Multiple sequence alignment - TraesCS6D01G225400

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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 TraesCS6D01G225400 chr6D 100.000 3826 0 0 1 3826 317083668 317079843 0.000000e+00 7066.0
1 TraesCS6D01G225400 chr6B 92.236 2254 89 37 600 2842 507467488 507469666 0.000000e+00 3114.0
2 TraesCS6D01G225400 chr6B 96.793 873 24 3 2955 3826 507469729 507470598 0.000000e+00 1454.0
3 TraesCS6D01G225400 chr6B 93.688 301 14 2 308 607 507467168 507467464 2.710000e-121 446.0
4 TraesCS6D01G225400 chr6B 91.772 158 9 3 136 289 507462175 507462332 2.310000e-52 217.0
5 TraesCS6D01G225400 chr6B 89.333 150 13 3 1 149 507462009 507462156 6.530000e-43 185.0
6 TraesCS6D01G225400 chr6A 96.703 1274 32 2 1581 2845 454681100 454679828 0.000000e+00 2111.0
7 TraesCS6D01G225400 chr6A 96.008 952 29 6 2882 3826 454679829 454678880 0.000000e+00 1539.0
8 TraesCS6D01G225400 chr6A 92.298 831 27 13 707 1530 454681924 454681124 0.000000e+00 1146.0
9 TraesCS6D01G225400 chr6A 91.925 322 12 8 381 698 454682514 454682203 4.540000e-119 438.0
10 TraesCS6D01G225400 chr6A 88.214 280 24 6 1 277 454696727 454696454 3.690000e-85 326.0
11 TraesCS6D01G225400 chr7A 87.209 86 3 6 497 578 673830402 673830321 1.460000e-14 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 TraesCS6D01G225400 chr6D 317079843 317083668 3825 True 7066.000000 7066 100.0000 1 3826 1 chr6D.!!$R1 3825
1 TraesCS6D01G225400 chr6B 507467168 507470598 3430 False 1671.333333 3114 94.2390 308 3826 3 chr6B.!!$F2 3518
2 TraesCS6D01G225400 chr6A 454678880 454682514 3634 True 1308.500000 2111 94.2335 381 3826 4 chr6A.!!$R2 3445

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
563 569 0.028505 CAGCAGCGGTATACGTACGT 59.971 55.0 25.98 25.98 46.52 3.57 F
1564 1898 0.109689 GCTAGCGGCCGATAGTACAG 60.110 60.0 41.04 25.81 36.58 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1900 0.388520 GCTGGCCCGAAATTTGTCAC 60.389 55.0 0.0 0.0 0.00 3.67 R
2869 3212 0.108945 CCAACGTACTCCCTCCGTTC 60.109 60.0 0.0 0.0 42.34 3.95 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.931512 GGACTCTTCCTCGTCTCAAG 57.068 55.000 0.00 0.00 39.13 3.02
20 21 2.164338 GGACTCTTCCTCGTCTCAAGT 58.836 52.381 0.00 0.00 39.13 3.16
21 22 2.094957 GGACTCTTCCTCGTCTCAAGTG 60.095 54.545 0.00 0.00 39.13 3.16
22 23 1.271102 ACTCTTCCTCGTCTCAAGTGC 59.729 52.381 0.00 0.00 0.00 4.40
23 24 0.241213 TCTTCCTCGTCTCAAGTGCG 59.759 55.000 0.00 0.00 0.00 5.34
24 25 1.347817 CTTCCTCGTCTCAAGTGCGC 61.348 60.000 0.00 0.00 0.00 6.09
25 26 2.049156 CCTCGTCTCAAGTGCGCA 60.049 61.111 5.66 5.66 0.00 6.09
26 27 2.091112 CCTCGTCTCAAGTGCGCAG 61.091 63.158 12.22 0.00 0.00 5.18
41 42 2.257974 CGCAGCGTACTAAGTTCTCA 57.742 50.000 6.65 0.00 0.00 3.27
42 43 1.912110 CGCAGCGTACTAAGTTCTCAC 59.088 52.381 6.65 0.00 0.00 3.51
43 44 2.667448 CGCAGCGTACTAAGTTCTCACA 60.667 50.000 6.65 0.00 0.00 3.58
44 45 3.512680 GCAGCGTACTAAGTTCTCACAT 58.487 45.455 0.00 0.00 0.00 3.21
45 46 3.304559 GCAGCGTACTAAGTTCTCACATG 59.695 47.826 0.00 0.00 0.00 3.21
46 47 3.304559 CAGCGTACTAAGTTCTCACATGC 59.695 47.826 0.00 0.00 0.00 4.06
47 48 3.056821 AGCGTACTAAGTTCTCACATGCA 60.057 43.478 0.00 0.00 0.00 3.96
48 49 3.865745 GCGTACTAAGTTCTCACATGCAT 59.134 43.478 0.00 0.00 0.00 3.96
49 50 5.041287 GCGTACTAAGTTCTCACATGCATA 58.959 41.667 0.00 0.00 0.00 3.14
50 51 5.174035 GCGTACTAAGTTCTCACATGCATAG 59.826 44.000 0.00 0.00 0.00 2.23
51 52 5.687730 CGTACTAAGTTCTCACATGCATAGG 59.312 44.000 0.00 0.00 0.00 2.57
52 53 5.028549 ACTAAGTTCTCACATGCATAGGG 57.971 43.478 0.00 0.00 0.00 3.53
53 54 4.716784 ACTAAGTTCTCACATGCATAGGGA 59.283 41.667 0.00 0.00 0.00 4.20
54 55 4.574674 AAGTTCTCACATGCATAGGGAA 57.425 40.909 9.01 9.01 0.00 3.97
55 56 3.878778 AGTTCTCACATGCATAGGGAAC 58.121 45.455 25.49 25.49 33.91 3.62
56 57 3.264193 AGTTCTCACATGCATAGGGAACA 59.736 43.478 30.35 7.39 35.49 3.18
57 58 4.080129 AGTTCTCACATGCATAGGGAACAT 60.080 41.667 30.35 19.50 35.49 2.71
58 59 4.077300 TCTCACATGCATAGGGAACATC 57.923 45.455 0.00 0.00 0.00 3.06
59 60 2.804527 CTCACATGCATAGGGAACATCG 59.195 50.000 0.00 0.00 0.00 3.84
60 61 1.875514 CACATGCATAGGGAACATCGG 59.124 52.381 0.00 0.00 0.00 4.18
61 62 1.490490 ACATGCATAGGGAACATCGGT 59.510 47.619 0.00 0.00 0.00 4.69
62 63 1.875514 CATGCATAGGGAACATCGGTG 59.124 52.381 0.00 0.00 0.00 4.94
63 64 0.180171 TGCATAGGGAACATCGGTGG 59.820 55.000 0.00 0.00 0.00 4.61
64 65 1.166531 GCATAGGGAACATCGGTGGC 61.167 60.000 0.00 0.00 0.00 5.01
65 66 0.880278 CATAGGGAACATCGGTGGCG 60.880 60.000 0.00 0.00 0.00 5.69
66 67 2.660258 ATAGGGAACATCGGTGGCGC 62.660 60.000 0.00 0.00 0.00 6.53
79 80 4.459331 GGCGCCGACACGTACGTA 62.459 66.667 22.34 0.00 34.88 3.57
80 81 2.941013 GCGCCGACACGTACGTAG 60.941 66.667 22.34 17.19 34.88 3.51
81 82 2.778026 CGCCGACACGTACGTAGA 59.222 61.111 22.34 0.00 0.00 2.59
82 83 1.296432 CGCCGACACGTACGTAGAG 60.296 63.158 22.34 11.73 0.00 2.43
83 84 1.582168 GCCGACACGTACGTAGAGC 60.582 63.158 22.34 17.11 0.00 4.09
102 103 5.744666 GAGCGTAGTTCTCTCTATCAAGT 57.255 43.478 0.00 0.00 33.98 3.16
103 104 6.847956 GAGCGTAGTTCTCTCTATCAAGTA 57.152 41.667 0.00 0.00 33.98 2.24
104 105 7.429636 GAGCGTAGTTCTCTCTATCAAGTAT 57.570 40.000 0.00 0.00 33.98 2.12
105 106 7.429636 AGCGTAGTTCTCTCTATCAAGTATC 57.570 40.000 0.00 0.00 0.00 2.24
106 107 6.993308 AGCGTAGTTCTCTCTATCAAGTATCA 59.007 38.462 0.00 0.00 0.00 2.15
107 108 7.499563 AGCGTAGTTCTCTCTATCAAGTATCAA 59.500 37.037 0.00 0.00 0.00 2.57
108 109 7.588488 GCGTAGTTCTCTCTATCAAGTATCAAC 59.412 40.741 0.00 0.00 0.00 3.18
109 110 8.071368 CGTAGTTCTCTCTATCAAGTATCAACC 58.929 40.741 0.00 0.00 0.00 3.77
110 111 7.033530 AGTTCTCTCTATCAAGTATCAACCG 57.966 40.000 0.00 0.00 0.00 4.44
111 112 6.829298 AGTTCTCTCTATCAAGTATCAACCGA 59.171 38.462 0.00 0.00 0.00 4.69
112 113 6.869315 TCTCTCTATCAAGTATCAACCGAG 57.131 41.667 0.00 0.00 0.00 4.63
113 114 5.765677 TCTCTCTATCAAGTATCAACCGAGG 59.234 44.000 0.00 0.00 0.00 4.63
114 115 5.691896 TCTCTATCAAGTATCAACCGAGGA 58.308 41.667 0.00 0.00 0.00 3.71
115 116 5.765677 TCTCTATCAAGTATCAACCGAGGAG 59.234 44.000 0.00 0.00 0.00 3.69
116 117 5.691896 TCTATCAAGTATCAACCGAGGAGA 58.308 41.667 0.00 0.00 0.00 3.71
117 118 4.927978 ATCAAGTATCAACCGAGGAGAG 57.072 45.455 0.00 0.00 0.00 3.20
118 119 3.964411 TCAAGTATCAACCGAGGAGAGA 58.036 45.455 0.00 0.00 0.00 3.10
119 120 4.341487 TCAAGTATCAACCGAGGAGAGAA 58.659 43.478 0.00 0.00 0.00 2.87
120 121 4.770531 TCAAGTATCAACCGAGGAGAGAAA 59.229 41.667 0.00 0.00 0.00 2.52
121 122 4.993029 AGTATCAACCGAGGAGAGAAAG 57.007 45.455 0.00 0.00 0.00 2.62
122 123 2.682155 ATCAACCGAGGAGAGAAAGC 57.318 50.000 0.00 0.00 0.00 3.51
123 124 0.608640 TCAACCGAGGAGAGAAAGCC 59.391 55.000 0.00 0.00 0.00 4.35
124 125 0.321671 CAACCGAGGAGAGAAAGCCA 59.678 55.000 0.00 0.00 0.00 4.75
125 126 0.321996 AACCGAGGAGAGAAAGCCAC 59.678 55.000 0.00 0.00 0.00 5.01
126 127 0.832135 ACCGAGGAGAGAAAGCCACA 60.832 55.000 0.00 0.00 0.00 4.17
127 128 0.539051 CCGAGGAGAGAAAGCCACAT 59.461 55.000 0.00 0.00 0.00 3.21
128 129 1.065854 CCGAGGAGAGAAAGCCACATT 60.066 52.381 0.00 0.00 0.00 2.71
129 130 2.168521 CCGAGGAGAGAAAGCCACATTA 59.831 50.000 0.00 0.00 0.00 1.90
130 131 3.452474 CGAGGAGAGAAAGCCACATTAG 58.548 50.000 0.00 0.00 0.00 1.73
131 132 3.202097 GAGGAGAGAAAGCCACATTAGC 58.798 50.000 0.00 0.00 0.00 3.09
132 133 2.573462 AGGAGAGAAAGCCACATTAGCA 59.427 45.455 0.00 0.00 0.00 3.49
133 134 3.009473 AGGAGAGAAAGCCACATTAGCAA 59.991 43.478 0.00 0.00 0.00 3.91
134 135 3.376546 GGAGAGAAAGCCACATTAGCAAG 59.623 47.826 0.00 0.00 0.00 4.01
135 136 3.350833 AGAGAAAGCCACATTAGCAAGG 58.649 45.455 0.00 0.00 0.00 3.61
136 137 3.009473 AGAGAAAGCCACATTAGCAAGGA 59.991 43.478 0.00 0.00 0.00 3.36
137 138 3.950395 GAGAAAGCCACATTAGCAAGGAT 59.050 43.478 0.00 0.00 0.00 3.24
138 139 3.698040 AGAAAGCCACATTAGCAAGGATG 59.302 43.478 0.00 0.00 0.00 3.51
158 159 9.897744 AAGGATGCATACATGATAATTTTAACG 57.102 29.630 12.53 0.00 36.35 3.18
159 160 9.283768 AGGATGCATACATGATAATTTTAACGA 57.716 29.630 12.53 0.00 36.35 3.85
160 161 9.546909 GGATGCATACATGATAATTTTAACGAG 57.453 33.333 3.28 0.00 36.35 4.18
168 169 9.250624 ACATGATAATTTTAACGAGTAGAGCTC 57.749 33.333 5.27 5.27 40.77 4.09
169 170 8.704234 CATGATAATTTTAACGAGTAGAGCTCC 58.296 37.037 10.93 0.00 41.10 4.70
170 171 8.008513 TGATAATTTTAACGAGTAGAGCTCCT 57.991 34.615 10.93 0.16 41.10 3.69
171 172 9.128404 TGATAATTTTAACGAGTAGAGCTCCTA 57.872 33.333 10.93 0.00 41.10 2.94
172 173 9.615295 GATAATTTTAACGAGTAGAGCTCCTAG 57.385 37.037 10.93 4.32 41.10 3.02
173 174 7.642082 AATTTTAACGAGTAGAGCTCCTAGA 57.358 36.000 10.93 0.00 41.10 2.43
174 175 7.826918 ATTTTAACGAGTAGAGCTCCTAGAT 57.173 36.000 10.93 0.00 41.10 1.98
175 176 6.621316 TTTAACGAGTAGAGCTCCTAGATG 57.379 41.667 10.93 0.00 41.10 2.90
176 177 3.134574 ACGAGTAGAGCTCCTAGATGG 57.865 52.381 10.93 0.00 41.10 3.51
177 178 2.706723 ACGAGTAGAGCTCCTAGATGGA 59.293 50.000 10.93 0.00 43.86 3.41
178 179 3.329520 ACGAGTAGAGCTCCTAGATGGAT 59.670 47.826 10.93 0.00 45.16 3.41
179 180 3.689161 CGAGTAGAGCTCCTAGATGGATG 59.311 52.174 10.93 0.00 45.16 3.51
180 181 4.564613 CGAGTAGAGCTCCTAGATGGATGA 60.565 50.000 10.93 0.00 45.16 2.92
181 182 4.922206 AGTAGAGCTCCTAGATGGATGAG 58.078 47.826 10.93 0.00 45.16 2.90
182 183 3.901570 AGAGCTCCTAGATGGATGAGT 57.098 47.619 10.93 0.00 45.16 3.41
183 184 5.550011 AGTAGAGCTCCTAGATGGATGAGTA 59.450 44.000 10.93 0.00 45.16 2.59
184 185 4.662278 AGAGCTCCTAGATGGATGAGTAC 58.338 47.826 10.93 0.00 45.16 2.73
185 186 3.417101 AGCTCCTAGATGGATGAGTACG 58.583 50.000 0.00 0.00 45.16 3.67
186 187 3.150767 GCTCCTAGATGGATGAGTACGT 58.849 50.000 0.00 0.00 45.16 3.57
187 188 4.041815 AGCTCCTAGATGGATGAGTACGTA 59.958 45.833 0.00 0.00 45.16 3.57
188 189 4.393680 GCTCCTAGATGGATGAGTACGTAG 59.606 50.000 0.00 0.00 45.16 3.51
189 190 4.907809 TCCTAGATGGATGAGTACGTAGG 58.092 47.826 0.00 0.00 40.56 3.18
190 191 4.350225 TCCTAGATGGATGAGTACGTAGGT 59.650 45.833 0.00 0.00 40.56 3.08
191 192 5.071370 CCTAGATGGATGAGTACGTAGGTT 58.929 45.833 0.00 0.00 38.35 3.50
192 193 5.181622 CCTAGATGGATGAGTACGTAGGTTC 59.818 48.000 0.00 0.00 38.35 3.62
193 194 3.564644 AGATGGATGAGTACGTAGGTTCG 59.435 47.826 0.00 0.00 0.00 3.95
194 195 1.402968 TGGATGAGTACGTAGGTTCGC 59.597 52.381 0.00 0.00 0.00 4.70
195 196 1.674962 GGATGAGTACGTAGGTTCGCT 59.325 52.381 0.00 0.00 0.00 4.93
196 197 2.098770 GGATGAGTACGTAGGTTCGCTT 59.901 50.000 0.00 0.00 0.00 4.68
197 198 3.428589 GGATGAGTACGTAGGTTCGCTTT 60.429 47.826 0.00 0.00 0.00 3.51
198 199 4.201950 GGATGAGTACGTAGGTTCGCTTTA 60.202 45.833 0.00 0.00 0.00 1.85
199 200 4.970662 TGAGTACGTAGGTTCGCTTTAT 57.029 40.909 0.00 0.00 0.00 1.40
200 201 6.293626 GGATGAGTACGTAGGTTCGCTTTATA 60.294 42.308 0.00 0.00 0.00 0.98
201 202 6.624352 TGAGTACGTAGGTTCGCTTTATAT 57.376 37.500 0.00 0.00 0.00 0.86
202 203 7.031226 TGAGTACGTAGGTTCGCTTTATATT 57.969 36.000 0.00 0.00 0.00 1.28
203 204 6.914215 TGAGTACGTAGGTTCGCTTTATATTG 59.086 38.462 0.00 0.00 0.00 1.90
204 205 6.799512 AGTACGTAGGTTCGCTTTATATTGT 58.200 36.000 0.00 0.00 0.00 2.71
205 206 7.930217 AGTACGTAGGTTCGCTTTATATTGTA 58.070 34.615 0.00 0.00 0.00 2.41
206 207 7.857885 AGTACGTAGGTTCGCTTTATATTGTAC 59.142 37.037 0.00 0.00 0.00 2.90
207 208 6.799512 ACGTAGGTTCGCTTTATATTGTACT 58.200 36.000 0.00 0.00 0.00 2.73
208 209 7.260603 ACGTAGGTTCGCTTTATATTGTACTT 58.739 34.615 0.00 0.00 0.00 2.24
209 210 8.405531 ACGTAGGTTCGCTTTATATTGTACTTA 58.594 33.333 0.00 0.00 0.00 2.24
210 211 8.685536 CGTAGGTTCGCTTTATATTGTACTTAC 58.314 37.037 0.00 0.00 0.00 2.34
211 212 7.689953 AGGTTCGCTTTATATTGTACTTACG 57.310 36.000 0.00 0.00 0.00 3.18
212 213 7.260603 AGGTTCGCTTTATATTGTACTTACGT 58.739 34.615 0.00 0.00 0.00 3.57
213 214 7.221452 AGGTTCGCTTTATATTGTACTTACGTG 59.779 37.037 0.00 0.00 0.00 4.49
214 215 7.332530 GTTCGCTTTATATTGTACTTACGTGG 58.667 38.462 0.00 0.00 0.00 4.94
215 216 6.794374 TCGCTTTATATTGTACTTACGTGGA 58.206 36.000 0.00 0.00 0.00 4.02
216 217 7.428020 TCGCTTTATATTGTACTTACGTGGAT 58.572 34.615 0.00 0.00 0.00 3.41
217 218 7.592533 TCGCTTTATATTGTACTTACGTGGATC 59.407 37.037 0.00 0.00 0.00 3.36
218 219 7.409026 CGCTTTATATTGTACTTACGTGGATCG 60.409 40.741 0.00 0.00 46.00 3.69
231 232 3.966154 CGTGGATCGTCTTAATGCTACT 58.034 45.455 0.00 0.00 34.52 2.57
232 233 3.731216 CGTGGATCGTCTTAATGCTACTG 59.269 47.826 0.00 0.00 34.52 2.74
233 234 4.683832 GTGGATCGTCTTAATGCTACTGT 58.316 43.478 0.00 0.00 0.00 3.55
234 235 4.504461 GTGGATCGTCTTAATGCTACTGTG 59.496 45.833 0.00 0.00 0.00 3.66
235 236 4.159693 TGGATCGTCTTAATGCTACTGTGT 59.840 41.667 0.00 0.00 0.00 3.72
236 237 4.504461 GGATCGTCTTAATGCTACTGTGTG 59.496 45.833 0.00 0.00 0.00 3.82
237 238 3.250744 TCGTCTTAATGCTACTGTGTGC 58.749 45.455 0.00 0.00 0.00 4.57
238 239 3.056821 TCGTCTTAATGCTACTGTGTGCT 60.057 43.478 8.58 0.00 0.00 4.40
239 240 3.061295 CGTCTTAATGCTACTGTGTGCTG 59.939 47.826 8.58 0.00 0.00 4.41
240 241 3.997021 GTCTTAATGCTACTGTGTGCTGT 59.003 43.478 8.58 0.00 0.00 4.40
241 242 3.996363 TCTTAATGCTACTGTGTGCTGTG 59.004 43.478 8.58 0.00 0.00 3.66
242 243 0.877071 AATGCTACTGTGTGCTGTGC 59.123 50.000 8.58 0.00 0.00 4.57
243 244 0.250424 ATGCTACTGTGTGCTGTGCA 60.250 50.000 8.58 0.00 36.23 4.57
244 245 0.250424 TGCTACTGTGTGCTGTGCAT 60.250 50.000 0.00 0.00 41.91 3.96
245 246 0.445436 GCTACTGTGTGCTGTGCATC 59.555 55.000 0.00 0.00 41.91 3.91
246 247 0.717784 CTACTGTGTGCTGTGCATCG 59.282 55.000 0.00 0.00 41.91 3.84
247 248 0.670239 TACTGTGTGCTGTGCATCGG 60.670 55.000 0.00 1.05 41.91 4.18
256 257 4.811761 GTGCATCGGCGGCGTTTC 62.812 66.667 31.06 17.91 45.35 2.78
258 259 3.799755 GCATCGGCGGCGTTTCTT 61.800 61.111 31.06 9.29 0.00 2.52
259 260 2.867472 CATCGGCGGCGTTTCTTT 59.133 55.556 31.06 7.50 0.00 2.52
260 261 1.226018 CATCGGCGGCGTTTCTTTC 60.226 57.895 31.06 0.00 0.00 2.62
261 262 1.375523 ATCGGCGGCGTTTCTTTCT 60.376 52.632 31.06 4.18 0.00 2.52
262 263 0.108520 ATCGGCGGCGTTTCTTTCTA 60.109 50.000 31.06 8.81 0.00 2.10
263 264 0.734942 TCGGCGGCGTTTCTTTCTAG 60.735 55.000 31.06 0.00 0.00 2.43
264 265 1.424240 GGCGGCGTTTCTTTCTAGC 59.576 57.895 9.37 0.00 0.00 3.42
265 266 1.296056 GGCGGCGTTTCTTTCTAGCA 61.296 55.000 9.37 0.00 0.00 3.49
266 267 0.515564 GCGGCGTTTCTTTCTAGCAA 59.484 50.000 9.37 0.00 0.00 3.91
267 268 1.130561 GCGGCGTTTCTTTCTAGCAAT 59.869 47.619 9.37 0.00 0.00 3.56
268 269 2.350498 GCGGCGTTTCTTTCTAGCAATA 59.650 45.455 9.37 0.00 0.00 1.90
269 270 3.544244 GCGGCGTTTCTTTCTAGCAATAG 60.544 47.826 9.37 0.00 0.00 1.73
270 271 3.544244 CGGCGTTTCTTTCTAGCAATAGC 60.544 47.826 0.00 0.00 42.56 2.97
289 290 9.370126 GCAATAGCTTGTGATTAATTAAGTACG 57.630 33.333 3.94 0.00 37.91 3.67
292 293 7.303634 AGCTTGTGATTAATTAAGTACGTGG 57.696 36.000 0.00 2.10 0.00 4.94
293 294 6.877322 AGCTTGTGATTAATTAAGTACGTGGT 59.123 34.615 0.00 5.28 0.00 4.16
294 295 8.036575 AGCTTGTGATTAATTAAGTACGTGGTA 58.963 33.333 0.00 0.00 0.00 3.25
295 296 8.325997 GCTTGTGATTAATTAAGTACGTGGTAG 58.674 37.037 0.00 2.04 0.00 3.18
296 297 9.577110 CTTGTGATTAATTAAGTACGTGGTAGA 57.423 33.333 0.00 0.00 0.00 2.59
306 307 5.747951 AGTACGTGGTAGATTACTACTGC 57.252 43.478 0.00 0.00 45.70 4.40
311 312 4.319333 CGTGGTAGATTACTACTGCCTACG 60.319 50.000 0.00 0.00 45.70 3.51
329 330 0.928229 CGCAAGAGTACATTACCCGC 59.072 55.000 0.00 0.00 43.02 6.13
355 356 1.742268 GAGAGCCCAGATGTTCTTTGC 59.258 52.381 0.00 0.00 0.00 3.68
373 374 2.633657 GAGCCATGGCAATACGCG 59.366 61.111 37.18 3.53 44.88 6.01
460 461 0.682852 TCCCGAACCGACACTGAATT 59.317 50.000 0.00 0.00 0.00 2.17
464 465 2.607187 CGAACCGACACTGAATTAGCT 58.393 47.619 0.00 0.00 0.00 3.32
482 484 1.067354 GCTAAACGAAGACCGGGAGAA 60.067 52.381 6.32 0.00 43.93 2.87
500 502 3.116300 AGAAATATAGTGCGTGTCTGCG 58.884 45.455 0.00 0.00 37.81 5.18
561 567 2.503256 GCAGCAGCGGTATACGTAC 58.497 57.895 0.00 0.00 46.52 3.67
562 568 1.266786 GCAGCAGCGGTATACGTACG 61.267 60.000 15.01 15.01 46.52 3.67
563 569 0.028505 CAGCAGCGGTATACGTACGT 59.971 55.000 25.98 25.98 46.52 3.57
607 644 3.178412 ACCAAACCCCCGAAATACATT 57.822 42.857 0.00 0.00 0.00 2.71
615 652 3.067106 CCCCGAAATACATTCATCCGAG 58.933 50.000 0.00 0.00 37.96 4.63
674 711 6.814954 TTCCTTAGCAGTATCATTCTCCTT 57.185 37.500 0.00 0.00 0.00 3.36
686 723 1.747444 TTCTCCTTCCTTCCCAGCTT 58.253 50.000 0.00 0.00 0.00 3.74
701 738 2.082943 GCTTTTGCCTTTCGCGCTC 61.083 57.895 5.56 0.00 42.08 5.03
709 1016 0.875059 CCTTTCGCGCTCCTTTCTTT 59.125 50.000 5.56 0.00 0.00 2.52
835 1142 3.844577 ACCACACCTATATATCGCGAC 57.155 47.619 12.93 0.00 0.00 5.19
916 1224 4.022416 GCTCATAATCGGTCTCACTCTCAT 60.022 45.833 0.00 0.00 0.00 2.90
947 1255 2.612567 CGATCGAGAGCCTCCTCCG 61.613 68.421 10.26 0.00 38.96 4.63
1552 1886 0.321653 AAACCTCCACTTGCTAGCGG 60.322 55.000 10.77 8.09 0.00 5.52
1553 1887 2.512515 CCTCCACTTGCTAGCGGC 60.513 66.667 10.77 0.00 42.22 6.53
1554 1888 2.512515 CTCCACTTGCTAGCGGCC 60.513 66.667 10.77 0.00 40.92 6.13
1555 1889 4.451150 TCCACTTGCTAGCGGCCG 62.451 66.667 24.05 24.05 40.92 6.13
1556 1890 4.451150 CCACTTGCTAGCGGCCGA 62.451 66.667 33.48 8.14 40.92 5.54
1557 1891 2.202932 CACTTGCTAGCGGCCGAT 60.203 61.111 33.48 28.73 40.92 4.18
1558 1892 1.067416 CACTTGCTAGCGGCCGATA 59.933 57.895 33.48 28.18 40.92 2.92
1559 1893 0.941463 CACTTGCTAGCGGCCGATAG 60.941 60.000 39.06 39.06 40.92 2.08
1560 1894 1.364171 CTTGCTAGCGGCCGATAGT 59.636 57.895 41.04 20.90 40.92 2.12
1561 1895 0.596577 CTTGCTAGCGGCCGATAGTA 59.403 55.000 41.04 37.21 40.92 1.82
1562 1896 0.313043 TTGCTAGCGGCCGATAGTAC 59.687 55.000 41.04 29.53 40.92 2.73
1563 1897 0.820482 TGCTAGCGGCCGATAGTACA 60.820 55.000 41.04 31.43 40.92 2.90
1564 1898 0.109689 GCTAGCGGCCGATAGTACAG 60.110 60.000 41.04 25.81 36.58 2.74
1565 1899 1.236628 CTAGCGGCCGATAGTACAGT 58.763 55.000 36.12 9.05 30.32 3.55
1566 1900 0.949397 TAGCGGCCGATAGTACAGTG 59.051 55.000 33.48 0.00 0.00 3.66
1567 1901 1.035932 AGCGGCCGATAGTACAGTGT 61.036 55.000 33.48 0.00 0.00 3.55
1568 1902 0.870307 GCGGCCGATAGTACAGTGTG 60.870 60.000 33.48 0.00 0.00 3.82
1569 1903 0.736636 CGGCCGATAGTACAGTGTGA 59.263 55.000 24.07 0.00 0.00 3.58
1570 1904 1.533338 CGGCCGATAGTACAGTGTGAC 60.533 57.143 24.07 0.48 0.00 3.67
1571 1905 1.475280 GGCCGATAGTACAGTGTGACA 59.525 52.381 5.88 0.00 0.00 3.58
1572 1906 2.094390 GGCCGATAGTACAGTGTGACAA 60.094 50.000 5.88 0.00 0.00 3.18
1573 1907 3.581755 GCCGATAGTACAGTGTGACAAA 58.418 45.455 5.88 0.00 0.00 2.83
1574 1908 4.181578 GCCGATAGTACAGTGTGACAAAT 58.818 43.478 5.88 0.00 0.00 2.32
1575 1909 4.630069 GCCGATAGTACAGTGTGACAAATT 59.370 41.667 5.88 0.00 0.00 1.82
1576 1910 5.121768 GCCGATAGTACAGTGTGACAAATTT 59.878 40.000 5.88 0.00 0.00 1.82
1577 1911 6.672357 GCCGATAGTACAGTGTGACAAATTTC 60.672 42.308 5.88 0.00 0.00 2.17
1578 1912 6.453791 CCGATAGTACAGTGTGACAAATTTCG 60.454 42.308 5.88 1.84 0.00 3.46
1579 1913 6.453791 CGATAGTACAGTGTGACAAATTTCGG 60.454 42.308 5.88 0.00 0.00 4.30
1580 1914 3.813166 AGTACAGTGTGACAAATTTCGGG 59.187 43.478 5.88 0.00 0.00 5.14
1581 1915 1.336755 ACAGTGTGACAAATTTCGGGC 59.663 47.619 0.00 0.00 0.00 6.13
1582 1916 0.958822 AGTGTGACAAATTTCGGGCC 59.041 50.000 0.00 0.00 0.00 5.80
1583 1917 0.671251 GTGTGACAAATTTCGGGCCA 59.329 50.000 4.39 0.00 0.00 5.36
1584 1918 0.958091 TGTGACAAATTTCGGGCCAG 59.042 50.000 4.39 0.00 0.00 4.85
1585 1919 0.388520 GTGACAAATTTCGGGCCAGC 60.389 55.000 4.39 0.00 0.00 4.85
1586 1920 1.154035 GACAAATTTCGGGCCAGCG 60.154 57.895 4.39 0.00 0.00 5.18
1627 1961 6.020971 TCGAAGCTGACATTTAACAGAGTA 57.979 37.500 0.00 0.00 36.38 2.59
1628 1962 6.631016 TCGAAGCTGACATTTAACAGAGTAT 58.369 36.000 0.00 0.00 36.38 2.12
1638 1972 9.760660 GACATTTAACAGAGTATCATGTGAAAC 57.239 33.333 0.00 0.00 37.82 2.78
1654 1988 1.197721 GAAACATTCTGCAGGTGGACG 59.802 52.381 15.13 0.00 0.00 4.79
1766 2109 2.897436 CATAGCTCTACACTGCAGCAA 58.103 47.619 15.27 0.00 35.46 3.91
2681 3024 1.140589 CGAGATGAAGAGGCACGCT 59.859 57.895 0.00 0.00 43.09 5.07
2828 3171 0.179111 GCGGCTATGTGCAGTAGTCA 60.179 55.000 10.31 0.00 45.15 3.41
2842 3185 7.094118 TGTGCAGTAGTCACATACAGTACATAA 60.094 37.037 0.00 0.00 39.29 1.90
2843 3186 7.921214 GTGCAGTAGTCACATACAGTACATAAT 59.079 37.037 0.00 0.00 31.29 1.28
2844 3187 9.127277 TGCAGTAGTCACATACAGTACATAATA 57.873 33.333 0.00 0.00 0.00 0.98
2877 3220 9.376075 TCTAGACGTATTTATATAGAACGGAGG 57.624 37.037 14.28 5.75 37.86 4.30
2878 3221 7.388460 AGACGTATTTATATAGAACGGAGGG 57.612 40.000 14.28 0.00 37.86 4.30
2879 3222 7.170965 AGACGTATTTATATAGAACGGAGGGA 58.829 38.462 14.28 0.00 37.86 4.20
2880 3223 7.336427 AGACGTATTTATATAGAACGGAGGGAG 59.664 40.741 14.28 0.00 37.86 4.30
3163 3508 6.815089 ACACATTTTTCAATCCAGCAACTAA 58.185 32.000 0.00 0.00 0.00 2.24
3164 3509 7.444299 ACACATTTTTCAATCCAGCAACTAAT 58.556 30.769 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.094957 CACTTGAGACGAGGAAGAGTCC 60.095 54.545 0.00 0.00 45.35 3.85
1 2 2.669950 GCACTTGAGACGAGGAAGAGTC 60.670 54.545 0.00 0.00 37.63 3.36
2 3 1.271102 GCACTTGAGACGAGGAAGAGT 59.729 52.381 0.00 0.00 0.00 3.24
3 4 1.730772 CGCACTTGAGACGAGGAAGAG 60.731 57.143 0.00 0.00 0.00 2.85
4 5 0.241213 CGCACTTGAGACGAGGAAGA 59.759 55.000 0.00 0.00 0.00 2.87
5 6 1.347817 GCGCACTTGAGACGAGGAAG 61.348 60.000 0.30 0.00 0.00 3.46
6 7 1.372997 GCGCACTTGAGACGAGGAA 60.373 57.895 0.30 0.00 0.00 3.36
7 8 2.258591 GCGCACTTGAGACGAGGA 59.741 61.111 0.30 0.00 0.00 3.71
8 9 2.049156 TGCGCACTTGAGACGAGG 60.049 61.111 5.66 0.00 0.00 4.63
9 10 2.724708 GCTGCGCACTTGAGACGAG 61.725 63.158 5.66 0.00 0.00 4.18
10 11 2.734723 GCTGCGCACTTGAGACGA 60.735 61.111 5.66 0.00 0.00 4.20
11 12 4.126390 CGCTGCGCACTTGAGACG 62.126 66.667 5.66 0.86 0.00 4.18
12 13 1.733041 TACGCTGCGCACTTGAGAC 60.733 57.895 23.51 0.00 0.00 3.36
13 14 1.733041 GTACGCTGCGCACTTGAGA 60.733 57.895 23.51 0.00 0.00 3.27
14 15 0.456142 TAGTACGCTGCGCACTTGAG 60.456 55.000 30.08 0.63 35.06 3.02
15 16 0.038983 TTAGTACGCTGCGCACTTGA 60.039 50.000 30.08 17.68 35.06 3.02
16 17 0.366871 CTTAGTACGCTGCGCACTTG 59.633 55.000 30.08 19.76 35.06 3.16
17 18 0.038526 ACTTAGTACGCTGCGCACTT 60.039 50.000 30.08 12.30 35.06 3.16
18 19 0.038526 AACTTAGTACGCTGCGCACT 60.039 50.000 28.32 28.32 37.27 4.40
19 20 0.365859 GAACTTAGTACGCTGCGCAC 59.634 55.000 23.51 20.16 0.00 5.34
20 21 0.242825 AGAACTTAGTACGCTGCGCA 59.757 50.000 23.51 10.98 0.00 6.09
21 22 0.915227 GAGAACTTAGTACGCTGCGC 59.085 55.000 23.51 0.00 0.00 6.09
22 23 1.912110 GTGAGAACTTAGTACGCTGCG 59.088 52.381 21.91 21.91 0.00 5.18
23 24 2.942710 TGTGAGAACTTAGTACGCTGC 58.057 47.619 0.00 0.00 0.00 5.25
24 25 3.304559 GCATGTGAGAACTTAGTACGCTG 59.695 47.826 0.00 0.00 0.00 5.18
25 26 3.056821 TGCATGTGAGAACTTAGTACGCT 60.057 43.478 0.00 0.00 0.00 5.07
26 27 3.250744 TGCATGTGAGAACTTAGTACGC 58.749 45.455 0.00 0.00 0.00 4.42
27 28 5.687730 CCTATGCATGTGAGAACTTAGTACG 59.312 44.000 10.16 0.00 0.00 3.67
28 29 5.986135 CCCTATGCATGTGAGAACTTAGTAC 59.014 44.000 10.16 0.00 0.00 2.73
29 30 5.897250 TCCCTATGCATGTGAGAACTTAGTA 59.103 40.000 10.16 0.00 0.00 1.82
30 31 4.716784 TCCCTATGCATGTGAGAACTTAGT 59.283 41.667 10.16 0.00 0.00 2.24
31 32 5.282055 TCCCTATGCATGTGAGAACTTAG 57.718 43.478 10.16 0.00 0.00 2.18
32 33 5.045942 TGTTCCCTATGCATGTGAGAACTTA 60.046 40.000 22.84 10.20 34.62 2.24
33 34 4.263462 TGTTCCCTATGCATGTGAGAACTT 60.263 41.667 22.84 0.00 34.62 2.66
34 35 3.264193 TGTTCCCTATGCATGTGAGAACT 59.736 43.478 22.84 0.00 34.62 3.01
35 36 3.609853 TGTTCCCTATGCATGTGAGAAC 58.390 45.455 10.16 16.04 34.23 3.01
36 37 3.998913 TGTTCCCTATGCATGTGAGAA 57.001 42.857 10.16 4.40 0.00 2.87
37 38 3.493176 CGATGTTCCCTATGCATGTGAGA 60.493 47.826 10.16 0.00 0.00 3.27
38 39 2.804527 CGATGTTCCCTATGCATGTGAG 59.195 50.000 10.16 0.00 0.00 3.51
39 40 2.485302 CCGATGTTCCCTATGCATGTGA 60.485 50.000 10.16 0.00 0.00 3.58
40 41 1.875514 CCGATGTTCCCTATGCATGTG 59.124 52.381 10.16 1.76 0.00 3.21
41 42 1.490490 ACCGATGTTCCCTATGCATGT 59.510 47.619 10.16 0.00 0.00 3.21
42 43 1.875514 CACCGATGTTCCCTATGCATG 59.124 52.381 10.16 0.00 0.00 4.06
43 44 1.202806 CCACCGATGTTCCCTATGCAT 60.203 52.381 3.79 3.79 0.00 3.96
44 45 0.180171 CCACCGATGTTCCCTATGCA 59.820 55.000 0.00 0.00 0.00 3.96
45 46 1.166531 GCCACCGATGTTCCCTATGC 61.167 60.000 0.00 0.00 0.00 3.14
46 47 0.880278 CGCCACCGATGTTCCCTATG 60.880 60.000 0.00 0.00 36.29 2.23
47 48 1.445942 CGCCACCGATGTTCCCTAT 59.554 57.895 0.00 0.00 36.29 2.57
48 49 2.897207 CGCCACCGATGTTCCCTA 59.103 61.111 0.00 0.00 36.29 3.53
49 50 4.778143 GCGCCACCGATGTTCCCT 62.778 66.667 0.00 0.00 36.29 4.20
62 63 4.459331 TACGTACGTGTCGGCGCC 62.459 66.667 30.25 19.07 34.19 6.53
63 64 2.941013 CTACGTACGTGTCGGCGC 60.941 66.667 30.25 0.00 34.19 6.53
64 65 1.296432 CTCTACGTACGTGTCGGCG 60.296 63.158 30.25 0.00 36.07 6.46
65 66 1.582168 GCTCTACGTACGTGTCGGC 60.582 63.158 30.25 22.25 0.00 5.54
66 67 1.296432 CGCTCTACGTACGTGTCGG 60.296 63.158 30.25 17.29 36.87 4.79
67 68 4.242499 CGCTCTACGTACGTGTCG 57.758 61.111 30.25 21.30 36.87 4.35
80 81 5.744666 ACTTGATAGAGAGAACTACGCTC 57.255 43.478 0.00 0.00 43.92 5.03
81 82 6.993308 TGATACTTGATAGAGAGAACTACGCT 59.007 38.462 0.00 0.00 0.00 5.07
82 83 7.192148 TGATACTTGATAGAGAGAACTACGC 57.808 40.000 0.00 0.00 0.00 4.42
83 84 8.071368 GGTTGATACTTGATAGAGAGAACTACG 58.929 40.741 0.00 0.00 0.00 3.51
84 85 8.071368 CGGTTGATACTTGATAGAGAGAACTAC 58.929 40.741 0.00 0.00 0.00 2.73
85 86 7.991460 TCGGTTGATACTTGATAGAGAGAACTA 59.009 37.037 0.00 0.00 0.00 2.24
86 87 6.829298 TCGGTTGATACTTGATAGAGAGAACT 59.171 38.462 0.00 0.00 0.00 3.01
87 88 7.028926 TCGGTTGATACTTGATAGAGAGAAC 57.971 40.000 0.00 0.00 0.00 3.01
88 89 6.263392 CCTCGGTTGATACTTGATAGAGAGAA 59.737 42.308 0.00 0.00 0.00 2.87
89 90 5.765677 CCTCGGTTGATACTTGATAGAGAGA 59.234 44.000 0.00 0.00 0.00 3.10
90 91 5.765677 TCCTCGGTTGATACTTGATAGAGAG 59.234 44.000 0.00 0.00 0.00 3.20
91 92 5.691896 TCCTCGGTTGATACTTGATAGAGA 58.308 41.667 0.00 0.00 0.00 3.10
92 93 5.765677 TCTCCTCGGTTGATACTTGATAGAG 59.234 44.000 0.00 0.00 0.00 2.43
93 94 5.691896 TCTCCTCGGTTGATACTTGATAGA 58.308 41.667 0.00 0.00 0.00 1.98
94 95 5.765677 TCTCTCCTCGGTTGATACTTGATAG 59.234 44.000 0.00 0.00 0.00 2.08
95 96 5.691896 TCTCTCCTCGGTTGATACTTGATA 58.308 41.667 0.00 0.00 0.00 2.15
96 97 4.537751 TCTCTCCTCGGTTGATACTTGAT 58.462 43.478 0.00 0.00 0.00 2.57
97 98 3.964411 TCTCTCCTCGGTTGATACTTGA 58.036 45.455 0.00 0.00 0.00 3.02
98 99 4.720649 TTCTCTCCTCGGTTGATACTTG 57.279 45.455 0.00 0.00 0.00 3.16
99 100 4.382147 GCTTTCTCTCCTCGGTTGATACTT 60.382 45.833 0.00 0.00 0.00 2.24
100 101 3.131400 GCTTTCTCTCCTCGGTTGATACT 59.869 47.826 0.00 0.00 0.00 2.12
101 102 3.449632 GCTTTCTCTCCTCGGTTGATAC 58.550 50.000 0.00 0.00 0.00 2.24
102 103 2.431057 GGCTTTCTCTCCTCGGTTGATA 59.569 50.000 0.00 0.00 0.00 2.15
103 104 1.208293 GGCTTTCTCTCCTCGGTTGAT 59.792 52.381 0.00 0.00 0.00 2.57
104 105 0.608640 GGCTTTCTCTCCTCGGTTGA 59.391 55.000 0.00 0.00 0.00 3.18
105 106 0.321671 TGGCTTTCTCTCCTCGGTTG 59.678 55.000 0.00 0.00 0.00 3.77
106 107 0.321996 GTGGCTTTCTCTCCTCGGTT 59.678 55.000 0.00 0.00 0.00 4.44
107 108 0.832135 TGTGGCTTTCTCTCCTCGGT 60.832 55.000 0.00 0.00 0.00 4.69
108 109 0.539051 ATGTGGCTTTCTCTCCTCGG 59.461 55.000 0.00 0.00 0.00 4.63
109 110 2.393271 AATGTGGCTTTCTCTCCTCG 57.607 50.000 0.00 0.00 0.00 4.63
110 111 3.202097 GCTAATGTGGCTTTCTCTCCTC 58.798 50.000 0.00 0.00 0.00 3.71
111 112 2.573462 TGCTAATGTGGCTTTCTCTCCT 59.427 45.455 0.00 0.00 0.00 3.69
112 113 2.991250 TGCTAATGTGGCTTTCTCTCC 58.009 47.619 0.00 0.00 0.00 3.71
113 114 3.376546 CCTTGCTAATGTGGCTTTCTCTC 59.623 47.826 0.00 0.00 0.00 3.20
114 115 3.009473 TCCTTGCTAATGTGGCTTTCTCT 59.991 43.478 0.00 0.00 0.00 3.10
115 116 3.347216 TCCTTGCTAATGTGGCTTTCTC 58.653 45.455 0.00 0.00 0.00 2.87
116 117 3.439857 TCCTTGCTAATGTGGCTTTCT 57.560 42.857 0.00 0.00 0.00 2.52
117 118 3.736126 GCATCCTTGCTAATGTGGCTTTC 60.736 47.826 0.00 0.00 45.77 2.62
118 119 2.167075 GCATCCTTGCTAATGTGGCTTT 59.833 45.455 0.00 0.00 45.77 3.51
119 120 1.753073 GCATCCTTGCTAATGTGGCTT 59.247 47.619 0.00 0.00 45.77 4.35
120 121 1.396653 GCATCCTTGCTAATGTGGCT 58.603 50.000 0.00 0.00 45.77 4.75
121 122 3.953201 GCATCCTTGCTAATGTGGC 57.047 52.632 0.00 0.00 45.77 5.01
132 133 9.897744 CGTTAAAATTATCATGTATGCATCCTT 57.102 29.630 0.19 0.00 31.99 3.36
133 134 9.283768 TCGTTAAAATTATCATGTATGCATCCT 57.716 29.630 0.19 0.00 31.99 3.24
134 135 9.546909 CTCGTTAAAATTATCATGTATGCATCC 57.453 33.333 0.19 0.00 31.99 3.51
142 143 9.250624 GAGCTCTACTCGTTAAAATTATCATGT 57.749 33.333 6.43 0.00 35.18 3.21
168 169 4.653868 ACCTACGTACTCATCCATCTAGG 58.346 47.826 0.00 0.00 39.47 3.02
169 170 5.107026 CGAACCTACGTACTCATCCATCTAG 60.107 48.000 0.00 0.00 0.00 2.43
170 171 4.753610 CGAACCTACGTACTCATCCATCTA 59.246 45.833 0.00 0.00 0.00 1.98
171 172 3.564644 CGAACCTACGTACTCATCCATCT 59.435 47.826 0.00 0.00 0.00 2.90
172 173 3.852572 GCGAACCTACGTACTCATCCATC 60.853 52.174 0.00 0.00 35.59 3.51
173 174 2.034305 GCGAACCTACGTACTCATCCAT 59.966 50.000 0.00 0.00 35.59 3.41
174 175 1.402968 GCGAACCTACGTACTCATCCA 59.597 52.381 0.00 0.00 35.59 3.41
175 176 1.674962 AGCGAACCTACGTACTCATCC 59.325 52.381 0.00 0.00 35.59 3.51
176 177 3.417690 AAGCGAACCTACGTACTCATC 57.582 47.619 0.00 0.00 35.59 2.92
177 178 3.863142 AAAGCGAACCTACGTACTCAT 57.137 42.857 0.00 0.00 35.59 2.90
178 179 4.970662 ATAAAGCGAACCTACGTACTCA 57.029 40.909 0.00 0.00 35.59 3.41
179 180 6.914757 ACAATATAAAGCGAACCTACGTACTC 59.085 38.462 0.00 0.00 35.59 2.59
180 181 6.799512 ACAATATAAAGCGAACCTACGTACT 58.200 36.000 0.00 0.00 35.59 2.73
181 182 7.857885 AGTACAATATAAAGCGAACCTACGTAC 59.142 37.037 0.00 0.00 35.59 3.67
182 183 7.930217 AGTACAATATAAAGCGAACCTACGTA 58.070 34.615 0.00 0.00 35.59 3.57
183 184 6.799512 AGTACAATATAAAGCGAACCTACGT 58.200 36.000 0.00 0.00 35.59 3.57
184 185 7.689953 AAGTACAATATAAAGCGAACCTACG 57.310 36.000 0.00 0.00 0.00 3.51
185 186 8.685536 CGTAAGTACAATATAAAGCGAACCTAC 58.314 37.037 0.00 0.00 0.00 3.18
186 187 8.786937 CGTAAGTACAATATAAAGCGAACCTA 57.213 34.615 0.00 0.00 0.00 3.08
187 188 7.689953 CGTAAGTACAATATAAAGCGAACCT 57.310 36.000 0.00 0.00 0.00 3.50
211 212 4.504461 CACAGTAGCATTAAGACGATCCAC 59.496 45.833 0.00 0.00 0.00 4.02
212 213 4.159693 ACACAGTAGCATTAAGACGATCCA 59.840 41.667 0.00 0.00 0.00 3.41
213 214 4.504461 CACACAGTAGCATTAAGACGATCC 59.496 45.833 0.00 0.00 0.00 3.36
214 215 4.026475 GCACACAGTAGCATTAAGACGATC 60.026 45.833 0.00 0.00 0.00 3.69
215 216 3.865745 GCACACAGTAGCATTAAGACGAT 59.134 43.478 0.00 0.00 0.00 3.73
216 217 3.056821 AGCACACAGTAGCATTAAGACGA 60.057 43.478 0.00 0.00 0.00 4.20
217 218 3.061295 CAGCACACAGTAGCATTAAGACG 59.939 47.826 0.49 0.00 0.00 4.18
218 219 3.997021 ACAGCACACAGTAGCATTAAGAC 59.003 43.478 0.49 0.00 0.00 3.01
219 220 3.996363 CACAGCACACAGTAGCATTAAGA 59.004 43.478 0.49 0.00 0.00 2.10
220 221 3.425359 GCACAGCACACAGTAGCATTAAG 60.425 47.826 0.49 0.00 0.00 1.85
221 222 2.483877 GCACAGCACACAGTAGCATTAA 59.516 45.455 0.49 0.00 0.00 1.40
222 223 2.076100 GCACAGCACACAGTAGCATTA 58.924 47.619 0.49 0.00 0.00 1.90
223 224 0.877071 GCACAGCACACAGTAGCATT 59.123 50.000 0.49 0.00 0.00 3.56
224 225 0.250424 TGCACAGCACACAGTAGCAT 60.250 50.000 0.49 0.00 31.71 3.79
225 226 0.250424 ATGCACAGCACACAGTAGCA 60.250 50.000 0.00 0.00 43.04 3.49
226 227 0.445436 GATGCACAGCACACAGTAGC 59.555 55.000 0.00 0.00 43.04 3.58
227 228 0.717784 CGATGCACAGCACACAGTAG 59.282 55.000 0.00 0.00 43.04 2.57
228 229 0.670239 CCGATGCACAGCACACAGTA 60.670 55.000 0.00 0.00 43.04 2.74
229 230 1.962822 CCGATGCACAGCACACAGT 60.963 57.895 0.00 0.00 43.04 3.55
230 231 2.865308 CCGATGCACAGCACACAG 59.135 61.111 0.00 0.00 43.04 3.66
231 232 3.356267 GCCGATGCACAGCACACA 61.356 61.111 0.00 0.00 43.04 3.72
232 233 4.450122 CGCCGATGCACAGCACAC 62.450 66.667 0.00 0.00 43.04 3.82
239 240 4.811761 GAAACGCCGCCGATGCAC 62.812 66.667 0.00 0.00 37.32 4.57
241 242 3.322706 AAAGAAACGCCGCCGATGC 62.323 57.895 0.00 0.00 38.29 3.91
242 243 1.226018 GAAAGAAACGCCGCCGATG 60.226 57.895 0.00 0.00 38.29 3.84
243 244 0.108520 TAGAAAGAAACGCCGCCGAT 60.109 50.000 0.00 0.00 38.29 4.18
244 245 0.734942 CTAGAAAGAAACGCCGCCGA 60.735 55.000 0.00 0.00 38.29 5.54
245 246 1.708027 CTAGAAAGAAACGCCGCCG 59.292 57.895 0.00 0.00 41.14 6.46
246 247 1.296056 TGCTAGAAAGAAACGCCGCC 61.296 55.000 0.00 0.00 0.00 6.13
247 248 0.515564 TTGCTAGAAAGAAACGCCGC 59.484 50.000 0.00 0.00 0.00 6.53
248 249 3.544244 GCTATTGCTAGAAAGAAACGCCG 60.544 47.826 0.00 0.00 36.03 6.46
249 250 3.941520 GCTATTGCTAGAAAGAAACGCC 58.058 45.455 0.00 0.00 36.03 5.68
263 264 9.370126 CGTACTTAATTAATCACAAGCTATTGC 57.630 33.333 0.00 0.00 40.27 3.56
266 267 9.042008 CCACGTACTTAATTAATCACAAGCTAT 57.958 33.333 0.00 0.00 0.00 2.97
267 268 8.036575 ACCACGTACTTAATTAATCACAAGCTA 58.963 33.333 0.00 0.00 0.00 3.32
268 269 6.877322 ACCACGTACTTAATTAATCACAAGCT 59.123 34.615 0.00 0.00 0.00 3.74
269 270 7.068692 ACCACGTACTTAATTAATCACAAGC 57.931 36.000 0.00 0.00 0.00 4.01
270 271 9.577110 TCTACCACGTACTTAATTAATCACAAG 57.423 33.333 0.00 0.00 0.00 3.16
280 281 8.348507 GCAGTAGTAATCTACCACGTACTTAAT 58.651 37.037 0.00 0.00 45.36 1.40
281 282 7.201732 GGCAGTAGTAATCTACCACGTACTTAA 60.202 40.741 0.00 0.00 45.36 1.85
282 283 6.260936 GGCAGTAGTAATCTACCACGTACTTA 59.739 42.308 0.00 0.00 45.36 2.24
283 284 5.067023 GGCAGTAGTAATCTACCACGTACTT 59.933 44.000 0.00 0.00 45.36 2.24
284 285 4.578105 GGCAGTAGTAATCTACCACGTACT 59.422 45.833 0.00 0.00 45.36 2.73
285 286 4.578105 AGGCAGTAGTAATCTACCACGTAC 59.422 45.833 0.00 0.00 45.36 3.67
286 287 4.785301 AGGCAGTAGTAATCTACCACGTA 58.215 43.478 0.00 0.00 45.36 3.57
287 288 3.629087 AGGCAGTAGTAATCTACCACGT 58.371 45.455 2.36 0.00 45.36 4.49
288 289 4.319333 CGTAGGCAGTAGTAATCTACCACG 60.319 50.000 2.36 0.00 45.36 4.94
289 290 4.556302 GCGTAGGCAGTAGTAATCTACCAC 60.556 50.000 1.75 0.00 45.36 4.16
290 291 3.567164 GCGTAGGCAGTAGTAATCTACCA 59.433 47.826 1.75 0.00 45.36 3.25
291 292 3.567164 TGCGTAGGCAGTAGTAATCTACC 59.433 47.826 5.89 0.00 46.21 3.18
292 293 4.825546 TGCGTAGGCAGTAGTAATCTAC 57.174 45.455 5.89 0.00 46.21 2.59
305 306 3.121544 GGTAATGTACTCTTGCGTAGGC 58.878 50.000 0.00 0.00 40.52 3.93
306 307 3.714391 GGGTAATGTACTCTTGCGTAGG 58.286 50.000 0.00 0.00 0.00 3.18
311 312 0.928229 CGCGGGTAATGTACTCTTGC 59.072 55.000 0.00 0.00 0.00 4.01
329 330 1.326213 ACATCTGGGCTCTCCACTCG 61.326 60.000 0.00 0.00 41.46 4.18
343 344 1.741706 CATGGCTCGCAAAGAACATCT 59.258 47.619 0.00 0.00 0.00 2.90
355 356 2.633657 GCGTATTGCCATGGCTCG 59.366 61.111 35.53 30.09 42.51 5.03
373 374 1.668419 ACTTTAGATGGATGCGTGGC 58.332 50.000 0.00 0.00 0.00 5.01
460 461 1.747355 CTCCCGGTCTTCGTTTAGCTA 59.253 52.381 0.00 0.00 37.11 3.32
464 465 3.967332 ATTTCTCCCGGTCTTCGTTTA 57.033 42.857 0.00 0.00 37.11 2.01
482 484 2.579207 ACGCAGACACGCACTATATT 57.421 45.000 0.00 0.00 36.19 1.28
500 502 0.452585 GGAGAGCGGAGTGAGTGTAC 59.547 60.000 0.00 0.00 0.00 2.90
582 588 1.043673 TTTCGGGGGTTTGGTTGGTG 61.044 55.000 0.00 0.00 0.00 4.17
607 644 1.351430 CGTTTCGCTTGCTCGGATGA 61.351 55.000 0.00 0.00 0.00 2.92
674 711 0.188342 AAGGCAAAAGCTGGGAAGGA 59.812 50.000 0.00 0.00 0.00 3.36
686 723 1.452145 AAAGGAGCGCGAAAGGCAAA 61.452 50.000 12.10 0.00 43.84 3.68
698 735 2.880890 TCAGTCAGCAAAAGAAAGGAGC 59.119 45.455 0.00 0.00 0.00 4.70
699 736 4.024218 CAGTCAGTCAGCAAAAGAAAGGAG 60.024 45.833 0.00 0.00 0.00 3.69
701 738 3.879295 TCAGTCAGTCAGCAAAAGAAAGG 59.121 43.478 0.00 0.00 0.00 3.11
709 1016 2.035832 TGAACGATCAGTCAGTCAGCAA 59.964 45.455 0.00 0.00 0.00 3.91
835 1142 3.707102 AGTTGAGCTAAGCTAAGTAGGGG 59.293 47.826 0.00 0.00 39.88 4.79
866 1173 0.546267 ACACACTGGAGAGGATGGCT 60.546 55.000 0.00 0.00 0.00 4.75
916 1224 2.340019 CTCGATCGACGGGAGTGAGAA 61.340 57.143 15.15 0.00 46.62 2.87
947 1255 2.187946 CGTGGAGGAGTGGATGGC 59.812 66.667 0.00 0.00 0.00 4.40
1552 1886 2.933495 TGTCACACTGTACTATCGGC 57.067 50.000 0.00 0.00 0.00 5.54
1553 1887 6.453791 CGAAATTTGTCACACTGTACTATCGG 60.454 42.308 0.00 0.00 0.00 4.18
1554 1888 6.453791 CCGAAATTTGTCACACTGTACTATCG 60.454 42.308 0.00 0.00 0.00 2.92
1555 1889 6.183360 CCCGAAATTTGTCACACTGTACTATC 60.183 42.308 0.00 0.00 0.00 2.08
1556 1890 5.642063 CCCGAAATTTGTCACACTGTACTAT 59.358 40.000 0.00 0.00 0.00 2.12
1557 1891 4.992319 CCCGAAATTTGTCACACTGTACTA 59.008 41.667 0.00 0.00 0.00 1.82
1558 1892 3.813166 CCCGAAATTTGTCACACTGTACT 59.187 43.478 0.00 0.00 0.00 2.73
1559 1893 3.608474 GCCCGAAATTTGTCACACTGTAC 60.608 47.826 0.00 0.00 0.00 2.90
1560 1894 2.550606 GCCCGAAATTTGTCACACTGTA 59.449 45.455 0.00 0.00 0.00 2.74
1561 1895 1.336755 GCCCGAAATTTGTCACACTGT 59.663 47.619 0.00 0.00 0.00 3.55
1562 1896 1.335872 GGCCCGAAATTTGTCACACTG 60.336 52.381 0.00 0.00 0.00 3.66
1563 1897 0.958822 GGCCCGAAATTTGTCACACT 59.041 50.000 0.00 0.00 0.00 3.55
1564 1898 0.671251 TGGCCCGAAATTTGTCACAC 59.329 50.000 0.00 0.00 0.00 3.82
1565 1899 0.958091 CTGGCCCGAAATTTGTCACA 59.042 50.000 0.00 0.00 0.00 3.58
1566 1900 0.388520 GCTGGCCCGAAATTTGTCAC 60.389 55.000 0.00 0.00 0.00 3.67
1567 1901 1.861542 CGCTGGCCCGAAATTTGTCA 61.862 55.000 0.00 0.00 0.00 3.58
1568 1902 1.154035 CGCTGGCCCGAAATTTGTC 60.154 57.895 0.00 0.00 0.00 3.18
1569 1903 1.862602 GACGCTGGCCCGAAATTTGT 61.863 55.000 8.49 0.00 0.00 2.83
1570 1904 1.154035 GACGCTGGCCCGAAATTTG 60.154 57.895 8.49 0.00 0.00 2.32
1571 1905 2.686816 CGACGCTGGCCCGAAATTT 61.687 57.895 8.49 0.00 0.00 1.82
1572 1906 3.124921 CGACGCTGGCCCGAAATT 61.125 61.111 8.49 0.00 0.00 1.82
1586 1920 1.658968 GAATGTTTCACACGTGCGAC 58.341 50.000 17.22 9.67 0.00 5.19
1627 1961 4.082408 CACCTGCAGAATGTTTCACATGAT 60.082 41.667 17.39 0.00 37.97 2.45
1628 1962 3.253921 CACCTGCAGAATGTTTCACATGA 59.746 43.478 17.39 0.00 37.97 3.07
1638 1972 0.742281 CTCCGTCCACCTGCAGAATG 60.742 60.000 17.39 13.04 40.87 2.67
1654 1988 1.968540 ACGCCAAAGAAGCTGCTCC 60.969 57.895 1.00 0.00 0.00 4.70
1766 2109 2.630889 TCTTCTCCCAGACCATGAGT 57.369 50.000 0.00 0.00 0.00 3.41
2129 2472 1.712018 CGTGCTGGATCTCCGTCGTA 61.712 60.000 0.00 0.00 39.43 3.43
2132 2475 2.105128 CCGTGCTGGATCTCCGTC 59.895 66.667 0.00 0.00 42.00 4.79
2811 3154 2.672961 TGTGACTACTGCACATAGCC 57.327 50.000 0.00 0.00 44.83 3.93
2851 3194 9.376075 CCTCCGTTCTATATAAATACGTCTAGA 57.624 37.037 0.00 0.00 0.00 2.43
2852 3195 8.610896 CCCTCCGTTCTATATAAATACGTCTAG 58.389 40.741 0.00 0.00 0.00 2.43
2853 3196 8.321353 TCCCTCCGTTCTATATAAATACGTCTA 58.679 37.037 0.00 0.00 0.00 2.59
2854 3197 7.170965 TCCCTCCGTTCTATATAAATACGTCT 58.829 38.462 0.00 0.00 0.00 4.18
2855 3198 7.120432 ACTCCCTCCGTTCTATATAAATACGTC 59.880 40.741 0.00 0.00 0.00 4.34
2856 3199 6.944862 ACTCCCTCCGTTCTATATAAATACGT 59.055 38.462 0.00 0.00 0.00 3.57
2857 3200 7.388460 ACTCCCTCCGTTCTATATAAATACG 57.612 40.000 0.00 0.00 0.00 3.06
2858 3201 8.394121 CGTACTCCCTCCGTTCTATATAAATAC 58.606 40.741 0.00 0.00 0.00 1.89
2859 3202 8.103305 ACGTACTCCCTCCGTTCTATATAAATA 58.897 37.037 0.00 0.00 0.00 1.40
2860 3203 6.944862 ACGTACTCCCTCCGTTCTATATAAAT 59.055 38.462 0.00 0.00 0.00 1.40
2861 3204 6.299141 ACGTACTCCCTCCGTTCTATATAAA 58.701 40.000 0.00 0.00 0.00 1.40
2862 3205 5.869579 ACGTACTCCCTCCGTTCTATATAA 58.130 41.667 0.00 0.00 0.00 0.98
2863 3206 5.489792 ACGTACTCCCTCCGTTCTATATA 57.510 43.478 0.00 0.00 0.00 0.86
2864 3207 4.363991 ACGTACTCCCTCCGTTCTATAT 57.636 45.455 0.00 0.00 0.00 0.86
2865 3208 3.845781 ACGTACTCCCTCCGTTCTATA 57.154 47.619 0.00 0.00 0.00 1.31
2866 3209 2.686915 CAACGTACTCCCTCCGTTCTAT 59.313 50.000 0.00 0.00 42.34 1.98
2867 3210 2.086869 CAACGTACTCCCTCCGTTCTA 58.913 52.381 0.00 0.00 42.34 2.10
2868 3211 0.886563 CAACGTACTCCCTCCGTTCT 59.113 55.000 0.00 0.00 42.34 3.01
2869 3212 0.108945 CCAACGTACTCCCTCCGTTC 60.109 60.000 0.00 0.00 42.34 3.95
2870 3213 0.829182 ACCAACGTACTCCCTCCGTT 60.829 55.000 0.00 0.00 44.81 4.44
2871 3214 0.829182 AACCAACGTACTCCCTCCGT 60.829 55.000 0.00 0.00 36.17 4.69
2872 3215 0.319405 AAACCAACGTACTCCCTCCG 59.681 55.000 0.00 0.00 0.00 4.63
2873 3216 2.148768 CAAAACCAACGTACTCCCTCC 58.851 52.381 0.00 0.00 0.00 4.30
2874 3217 2.148768 CCAAAACCAACGTACTCCCTC 58.851 52.381 0.00 0.00 0.00 4.30
2875 3218 1.770061 TCCAAAACCAACGTACTCCCT 59.230 47.619 0.00 0.00 0.00 4.20
2876 3219 2.148768 CTCCAAAACCAACGTACTCCC 58.851 52.381 0.00 0.00 0.00 4.30
2877 3220 3.116079 TCTCCAAAACCAACGTACTCC 57.884 47.619 0.00 0.00 0.00 3.85
2878 3221 6.980051 AATATCTCCAAAACCAACGTACTC 57.020 37.500 0.00 0.00 0.00 2.59
2879 3222 6.373495 GGAAATATCTCCAAAACCAACGTACT 59.627 38.462 0.00 0.00 35.36 2.73
2880 3223 6.373495 AGGAAATATCTCCAAAACCAACGTAC 59.627 38.462 0.00 0.00 38.02 3.67
2887 3230 8.459635 GTGTAGAAAGGAAATATCTCCAAAACC 58.540 37.037 0.00 0.00 38.02 3.27
2945 3288 5.618798 GCTCTCGCATTTCTTTCATATTTCG 59.381 40.000 0.00 0.00 35.78 3.46
3122 3465 7.996098 AAATGTGTACTATACTTTTGGTGCT 57.004 32.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.