00 0.00 5.28
185 186 4.309933 ACGACCCTAAACTCTTAAAACCG 58.690 43.478 0.00 0.00 0.00 4.44
186 187 7.388776 ACATTACGACCCTAAACTCTTAAAACC 59.611 37.037 0.00 0.00 0.00 3.27
187 188 8.315391 ACATTACGACCCTAAACTCTTAAAAC 57.685 34.615 0.00 0.00 0.00 2.43
188 189 9.643693 CTACATTACGACCCTAAACTCTTAAAA 57.356 33.333 0.00 0.00 0.00 1.52
189 190 9.023962 TCTACATTACGACCCTAAACTCTTAAA 57.976 33.333 0.00 0.00 0.00 1.52
190 191 8.462016 GTCTACATTACGACCCTAAACTCTTAA 58.538 37.037 0.00 0.00 0.00 1.85
191 192 7.201644 CGTCTACATTACGACCCTAAACTCTTA 60.202 40.741 0.00 0.00 42.90 2.10
192 193 6.404074 CGTCTACATTACGACCCTAAACTCTT 60.404 42.308 0.00 0.00 42.90 2.85
193 194 5.065731 CGTCTACATTACGACCCTAAACTCT 59.934 44.000 0.00 0.00 42.90 3.24
194 195 5.269313 CGTCTACATTACGACCCTAAACTC 58.731 45.833 0.00 0.00 42.90 3.01
195 196 4.096984 CCGTCTACATTACGACCCTAAACT 59.903 45.833 0.00 0.00 42.90 2.66
196 197 4.142381 ACCGTCTACATTACGACCCTAAAC 60.142 45.833 0.00 0.00 42.90 2.01
197 198 4.016444 ACCGTCTACATTACGACCCTAAA 58.984 43.478 0.00 0.00 42.90 1.85
198 199 3.620488 ACCGTCTACATTACGACCCTAA 58.380 45.455 0.00 0.00 42.90 2.69
199 200 3.281727 ACCGTCTACATTACGACCCTA 57.718 47.619 0.00 0.00 42.90 3.53
200 201 2.134789 ACCGTCTACATTACGACCCT 57.865 50.000 0.00 0.00 42.90 4.34
201 202 4.036734 TCAATACCGTCTACATTACGACCC 59.963 45.833 0.00 0.00 42.90 4.46
202 203 5.173774 TCAATACCGTCTACATTACGACC 57.826 43.478 0.00 0.00 42.90 4.79
203 204 6.261118 AGTTCAATACCGTCTACATTACGAC 58.739 40.000 0.00 0.00 42.90 4.34
204 205 6.441093 AGTTCAATACCGTCTACATTACGA 57.559 37.500 0.00 0.00 42.90 3.43
205 206 6.075728 CGAAGTTCAATACCGTCTACATTACG 60.076 42.308 3.32 0.00 40.01 3.18
206 207 6.197842 CCGAAGTTCAATACCGTCTACATTAC 59.802 42.308 3.32 0.00 0.00 1.89
207 208 6.095300 TCCGAAGTTCAATACCGTCTACATTA 59.905 38.462 3.32 0.00 0.00 1.90
208 209 5.105635 TCCGAAGTTCAATACCGTCTACATT 60.106 40.000 3.32 0.00 0.00 2.71
209 210 4.400251 TCCGAAGTTCAATACCGTCTACAT 59.600 41.667 3.32 0.00 0.00 2.29
210 211 3.758023 TCCGAAGTTCAATACCGTCTACA 59.242 43.478 3.32 0.00 0.00 2.74
211 212 4.142513 ACTCCGAAGTTCAATACCGTCTAC 60.143 45.833 3.32 0.00 28.74 2.59
212 213 4.012374 ACTCCGAAGTTCAATACCGTCTA 58.988 43.478 3.32 0.00 28.74 2.59
213 214 2.824341 ACTCCGAAGTTCAATACCGTCT 59.176 45.455 3.32 0.00 28.74 4.18
214 215 3.227810 ACTCCGAAGTTCAATACCGTC 57.772 47.619 3.32 0.00 28.74 4.79
215 216 3.006110 TCAACTCCGAAGTTCAATACCGT 59.994 43.478 3.32 0.00 43.99 4.83
216 217 3.581755 TCAACTCCGAAGTTCAATACCG 58.418 45.455 3.32 0.00 43.99 4.02
217 218 5.934935 TTTCAACTCCGAAGTTCAATACC 57.065 39.130 3.32 0.00 43.99 2.73
218 219 7.640240 GCATATTTCAACTCCGAAGTTCAATAC 59.360 37.037 3.32 0.00 43.99 1.89
219 220 7.335673 TGCATATTTCAACTCCGAAGTTCAATA 59.664 33.333 3.32 0.00 43.99 1.90
220 221 6.150976 TGCATATTTCAACTCCGAAGTTCAAT 59.849 34.615 3.32 0.00 43.99 2.57
221 222 5.471797 TGCATATTTCAACTCCGAAGTTCAA 59.528 36.000 3.32 0.00 43.99 2.69
222 223 5.000591 TGCATATTTCAACTCCGAAGTTCA 58.999 37.500 3.32 0.00 43.99 3.18
223 224 5.324697 GTGCATATTTCAACTCCGAAGTTC 58.675 41.667 0.00 0.00 43.99 3.01
224 225 4.156008 GGTGCATATTTCAACTCCGAAGTT 59.844 41.667 0.00 0.00 46.80 2.66
225 226 3.689649 GGTGCATATTTCAACTCCGAAGT 59.310 43.478 0.00 0.00 37.32 3.01
226 227 3.941483 AGGTGCATATTTCAACTCCGAAG 59.059 43.478 0.00 0.00 0.00 3.79
260 261 7.354025 ACGAACAATGTTGAATCGTGTAATA 57.646 32.000 21.07 0.00 45.09 0.98
261 262 6.236017 ACGAACAATGTTGAATCGTGTAAT 57.764 33.333 21.07 5.74 45.09 1.89
262 263 5.660629 ACGAACAATGTTGAATCGTGTAA 57.339 34.783 21.07 0.00 45.09 2.41
282 283 3.001634 CCATGTTGAATCTGGATCGAACG 59.998 47.826 0.00 0.00 31.38 3.95
284 285 4.220693 ACCATGTTGAATCTGGATCGAA 57.779 40.909 3.41 0.00 34.08 3.71
303 304 3.915437 TTCATTCGCTTTCCTCAAACC 57.085 42.857 0.00 0.00 0.00 3.27
307 308 2.164219 GCCATTTCATTCGCTTTCCTCA 59.836 45.455 0.00 0.00 0.00 3.86
342 343 8.087750 TGACAAATTTGAAACACAAGAAACTCT 58.912 29.630 24.64 0.00 39.77 3.24
346 347 8.600449 AACTGACAAATTTGAAACACAAGAAA 57.400 26.923 24.64 0.00 39.77 2.52
369 370 0.392336 TGCATCACAGCCCCAAAAAC 59.608 50.000 0.00 0.00 0.00 2.43
386 387 4.809815 TTTGCAAAATAAAAGCAGGTGC 57.190 36.364 10.02 0.00 39.72 5.01
409 410 2.333926 CTCTTGGCGTCGTTCAATACA 58.666 47.619 0.00 0.00 0.00 2.29
410 411 1.659098 CCTCTTGGCGTCGTTCAATAC 59.341 52.381 0.00 0.00 0.00 1.89
444 446 8.926715 AATAATTGCGAGGGAATAAAAGAAAC 57.073 30.769 0.00 0.00 0.00 2.78
585 587 2.267351 CCACAGCGGCATCAACCAA 61.267 57.895 1.45 0.00 0.00 3.67
612 614 3.036429 GCAGGGAGATCAGGGCGTT 62.036 63.158 0.00 0.00 0.00 4.84
646 648 2.126071 CGCGGTTGAGGATGTCGT 60.126 61.111 0.00 0.00 0.00 4.34
731 733 1.215655 GATGGCGCCAACGTAGCTAG 61.216 60.000 36.33 0.00 42.83 3.42
732 734 1.227147 GATGGCGCCAACGTAGCTA 60.227 57.895 36.33 6.47 42.83 3.32
733 735 2.511600 GATGGCGCCAACGTAGCT 60.512 61.111 36.33 16.00 42.83 3.32
749 751 6.930164 TCTTATTACTTTGCAGGTTGTTACGA 59.070 34.615 0.00 0.00 0.00 3.43
925 1631 0.598562 GAAGGAGCAGTGTCTGTCGA 59.401 55.000 0.00 0.00 33.43 4.20
926 1632 0.389166 GGAAGGAGCAGTGTCTGTCG 60.389 60.000 0.00 0.00 33.43 4.35
927 1633 0.972883 AGGAAGGAGCAGTGTCTGTC 59.027 55.000 0.00 0.00 33.43 3.51
928 1634 0.683973 CAGGAAGGAGCAGTGTCTGT 59.316 55.000 0.00 0.00 33.43 3.41
952 1683 3.509296 GAGTCGTCGCCGATCGGAG 62.509 68.421 37.64 33.45 46.30 4.63
1056 1854 1.903877 CGCCCATGACCCAAGAGACT 61.904 60.000 0.00 0.00 0.00 3.24
1098 1896 1.157870 CGTAGGGATCCGCGCATTTT 61.158 55.000 8.75 0.00 0.00 1.82
1101 1899 2.910479 TCGTAGGGATCCGCGCAT 60.910 61.111 8.75 0.00 0.00 4.73
1395 2199 2.970974 GAACTGCTCGTGCTTGGCC 61.971 63.158 11.19 0.00 40.48 5.36
1574 6871 2.814336 ACCAAAAACTCATCTTCTCGCC 59.186 45.455 0.00 0.00 0.00 5.54
1590 6887 2.843545 GCCAGGGACCTCACCAAA 59.156 61.111 0.00 0.00 0.00 3.28
1624 6921 0.739561 CCGAAAAACCCCAACGTCAA 59.260 50.000 0.00 0.00 0.00 3.18
1723 7020 1.216122 GAAGCAGCTTCTCTATGGCG 58.784 55.000 25.51 0.00 37.49 5.69
1755 7115 8.487313 TTGTAGCACGTCATTTACAGATTAAT 57.513 30.769 0.00 0.00 0.00 1.40
1756 7116 7.064134 CCTTGTAGCACGTCATTTACAGATTAA 59.936 37.037 0.00 0.00 0.00 1.40
1819 7189 5.220529 GGGTTTACAAATAACGACATCTCCG 60.221 44.000 0.00 0.00 0.00 4.63
1821 7191 6.980051 AGGGTTTACAAATAACGACATCTC 57.020 37.500 0.00 0.00 0.00 2.75
1849 7220 7.333779 TCATCCATGATACATACATTCCCTT 57.666 36.000 0.00 0.00 0.00 3.95
1852 7223 7.984422 TGTTCATCCATGATACATACATTCC 57.016 36.000 0.00 0.00 36.56 3.01
1888 7281 8.837099 AATTCCCATACACATCCTCATAAAAA 57.163 30.769 0.00 0.00 0.00 1.94
1889 7282 8.837099 AAATTCCCATACACATCCTCATAAAA 57.163 30.769 0.00 0.00 0.00 1.52
1907 7314 8.149973 TCGTGTGAGCTAATTATTAAATTCCC 57.850 34.615 0.00 0.00 36.67 3.97
1918 7325 2.093500 TGAGCCATCGTGTGAGCTAATT 60.093 45.455 0.00 0.00 35.41 1.40
1920 7327 0.894835 TGAGCCATCGTGTGAGCTAA 59.105 50.000 0.00 0.00 35.41 3.09
1922 7329 0.035317 TTTGAGCCATCGTGTGAGCT 59.965 50.000 0.00 0.00 37.15 4.09
1923 7330 0.874390 TTTTGAGCCATCGTGTGAGC 59.126 50.000 0.00 0.00 0.00 4.26
1924 7331 3.837213 AATTTTGAGCCATCGTGTGAG 57.163 42.857 0.00 0.00 0.00 3.51
1925 7332 4.759693 ACTTAATTTTGAGCCATCGTGTGA 59.240 37.500 0.00 0.00 0.00 3.58
1926 7333 5.046910 ACTTAATTTTGAGCCATCGTGTG 57.953 39.130 0.00 0.00 0.00 3.82
2007 7419 5.918608 ACAGACCATGTGATATCTTACACC 58.081 41.667 3.98 0.00 41.91 4.16
2166 8909 5.956642 TCAAAACTGGTGTCCAAAACTAAC 58.043 37.500 0.00 0.00 30.80 2.34
2167 8910 6.783708 ATCAAAACTGGTGTCCAAAACTAA 57.216 33.333 0.00 0.00 30.80 2.24
2183 8926 9.181805 TCGATCGAGATGTTAGATTATCAAAAC 57.818 33.333 15.15 0.00 0.00 2.43
2184 8927 9.914131 ATCGATCGAGATGTTAGATTATCAAAA 57.086 29.630 23.84 0.00 0.00 2.44
2256 9241 2.708861 AGGCCGGTGTAATTGATATCCA 59.291 45.455 1.90 0.00 0.00 3.41
2314 9299 5.736486 TTTCGTTGTTGTGTGCATACTTA 57.264 34.783 15.05 0.15 0.00 2.24
2315 9300 4.624336 TTTCGTTGTTGTGTGCATACTT 57.376 36.364 15.05 0.00 0.00 2.24
2361 9358 1.883021 GACATGACTTTTGGGGGCG 59.117 57.895 0.00 0.00 0.00 6.13
2362 9359 0.608035 TCGACATGACTTTTGGGGGC 60.608 55.000 0.00 0.00 0.00 5.80
2405 9402 4.941263 TGTTATATCAGGTGTTGTTGCTCC 59.059 41.667 0.00 0.00 0.00 4.70
2419 9416 8.983789 TGTATTGTCAAGGGTAGTGTTATATCA 58.016 33.333 0.00 0.00 0.00 2.15
2420 9417 9.257651 GTGTATTGTCAAGGGTAGTGTTATATC 57.742 37.037 0.00 0.00 0.00 1.63
2421 9418 8.764558 TGTGTATTGTCAAGGGTAGTGTTATAT 58.235 33.333 0.00 0.00 0.00 0.86
2422 9419 8.136563 TGTGTATTGTCAAGGGTAGTGTTATA 57.863 34.615 0.00 0.00 0.00 0.98
2423 9420 7.011499 TGTGTATTGTCAAGGGTAGTGTTAT 57.989 36.000 0.00 0.00 0.00 1.89
2500 9497 3.106407 GTCGACTGTGGCGTCTGC 61.106 66.667 8.70 0.00 41.71 4.26
2505 9502 1.712018 TAGATCCGTCGACTGTGGCG 61.712 60.000 14.70 0.00 0.00 5.69
2512 9509 2.814919 AGTGGATGATAGATCCGTCGAC 59.185 50.000 5.18 5.18 41.03 4.20
2516 9513 5.070446 TGCTTTTAGTGGATGATAGATCCGT 59.930 40.000 0.00 0.00 41.03 4.69
2522 9519 8.896744 TCTTGATTTGCTTTTAGTGGATGATAG 58.103 33.333 0.00 0.00 0.00 2.08
2557 9554 2.361357 CGGACTCACTCTCCGGGT 60.361 66.667 0.00 0.00 45.90 5.28
2594 9593 4.044426 TCATGTACGCAATCGAGATGAAG 58.956 43.478 5.26 1.40 39.41 3.02
2683 9749 4.966366 GCGCTTAGTTGATGAATGATGAAC 59.034 41.667 0.00 0.00 0.00 3.18
2685 9751 4.190772 TGCGCTTAGTTGATGAATGATGA 58.809 39.130 9.73 0.00 0.00 2.92
2687 9753 5.565592 TTTGCGCTTAGTTGATGAATGAT 57.434 34.783 9.73 0.00 0.00 2.45
2688 9754 5.449041 GGATTTGCGCTTAGTTGATGAATGA 60.449 40.000 9.73 0.00 0.00 2.57
2689 9755 4.736793 GGATTTGCGCTTAGTTGATGAATG 59.263 41.667 9.73 0.00 0.00 2.67
2690 9756 4.641989 AGGATTTGCGCTTAGTTGATGAAT 59.358 37.500 9.73 0.00 0.00 2.57
2704 9770 6.618287 TTGGAATATGAGTTAGGATTTGCG 57.382 37.500 0.00 0.00 0.00 4.85
2723 9789 5.611374 GCTATATGTCAACTTAGGCTTGGA 58.389 41.667 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.