Multiple sequence alignment - TraesCS2B01G166500

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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 TraesCS2B01G166500 chr2B 100.000 2310 0 0 673 2982 139345066 139347375 0.000000e+00 4266
1 TraesCS2B01G166500 chr2B 100.000 324 0 0 1 324 139344394 139344717 1.530000e-167 599
2 TraesCS2B01G166500 chr7B 97.023 974 29 0 673 1646 532148577 532149550 0.000000e+00 1639
3 TraesCS2B01G166500 chr7B 96.608 973 33 0 674 1646 69990327 69989355 0.000000e+00 1615
4 TraesCS2B01G166500 chr7B 98.352 728 12 0 1640 2367 532151410 532152137 0.000000e+00 1279
5 TraesCS2B01G166500 chr7B 97.940 728 15 0 1640 2367 69987492 69986765 0.000000e+00 1262
6 TraesCS2B01G166500 chr7B 95.560 518 21 1 1129 1646 679679232 679678717 0.000000e+00 828
7 TraesCS2B01G166500 chr7B 91.241 411 30 4 673 1077 679679653 679679243 3.360000e-154 555
8 TraesCS2B01G166500 chr7A 99.040 729 6 1 1640 2367 137843570 137844298 0.000000e+00 1306
9 TraesCS2B01G166500 chr7A 98.230 678 12 0 673 1350 137842424 137843101 0.000000e+00 1186
10 TraesCS2B01G166500 chr7A 91.824 795 44 6 673 1448 641312229 641313021 0.000000e+00 1088
11 TraesCS2B01G166500 chr7A 98.326 239 3 1 1407 1645 137843101 137843338 4.600000e-113 418
12 TraesCS2B01G166500 chr3A 97.649 723 17 0 673 1395 674334774 674335496 0.000000e+00 1242
13 TraesCS2B01G166500 chr1B 96.291 728 26 1 1640 2367 17703902 17703176 0.000000e+00 1194
14 TraesCS2B01G166500 chr1B 86.730 633 40 5 830 1456 17705119 17704525 0.000000e+00 664
15 TraesCS2B01G166500 chr7D 96.149 727 28 0 1640 2366 113749427 113748701 0.000000e+00 1188
16 TraesCS2B01G166500 chr6D 95.907 733 30 0 1640 2372 453935779 453935047 0.000000e+00 1188
17 TraesCS2B01G166500 chr6D 86.232 828 55 29 673 1460 453936939 453936131 0.000000e+00 843
18 TraesCS2B01G166500 chr6D 97.701 87 2 0 673 759 97260944 97260858 1.850000e-32 150
19 TraesCS2B01G166500 chr4D 96.016 728 28 1 1640 2367 97719833 97720559 0.000000e+00 1182
20 TraesCS2B01G166500 chr4D 85.283 829 59 35 673 1460 97718675 97719481 0.000000e+00 797
21 TraesCS2B01G166500 chr4D 94.118 85 5 0 886 970 97718942 97719026 2.410000e-26 130
22 TraesCS2B01G166500 chr5D 95.742 728 30 1 1640 2367 332219835 332219109 0.000000e+00 1171
23 TraesCS2B01G166500 chr5D 86.716 813 36 17 673 1460 332220952 332220187 0.000000e+00 837
24 TraesCS2B01G166500 chr3B 95.742 728 29 2 1640 2367 736664364 736665089 0.000000e+00 1171
25 TraesCS2B01G166500 chr2A 89.681 407 17 10 2371 2772 86905847 86906233 2.060000e-136 496
26 TraesCS2B01G166500 chr2A 86.517 267 28 6 1 263 86965591 86965853 1.350000e-73 287
27 TraesCS2B01G166500 chr2A 92.670 191 13 1 2793 2982 86907493 86907683 1.050000e-69 274
28 TraesCS2B01G166500 chr2D 85.156 384 41 8 2371 2749 86497728 86498100 2.170000e-101 379
29 TraesCS2B01G166500 chr2D 85.502 269 33 4 1 266 86497038 86497303 2.930000e-70 276
30 TraesCS2B01G166500 chr3D 86.296 270 29 7 1 266 611522989 611522724 1.350000e-73 287


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 TraesCS2B01G166500 chr2B 139344394 139347375 2981 False 2432.5 4266 100.000000 1 2982 2 chr2B.!!$F1 2981
1 TraesCS2B01G166500 chr7B 532148577 532152137 3560 False 1459.0 1639 97.687500 673 2367 2 chr7B.!!$F1 1694
2 TraesCS2B01G166500 chr7B 69986765 69990327 3562 True 1438.5 1615 97.274000 674 2367 2 chr7B.!!$R1 1693
3 TraesCS2B01G166500 chr7B 679678717 679679653 936 True 691.5 828 93.400500 673 1646 2 chr7B.!!$R2 973
4 TraesCS2B01G166500 chr7A 641312229 641313021 792 False 1088.0 1088 91.824000 673 1448 1 chr7A.!!$F1 775
5 TraesCS2B01G166500 chr7A 137842424 137844298 1874 False 970.0 1306 98.532000 673 2367 3 chr7A.!!$F2 1694
6 TraesCS2B01G166500 chr3A 674334774 674335496 722 False 1242.0 1242 97.649000 673 1395 1 chr3A.!!$F1 722
7 TraesCS2B01G166500 chr1B 17703176 17705119 1943 True 929.0 1194 91.510500 830 2367 2 chr1B.!!$R1 1537
8 TraesCS2B01G166500 chr7D 113748701 113749427 726 True 1188.0 1188 96.149000 1640 2366 1 chr7D.!!$R1 726
9 TraesCS2B01G166500 chr6D 453935047 453936939 1892 True 1015.5 1188 91.069500 673 2372 2 chr6D.!!$R2 1699
10 TraesCS2B01G166500 chr4D 97718675 97720559 1884 False 703.0 1182 91.805667 673 2367 3 chr4D.!!$F1 1694
11 TraesCS2B01G166500 chr5D 332219109 332220952 1843 True 1004.0 1171 91.229000 673 2367 2 chr5D.!!$R1 1694
12 TraesCS2B01G166500 chr3B 736664364 736665089 725 False 1171.0 1171 95.742000 1640 2367 1 chr3B.!!$F1 727
13 TraesCS2B01G166500 chr2A 86905847 86907683 1836 False 385.0 496 91.175500 2371 2982 2 chr2A.!!$F2 611
14 TraesCS2B01G166500 chr2D 86497038 86498100 1062 False 327.5 379 85.329000 1 2749 2 chr2D.!!$F1 2748

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
258 259 0.038435 TGCCGTTGTGAAATGCCATG 60.038 50.0 0.0 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 4337 1.047002 TGGCCCAAAATGTCCAACTG 58.953 50.0 0.0 0.0 0.0 3.16 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
24 25 3.391296 GTCTGGTGGGGAATGCTCTATTA 59.609 47.826 0.00 0.00 0.00 0.98
43 44 3.754766 GGGTGTTCCCGTAGTGATC 57.245 57.895 0.00 0.00 44.74 2.92
44 45 0.179119 GGGTGTTCCCGTAGTGATCG 60.179 60.000 0.00 0.00 44.74 3.69
45 46 0.813184 GGTGTTCCCGTAGTGATCGA 59.187 55.000 0.00 0.00 0.00 3.59
46 47 1.407979 GGTGTTCCCGTAGTGATCGAT 59.592 52.381 0.00 0.00 0.00 3.59
47 48 2.460918 GTGTTCCCGTAGTGATCGATG 58.539 52.381 0.54 0.00 0.00 3.84
48 49 2.097036 TGTTCCCGTAGTGATCGATGT 58.903 47.619 0.54 0.00 0.00 3.06
49 50 2.159296 TGTTCCCGTAGTGATCGATGTG 60.159 50.000 0.54 0.00 0.00 3.21
50 51 2.047002 TCCCGTAGTGATCGATGTGA 57.953 50.000 0.54 0.00 0.00 3.58
51 52 1.947456 TCCCGTAGTGATCGATGTGAG 59.053 52.381 0.54 0.00 0.00 3.51
52 53 1.676529 CCCGTAGTGATCGATGTGAGT 59.323 52.381 0.54 0.00 0.00 3.41
53 54 2.541794 CCCGTAGTGATCGATGTGAGTG 60.542 54.545 0.54 0.00 0.00 3.51
54 55 2.354821 CCGTAGTGATCGATGTGAGTGA 59.645 50.000 0.54 0.00 0.00 3.41
55 56 3.181500 CCGTAGTGATCGATGTGAGTGAA 60.181 47.826 0.54 0.00 0.00 3.18
56 57 4.498177 CCGTAGTGATCGATGTGAGTGAAT 60.498 45.833 0.54 0.00 0.00 2.57
57 58 4.672862 CGTAGTGATCGATGTGAGTGAATC 59.327 45.833 0.54 0.00 0.00 2.52
58 59 4.998671 AGTGATCGATGTGAGTGAATCT 57.001 40.909 0.54 0.00 0.00 2.40
59 60 5.336150 AGTGATCGATGTGAGTGAATCTT 57.664 39.130 0.54 0.00 0.00 2.40
60 61 5.728471 AGTGATCGATGTGAGTGAATCTTT 58.272 37.500 0.54 0.00 0.00 2.52
61 62 5.809562 AGTGATCGATGTGAGTGAATCTTTC 59.190 40.000 0.54 0.00 0.00 2.62
62 63 5.578336 GTGATCGATGTGAGTGAATCTTTCA 59.422 40.000 0.54 0.00 37.33 2.69
63 64 6.091305 GTGATCGATGTGAGTGAATCTTTCAA 59.909 38.462 0.54 0.00 42.15 2.69
64 65 6.312180 TGATCGATGTGAGTGAATCTTTCAAG 59.688 38.462 0.54 0.00 42.15 3.02
65 66 5.541845 TCGATGTGAGTGAATCTTTCAAGT 58.458 37.500 0.00 0.00 42.15 3.16
66 67 5.635280 TCGATGTGAGTGAATCTTTCAAGTC 59.365 40.000 0.00 0.00 42.15 3.01
67 68 5.163913 CGATGTGAGTGAATCTTTCAAGTCC 60.164 44.000 0.00 0.00 42.15 3.85
68 69 5.296151 TGTGAGTGAATCTTTCAAGTCCT 57.704 39.130 0.00 0.00 42.15 3.85
69 70 5.684704 TGTGAGTGAATCTTTCAAGTCCTT 58.315 37.500 0.00 0.00 42.15 3.36
70 71 6.122277 TGTGAGTGAATCTTTCAAGTCCTTT 58.878 36.000 0.00 0.00 42.15 3.11
71 72 6.603201 TGTGAGTGAATCTTTCAAGTCCTTTT 59.397 34.615 0.00 0.00 42.15 2.27
72 73 6.914757 GTGAGTGAATCTTTCAAGTCCTTTTG 59.085 38.462 0.00 0.00 42.15 2.44
73 74 6.828273 TGAGTGAATCTTTCAAGTCCTTTTGA 59.172 34.615 0.00 0.00 42.15 2.69
74 75 7.503566 TGAGTGAATCTTTCAAGTCCTTTTGAT 59.496 33.333 0.00 0.00 42.15 2.57
75 76 7.880105 AGTGAATCTTTCAAGTCCTTTTGATC 58.120 34.615 0.00 0.00 42.15 2.92
76 77 7.723172 AGTGAATCTTTCAAGTCCTTTTGATCT 59.277 33.333 0.00 0.00 42.15 2.75
77 78 7.806960 GTGAATCTTTCAAGTCCTTTTGATCTG 59.193 37.037 0.00 0.00 42.15 2.90
78 79 5.695851 TCTTTCAAGTCCTTTTGATCTGC 57.304 39.130 0.00 0.00 36.97 4.26
79 80 5.132502 TCTTTCAAGTCCTTTTGATCTGCA 58.867 37.500 0.00 0.00 36.97 4.41
80 81 5.593909 TCTTTCAAGTCCTTTTGATCTGCAA 59.406 36.000 0.00 0.00 36.97 4.08
81 82 5.850557 TTCAAGTCCTTTTGATCTGCAAA 57.149 34.783 0.00 0.00 44.38 3.68
90 91 4.979943 TTTGATCTGCAAAACACTGTGA 57.020 36.364 15.86 0.00 43.18 3.58
91 92 4.979943 TTGATCTGCAAAACACTGTGAA 57.020 36.364 15.86 0.00 32.46 3.18
92 93 5.518848 TTGATCTGCAAAACACTGTGAAT 57.481 34.783 15.86 0.00 32.46 2.57
93 94 6.631971 TTGATCTGCAAAACACTGTGAATA 57.368 33.333 15.86 0.00 32.46 1.75
94 95 6.822667 TGATCTGCAAAACACTGTGAATAT 57.177 33.333 15.86 0.00 0.00 1.28
95 96 7.218228 TGATCTGCAAAACACTGTGAATATT 57.782 32.000 15.86 1.27 0.00 1.28
96 97 8.334263 TGATCTGCAAAACACTGTGAATATTA 57.666 30.769 15.86 0.00 0.00 0.98
97 98 8.959548 TGATCTGCAAAACACTGTGAATATTAT 58.040 29.630 15.86 0.00 0.00 1.28
98 99 9.229784 GATCTGCAAAACACTGTGAATATTATG 57.770 33.333 15.86 4.77 0.00 1.90
99 100 7.537715 TCTGCAAAACACTGTGAATATTATGG 58.462 34.615 15.86 0.00 0.00 2.74
100 101 7.392953 TCTGCAAAACACTGTGAATATTATGGA 59.607 33.333 15.86 4.13 0.00 3.41
101 102 7.312154 TGCAAAACACTGTGAATATTATGGAC 58.688 34.615 15.86 0.00 0.00 4.02
102 103 7.176515 TGCAAAACACTGTGAATATTATGGACT 59.823 33.333 15.86 0.00 0.00 3.85
103 104 7.485913 GCAAAACACTGTGAATATTATGGACTG 59.514 37.037 15.86 0.45 0.00 3.51
104 105 8.729756 CAAAACACTGTGAATATTATGGACTGA 58.270 33.333 15.86 0.00 0.00 3.41
105 106 8.862325 AAACACTGTGAATATTATGGACTGAA 57.138 30.769 15.86 0.00 0.00 3.02
106 107 9.466497 AAACACTGTGAATATTATGGACTGAAT 57.534 29.630 15.86 0.00 0.00 2.57
174 175 5.181690 TGTGCTCCACATTGTTTAAGTTC 57.818 39.130 0.00 0.00 39.62 3.01
175 176 4.887071 TGTGCTCCACATTGTTTAAGTTCT 59.113 37.500 0.00 0.00 39.62 3.01
176 177 5.359576 TGTGCTCCACATTGTTTAAGTTCTT 59.640 36.000 0.00 0.00 39.62 2.52
177 178 5.687285 GTGCTCCACATTGTTTAAGTTCTTG 59.313 40.000 0.00 0.00 34.08 3.02
178 179 5.592282 TGCTCCACATTGTTTAAGTTCTTGA 59.408 36.000 0.00 0.00 0.00 3.02
179 180 5.915196 GCTCCACATTGTTTAAGTTCTTGAC 59.085 40.000 0.00 0.00 0.00 3.18
180 181 6.385649 TCCACATTGTTTAAGTTCTTGACC 57.614 37.500 0.00 0.00 0.00 4.02
181 182 5.888724 TCCACATTGTTTAAGTTCTTGACCA 59.111 36.000 0.00 0.00 0.00 4.02
182 183 6.549364 TCCACATTGTTTAAGTTCTTGACCAT 59.451 34.615 0.00 0.00 0.00 3.55
183 184 7.069331 TCCACATTGTTTAAGTTCTTGACCATT 59.931 33.333 0.00 0.00 0.00 3.16
184 185 7.710475 CCACATTGTTTAAGTTCTTGACCATTT 59.290 33.333 0.00 0.00 0.00 2.32
185 186 9.097257 CACATTGTTTAAGTTCTTGACCATTTT 57.903 29.630 0.00 0.00 0.00 1.82
186 187 9.665719 ACATTGTTTAAGTTCTTGACCATTTTT 57.334 25.926 0.00 0.00 0.00 1.94
187 188 9.919348 CATTGTTTAAGTTCTTGACCATTTTTG 57.081 29.630 0.00 0.00 0.00 2.44
188 189 9.665719 ATTGTTTAAGTTCTTGACCATTTTTGT 57.334 25.926 0.00 0.00 0.00 2.83
189 190 8.472683 TGTTTAAGTTCTTGACCATTTTTGTG 57.527 30.769 0.00 0.00 0.00 3.33
190 191 7.064016 TGTTTAAGTTCTTGACCATTTTTGTGC 59.936 33.333 0.00 0.00 0.00 4.57
191 192 5.343307 AAGTTCTTGACCATTTTTGTGCT 57.657 34.783 0.00 0.00 0.00 4.40
192 193 5.343307 AGTTCTTGACCATTTTTGTGCTT 57.657 34.783 0.00 0.00 0.00 3.91
193 194 6.463995 AGTTCTTGACCATTTTTGTGCTTA 57.536 33.333 0.00 0.00 0.00 3.09
194 195 7.054491 AGTTCTTGACCATTTTTGTGCTTAT 57.946 32.000 0.00 0.00 0.00 1.73
195 196 8.177119 AGTTCTTGACCATTTTTGTGCTTATA 57.823 30.769 0.00 0.00 0.00 0.98
196 197 8.299570 AGTTCTTGACCATTTTTGTGCTTATAG 58.700 33.333 0.00 0.00 0.00 1.31
197 198 7.759489 TCTTGACCATTTTTGTGCTTATAGT 57.241 32.000 0.00 0.00 0.00 2.12
198 199 8.177119 TCTTGACCATTTTTGTGCTTATAGTT 57.823 30.769 0.00 0.00 0.00 2.24
199 200 8.637986 TCTTGACCATTTTTGTGCTTATAGTTT 58.362 29.630 0.00 0.00 0.00 2.66
200 201 8.810652 TTGACCATTTTTGTGCTTATAGTTTC 57.189 30.769 0.00 0.00 0.00 2.78
201 202 7.946207 TGACCATTTTTGTGCTTATAGTTTCA 58.054 30.769 0.00 0.00 0.00 2.69
202 203 8.081633 TGACCATTTTTGTGCTTATAGTTTCAG 58.918 33.333 0.00 0.00 0.00 3.02
203 204 8.177119 ACCATTTTTGTGCTTATAGTTTCAGA 57.823 30.769 0.00 0.00 0.00 3.27
204 205 8.299570 ACCATTTTTGTGCTTATAGTTTCAGAG 58.700 33.333 0.00 0.00 0.00 3.35
205 206 8.299570 CCATTTTTGTGCTTATAGTTTCAGAGT 58.700 33.333 0.00 0.00 0.00 3.24
206 207 9.683069 CATTTTTGTGCTTATAGTTTCAGAGTT 57.317 29.630 0.00 0.00 0.00 3.01
207 208 9.899226 ATTTTTGTGCTTATAGTTTCAGAGTTC 57.101 29.630 0.00 0.00 0.00 3.01
208 209 8.677148 TTTTGTGCTTATAGTTTCAGAGTTCT 57.323 30.769 0.00 0.00 0.00 3.01
209 210 8.677148 TTTGTGCTTATAGTTTCAGAGTTCTT 57.323 30.769 0.00 0.00 0.00 2.52
210 211 8.677148 TTGTGCTTATAGTTTCAGAGTTCTTT 57.323 30.769 0.00 0.00 0.00 2.52
211 212 8.677148 TGTGCTTATAGTTTCAGAGTTCTTTT 57.323 30.769 0.00 0.00 0.00 2.27
212 213 9.120538 TGTGCTTATAGTTTCAGAGTTCTTTTT 57.879 29.630 0.00 0.00 0.00 1.94
236 237 7.784633 TTTTCCTTTTGCCTTCTACAATTTG 57.215 32.000 0.00 0.00 0.00 2.32
237 238 5.467035 TCCTTTTGCCTTCTACAATTTGG 57.533 39.130 0.78 0.00 0.00 3.28
238 239 5.144100 TCCTTTTGCCTTCTACAATTTGGA 58.856 37.500 0.78 0.00 0.00 3.53
239 240 5.779771 TCCTTTTGCCTTCTACAATTTGGAT 59.220 36.000 0.78 0.00 0.00 3.41
240 241 5.870978 CCTTTTGCCTTCTACAATTTGGATG 59.129 40.000 0.78 0.00 0.00 3.51
241 242 4.454728 TTGCCTTCTACAATTTGGATGC 57.545 40.909 0.78 0.00 0.00 3.91
242 243 2.760092 TGCCTTCTACAATTTGGATGCC 59.240 45.455 0.78 0.00 0.00 4.40
243 244 2.223572 GCCTTCTACAATTTGGATGCCG 60.224 50.000 0.78 0.00 0.00 5.69
244 245 3.016736 CCTTCTACAATTTGGATGCCGT 58.983 45.455 0.78 0.00 0.00 5.68
245 246 3.443681 CCTTCTACAATTTGGATGCCGTT 59.556 43.478 0.78 0.00 0.00 4.44
246 247 4.414852 CTTCTACAATTTGGATGCCGTTG 58.585 43.478 0.78 0.00 0.00 4.10
247 248 3.417101 TCTACAATTTGGATGCCGTTGT 58.583 40.909 0.78 0.00 36.94 3.32
248 249 2.437200 ACAATTTGGATGCCGTTGTG 57.563 45.000 0.78 0.00 32.30 3.33
249 250 1.959985 ACAATTTGGATGCCGTTGTGA 59.040 42.857 0.78 0.00 32.30 3.58
250 251 2.363680 ACAATTTGGATGCCGTTGTGAA 59.636 40.909 0.78 0.00 32.30 3.18
251 252 3.181471 ACAATTTGGATGCCGTTGTGAAA 60.181 39.130 0.78 0.00 32.30 2.69
252 253 3.959535 ATTTGGATGCCGTTGTGAAAT 57.040 38.095 0.00 0.00 0.00 2.17
253 254 2.721274 TTGGATGCCGTTGTGAAATG 57.279 45.000 0.00 0.00 0.00 2.32
254 255 0.243365 TGGATGCCGTTGTGAAATGC 59.757 50.000 0.00 0.00 0.00 3.56
255 256 0.458370 GGATGCCGTTGTGAAATGCC 60.458 55.000 0.00 0.00 0.00 4.40
256 257 0.243365 GATGCCGTTGTGAAATGCCA 59.757 50.000 0.00 0.00 0.00 4.92
257 258 0.896923 ATGCCGTTGTGAAATGCCAT 59.103 45.000 0.00 0.00 0.00 4.40
258 259 0.038435 TGCCGTTGTGAAATGCCATG 60.038 50.000 0.00 0.00 0.00 3.66
259 260 0.243365 GCCGTTGTGAAATGCCATGA 59.757 50.000 0.00 0.00 0.00 3.07
260 261 1.135024 GCCGTTGTGAAATGCCATGAT 60.135 47.619 0.00 0.00 0.00 2.45
261 262 2.801063 CCGTTGTGAAATGCCATGATC 58.199 47.619 0.00 0.00 0.00 2.92
262 263 2.424601 CCGTTGTGAAATGCCATGATCT 59.575 45.455 0.00 0.00 0.00 2.75
263 264 3.431856 CGTTGTGAAATGCCATGATCTG 58.568 45.455 0.00 0.00 0.00 2.90
264 265 3.127376 CGTTGTGAAATGCCATGATCTGA 59.873 43.478 0.00 0.00 0.00 3.27
265 266 4.379708 CGTTGTGAAATGCCATGATCTGAA 60.380 41.667 0.00 0.00 0.00 3.02
266 267 4.976224 TGTGAAATGCCATGATCTGAAG 57.024 40.909 0.00 0.00 0.00 3.02
267 268 4.338012 TGTGAAATGCCATGATCTGAAGT 58.662 39.130 0.00 0.00 0.00 3.01
268 269 4.768448 TGTGAAATGCCATGATCTGAAGTT 59.232 37.500 0.00 0.00 0.00 2.66
269 270 5.244402 TGTGAAATGCCATGATCTGAAGTTT 59.756 36.000 0.00 0.00 0.00 2.66
270 271 5.575606 GTGAAATGCCATGATCTGAAGTTTG 59.424 40.000 0.00 0.00 0.00 2.93
271 272 5.477637 TGAAATGCCATGATCTGAAGTTTGA 59.522 36.000 0.00 0.00 0.00 2.69
272 273 5.578005 AATGCCATGATCTGAAGTTTGAG 57.422 39.130 0.00 0.00 0.00 3.02
273 274 4.025040 TGCCATGATCTGAAGTTTGAGT 57.975 40.909 0.00 0.00 0.00 3.41
274 275 4.401022 TGCCATGATCTGAAGTTTGAGTT 58.599 39.130 0.00 0.00 0.00 3.01
275 276 4.828939 TGCCATGATCTGAAGTTTGAGTTT 59.171 37.500 0.00 0.00 0.00 2.66
276 277 5.159209 GCCATGATCTGAAGTTTGAGTTTG 58.841 41.667 0.00 0.00 0.00 2.93
277 278 5.048504 GCCATGATCTGAAGTTTGAGTTTGA 60.049 40.000 0.00 0.00 0.00 2.69
278 279 6.609533 CCATGATCTGAAGTTTGAGTTTGAG 58.390 40.000 0.00 0.00 0.00 3.02
279 280 6.349115 CCATGATCTGAAGTTTGAGTTTGAGG 60.349 42.308 0.00 0.00 0.00 3.86
280 281 4.516698 TGATCTGAAGTTTGAGTTTGAGGC 59.483 41.667 0.00 0.00 0.00 4.70
281 282 4.156455 TCTGAAGTTTGAGTTTGAGGCT 57.844 40.909 0.00 0.00 0.00 4.58
282 283 3.879295 TCTGAAGTTTGAGTTTGAGGCTG 59.121 43.478 0.00 0.00 0.00 4.85
283 284 3.620488 TGAAGTTTGAGTTTGAGGCTGT 58.380 40.909 0.00 0.00 0.00 4.40
284 285 4.016444 TGAAGTTTGAGTTTGAGGCTGTT 58.984 39.130 0.00 0.00 0.00 3.16
285 286 5.189928 TGAAGTTTGAGTTTGAGGCTGTTA 58.810 37.500 0.00 0.00 0.00 2.41
286 287 5.650266 TGAAGTTTGAGTTTGAGGCTGTTAA 59.350 36.000 0.00 0.00 0.00 2.01
287 288 6.151985 TGAAGTTTGAGTTTGAGGCTGTTAAA 59.848 34.615 0.00 0.00 0.00 1.52
288 289 5.891451 AGTTTGAGTTTGAGGCTGTTAAAC 58.109 37.500 0.00 0.78 35.19 2.01
289 290 4.545823 TTGAGTTTGAGGCTGTTAAACG 57.454 40.909 0.00 0.00 38.84 3.60
290 291 2.289547 TGAGTTTGAGGCTGTTAAACGC 59.710 45.455 0.00 3.63 38.84 4.84
291 292 1.263217 AGTTTGAGGCTGTTAAACGCG 59.737 47.619 3.53 3.53 38.84 6.01
292 293 1.262151 GTTTGAGGCTGTTAAACGCGA 59.738 47.619 15.93 0.00 0.00 5.87
293 294 1.803334 TTGAGGCTGTTAAACGCGAT 58.197 45.000 15.93 0.00 0.00 4.58
294 295 1.075542 TGAGGCTGTTAAACGCGATG 58.924 50.000 15.93 0.00 0.00 3.84
295 296 0.247695 GAGGCTGTTAAACGCGATGC 60.248 55.000 15.93 0.00 0.00 3.91
296 297 0.953471 AGGCTGTTAAACGCGATGCA 60.953 50.000 15.93 3.18 0.00 3.96
297 298 0.521242 GGCTGTTAAACGCGATGCAG 60.521 55.000 15.93 14.09 0.00 4.41
298 299 0.442310 GCTGTTAAACGCGATGCAGA 59.558 50.000 15.93 0.00 0.00 4.26
299 300 1.062587 GCTGTTAAACGCGATGCAGAT 59.937 47.619 15.93 0.00 0.00 2.90
300 301 2.284150 GCTGTTAAACGCGATGCAGATA 59.716 45.455 15.93 0.00 0.00 1.98
301 302 3.059597 GCTGTTAAACGCGATGCAGATAT 60.060 43.478 15.93 0.00 0.00 1.63
302 303 4.448891 CTGTTAAACGCGATGCAGATATG 58.551 43.478 15.93 0.00 0.00 1.78
303 304 3.218398 GTTAAACGCGATGCAGATATGC 58.782 45.455 15.93 5.09 0.00 3.14
305 306 2.095282 CGCGATGCAGATATGCGC 59.905 61.111 7.97 0.00 42.42 6.09
306 307 3.247046 GCGATGCAGATATGCGCA 58.753 55.556 14.96 14.96 46.19 6.09
307 308 1.132029 GCGATGCAGATATGCGCAG 59.868 57.895 18.32 2.01 46.19 5.18
308 309 1.287041 GCGATGCAGATATGCGCAGA 61.287 55.000 18.32 13.18 46.19 4.26
309 310 0.437678 CGATGCAGATATGCGCAGAC 59.562 55.000 18.32 9.73 42.37 3.51
310 311 1.505425 GATGCAGATATGCGCAGACA 58.495 50.000 18.32 5.79 42.37 3.41
311 312 1.869132 GATGCAGATATGCGCAGACAA 59.131 47.619 18.32 0.99 42.37 3.18
312 313 1.292992 TGCAGATATGCGCAGACAAG 58.707 50.000 18.32 6.92 37.69 3.16
313 314 0.041488 GCAGATATGCGCAGACAAGC 60.041 55.000 18.32 13.63 0.00 4.01
314 315 1.579698 CAGATATGCGCAGACAAGCT 58.420 50.000 18.32 6.51 0.00 3.74
1142 1229 3.809832 CAGCAGGTAAATAGTCCAATCCG 59.190 47.826 0.00 0.00 0.00 4.18
2083 4337 9.155975 CCTGTTGTAGGTATCTATTAATCATGC 57.844 37.037 0.00 0.00 42.00 4.06
2126 4380 3.243168 GGAATGCATTATTCAAGCAGCGA 60.243 43.478 12.97 0.00 45.70 4.93
2367 4621 1.140852 CAATTCCTGGATCCGCCACTA 59.859 52.381 7.39 0.00 43.33 2.74
2380 4634 3.577848 TCCGCCACTAGTTTACCAGTTTA 59.422 43.478 0.00 0.00 0.00 2.01
2381 4635 3.681417 CCGCCACTAGTTTACCAGTTTAC 59.319 47.826 0.00 0.00 0.00 2.01
2395 4649 4.226394 ACCAGTTTACCATGTACCATGCTA 59.774 41.667 0.00 0.00 0.00 3.49
2432 4688 9.453572 GTATTTATGCATCTATCCAAGGAATCA 57.546 33.333 0.19 0.00 0.00 2.57
2449 4705 6.735556 AGGAATCATGTACCTTCCAGATTTT 58.264 36.000 16.02 0.00 40.77 1.82
2484 4740 7.270757 TGCACAGTACAGATTTTATTGTTGT 57.729 32.000 0.00 0.00 0.00 3.32
2485 4741 7.138081 TGCACAGTACAGATTTTATTGTTGTG 58.862 34.615 0.00 0.00 38.30 3.33
2486 4742 7.138736 GCACAGTACAGATTTTATTGTTGTGT 58.861 34.615 0.00 0.00 37.89 3.72
2487 4743 7.647715 GCACAGTACAGATTTTATTGTTGTGTT 59.352 33.333 0.00 0.00 37.89 3.32
2488 4744 8.957028 CACAGTACAGATTTTATTGTTGTGTTG 58.043 33.333 0.00 0.00 34.07 3.33
2489 4745 8.682710 ACAGTACAGATTTTATTGTTGTGTTGT 58.317 29.630 0.00 0.00 0.00 3.32
2490 4746 9.515020 CAGTACAGATTTTATTGTTGTGTTGTT 57.485 29.630 0.00 0.00 0.00 2.83
2491 4747 9.515020 AGTACAGATTTTATTGTTGTGTTGTTG 57.485 29.630 0.00 0.00 0.00 3.33
2532 4789 8.721478 GGCAACACATGAATTCGATAACTATAT 58.279 33.333 0.00 0.00 0.00 0.86
2590 4847 2.717639 ACTGGTGCTCTGTTTTCTGT 57.282 45.000 0.00 0.00 0.00 3.41
2609 4866 5.636837 TCTGTTCTTTGGTTCTTTTTGTCG 58.363 37.500 0.00 0.00 0.00 4.35
2627 4884 2.088423 TCGTTAAATTCCGCATGGCTT 58.912 42.857 0.00 0.00 34.14 4.35
2642 4902 4.813697 GCATGGCTTGGTTTTGTTTCTAAA 59.186 37.500 2.33 0.00 0.00 1.85
2717 4977 2.162681 GCTGACCTGTTGCCAGTTTAT 58.837 47.619 0.00 0.00 36.95 1.40
2772 5032 2.627945 CCTACGGCTGCTAATCAAACA 58.372 47.619 0.00 0.00 0.00 2.83
2773 5033 3.206150 CCTACGGCTGCTAATCAAACAT 58.794 45.455 0.00 0.00 0.00 2.71
2774 5034 3.002656 CCTACGGCTGCTAATCAAACATG 59.997 47.826 0.00 0.00 0.00 3.21
2781 6048 6.072838 CGGCTGCTAATCAAACATGAGAATAT 60.073 38.462 0.00 0.00 0.00 1.28
2782 6049 7.521099 CGGCTGCTAATCAAACATGAGAATATT 60.521 37.037 0.00 0.00 0.00 1.28
2811 6311 6.406400 CCTGTAAGAGGAGAGTGTTAATCTGG 60.406 46.154 0.00 0.00 46.33 3.86
2816 6316 5.723887 AGAGGAGAGTGTTAATCTGGAACAT 59.276 40.000 0.00 0.00 38.94 2.71
2844 6344 3.584406 TCTGCTGAGAGAACAAGTAGC 57.416 47.619 0.00 0.00 0.00 3.58
2872 6372 4.332828 AGAGAAGAAATTAACCAACCCCG 58.667 43.478 0.00 0.00 0.00 5.73
2873 6373 3.427573 AGAAGAAATTAACCAACCCCGG 58.572 45.455 0.00 0.00 0.00 5.73
2890 6390 3.729698 GGTTGCCGCCGGTTGTAC 61.730 66.667 4.45 0.00 0.00 2.90
2898 6398 2.084681 GCCGGTTGTACACGTCGAG 61.085 63.158 1.90 0.00 0.00 4.04
2901 6401 0.935831 CGGTTGTACACGTCGAGCAA 60.936 55.000 0.00 0.00 0.00 3.91
2909 6409 1.269723 ACACGTCGAGCAAAGATCTCA 59.730 47.619 0.00 0.00 0.00 3.27
2920 6420 2.638556 AAGATCTCACTGTTCCGACG 57.361 50.000 0.00 0.00 0.00 5.12
2926 6426 0.591659 TCACTGTTCCGACGACTCTG 59.408 55.000 0.00 0.00 0.00 3.35
2953 6453 4.462483 TGCTGATCCCAGAATTTGTTTACC 59.538 41.667 0.00 0.00 43.02 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.040412 CCCTAATAGAGCATTCCCCACC 59.960 54.545 0.00 0.00 0.00 4.61
9 10 2.711547 ACACCCTAATAGAGCATTCCCC 59.288 50.000 0.00 0.00 0.00 4.81
10 11 4.390264 GAACACCCTAATAGAGCATTCCC 58.610 47.826 0.00 0.00 0.00 3.97
24 25 1.192428 GATCACTACGGGAACACCCT 58.808 55.000 0.00 0.00 41.43 4.34
35 36 5.826586 AGATTCACTCACATCGATCACTAC 58.173 41.667 0.00 0.00 0.00 2.73
40 41 6.312426 ACTTGAAAGATTCACTCACATCGATC 59.688 38.462 0.00 0.00 39.87 3.69
41 42 6.169094 ACTTGAAAGATTCACTCACATCGAT 58.831 36.000 0.00 0.00 39.87 3.59
42 43 5.541845 ACTTGAAAGATTCACTCACATCGA 58.458 37.500 0.00 0.00 39.87 3.59
43 44 5.163913 GGACTTGAAAGATTCACTCACATCG 60.164 44.000 0.00 0.00 39.87 3.84
44 45 5.936956 AGGACTTGAAAGATTCACTCACATC 59.063 40.000 0.00 0.00 39.87 3.06
45 46 5.874093 AGGACTTGAAAGATTCACTCACAT 58.126 37.500 0.00 0.00 39.87 3.21
46 47 5.296151 AGGACTTGAAAGATTCACTCACA 57.704 39.130 0.00 0.00 39.87 3.58
47 48 6.625873 AAAGGACTTGAAAGATTCACTCAC 57.374 37.500 0.00 0.00 39.87 3.51
48 49 6.828273 TCAAAAGGACTTGAAAGATTCACTCA 59.172 34.615 0.00 0.00 39.87 3.41
49 50 7.264373 TCAAAAGGACTTGAAAGATTCACTC 57.736 36.000 0.00 0.00 39.87 3.51
50 51 7.723172 AGATCAAAAGGACTTGAAAGATTCACT 59.277 33.333 0.00 0.00 39.87 3.41
51 52 7.806960 CAGATCAAAAGGACTTGAAAGATTCAC 59.193 37.037 0.00 0.00 39.87 3.18
52 53 7.522725 GCAGATCAAAAGGACTTGAAAGATTCA 60.523 37.037 0.00 0.00 38.75 2.57
53 54 6.805760 GCAGATCAAAAGGACTTGAAAGATTC 59.194 38.462 0.00 0.00 38.75 2.52
54 55 6.266103 TGCAGATCAAAAGGACTTGAAAGATT 59.734 34.615 0.00 0.00 38.75 2.40
55 56 5.771666 TGCAGATCAAAAGGACTTGAAAGAT 59.228 36.000 0.00 0.00 38.75 2.40
56 57 5.132502 TGCAGATCAAAAGGACTTGAAAGA 58.867 37.500 0.00 0.00 38.75 2.52
57 58 5.443185 TGCAGATCAAAAGGACTTGAAAG 57.557 39.130 0.00 0.00 38.75 2.62
58 59 5.850557 TTGCAGATCAAAAGGACTTGAAA 57.149 34.783 0.00 0.00 38.75 2.69
59 60 5.850557 TTTGCAGATCAAAAGGACTTGAA 57.149 34.783 0.00 0.00 41.36 2.69
60 61 5.850557 TTTTGCAGATCAAAAGGACTTGA 57.149 34.783 0.00 0.00 46.44 3.02
69 70 4.979943 TCACAGTGTTTTGCAGATCAAA 57.020 36.364 0.00 0.00 42.50 2.69
70 71 4.979943 TTCACAGTGTTTTGCAGATCAA 57.020 36.364 0.00 0.00 0.00 2.57
71 72 6.822667 ATATTCACAGTGTTTTGCAGATCA 57.177 33.333 0.00 0.00 0.00 2.92
72 73 9.229784 CATAATATTCACAGTGTTTTGCAGATC 57.770 33.333 0.00 0.00 0.00 2.75
73 74 8.192774 CCATAATATTCACAGTGTTTTGCAGAT 58.807 33.333 0.00 0.00 0.00 2.90
74 75 7.392953 TCCATAATATTCACAGTGTTTTGCAGA 59.607 33.333 0.00 0.00 0.00 4.26
75 76 7.485913 GTCCATAATATTCACAGTGTTTTGCAG 59.514 37.037 0.00 0.00 0.00 4.41
76 77 7.176515 AGTCCATAATATTCACAGTGTTTTGCA 59.823 33.333 0.00 0.00 0.00 4.08
77 78 7.485913 CAGTCCATAATATTCACAGTGTTTTGC 59.514 37.037 0.00 0.00 0.00 3.68
78 79 8.729756 TCAGTCCATAATATTCACAGTGTTTTG 58.270 33.333 0.00 0.00 0.00 2.44
79 80 8.862325 TCAGTCCATAATATTCACAGTGTTTT 57.138 30.769 0.00 0.00 0.00 2.43
80 81 8.862325 TTCAGTCCATAATATTCACAGTGTTT 57.138 30.769 0.00 0.00 0.00 2.83
153 154 5.438761 AGAACTTAAACAATGTGGAGCAC 57.561 39.130 0.00 0.00 34.56 4.40
154 155 5.592282 TCAAGAACTTAAACAATGTGGAGCA 59.408 36.000 0.00 0.00 0.00 4.26
155 156 5.915196 GTCAAGAACTTAAACAATGTGGAGC 59.085 40.000 0.00 0.00 0.00 4.70
156 157 6.039270 TGGTCAAGAACTTAAACAATGTGGAG 59.961 38.462 0.00 0.00 0.00 3.86
157 158 5.888724 TGGTCAAGAACTTAAACAATGTGGA 59.111 36.000 0.00 0.00 0.00 4.02
158 159 6.142818 TGGTCAAGAACTTAAACAATGTGG 57.857 37.500 0.00 0.00 0.00 4.17
159 160 8.647143 AAATGGTCAAGAACTTAAACAATGTG 57.353 30.769 0.00 0.00 0.00 3.21
160 161 9.665719 AAAAATGGTCAAGAACTTAAACAATGT 57.334 25.926 0.00 0.00 0.00 2.71
161 162 9.919348 CAAAAATGGTCAAGAACTTAAACAATG 57.081 29.630 0.00 0.00 0.00 2.82
162 163 9.665719 ACAAAAATGGTCAAGAACTTAAACAAT 57.334 25.926 0.00 0.00 0.00 2.71
163 164 8.930760 CACAAAAATGGTCAAGAACTTAAACAA 58.069 29.630 0.00 0.00 0.00 2.83
164 165 7.064016 GCACAAAAATGGTCAAGAACTTAAACA 59.936 33.333 0.00 0.00 0.00 2.83
165 166 7.277760 AGCACAAAAATGGTCAAGAACTTAAAC 59.722 33.333 0.00 0.00 0.00 2.01
166 167 7.327214 AGCACAAAAATGGTCAAGAACTTAAA 58.673 30.769 0.00 0.00 0.00 1.52
167 168 6.872920 AGCACAAAAATGGTCAAGAACTTAA 58.127 32.000 0.00 0.00 0.00 1.85
168 169 6.463995 AGCACAAAAATGGTCAAGAACTTA 57.536 33.333 0.00 0.00 0.00 2.24
169 170 5.343307 AGCACAAAAATGGTCAAGAACTT 57.657 34.783 0.00 0.00 0.00 2.66
170 171 5.343307 AAGCACAAAAATGGTCAAGAACT 57.657 34.783 0.00 0.00 0.00 3.01
171 172 8.082242 ACTATAAGCACAAAAATGGTCAAGAAC 58.918 33.333 0.00 0.00 0.00 3.01
172 173 8.177119 ACTATAAGCACAAAAATGGTCAAGAA 57.823 30.769 0.00 0.00 0.00 2.52
173 174 7.759489 ACTATAAGCACAAAAATGGTCAAGA 57.241 32.000 0.00 0.00 0.00 3.02
174 175 8.816640 AAACTATAAGCACAAAAATGGTCAAG 57.183 30.769 0.00 0.00 0.00 3.02
175 176 8.417106 TGAAACTATAAGCACAAAAATGGTCAA 58.583 29.630 0.00 0.00 0.00 3.18
176 177 7.946207 TGAAACTATAAGCACAAAAATGGTCA 58.054 30.769 0.00 0.00 0.00 4.02
177 178 8.296713 TCTGAAACTATAAGCACAAAAATGGTC 58.703 33.333 0.00 0.00 0.00 4.02
178 179 8.177119 TCTGAAACTATAAGCACAAAAATGGT 57.823 30.769 0.00 0.00 0.00 3.55
179 180 8.299570 ACTCTGAAACTATAAGCACAAAAATGG 58.700 33.333 0.00 0.00 0.00 3.16
180 181 9.683069 AACTCTGAAACTATAAGCACAAAAATG 57.317 29.630 0.00 0.00 0.00 2.32
181 182 9.899226 GAACTCTGAAACTATAAGCACAAAAAT 57.101 29.630 0.00 0.00 0.00 1.82
182 183 9.120538 AGAACTCTGAAACTATAAGCACAAAAA 57.879 29.630 0.00 0.00 0.00 1.94
183 184 8.677148 AGAACTCTGAAACTATAAGCACAAAA 57.323 30.769 0.00 0.00 0.00 2.44
184 185 8.677148 AAGAACTCTGAAACTATAAGCACAAA 57.323 30.769 0.00 0.00 0.00 2.83
185 186 8.677148 AAAGAACTCTGAAACTATAAGCACAA 57.323 30.769 0.00 0.00 0.00 3.33
186 187 8.677148 AAAAGAACTCTGAAACTATAAGCACA 57.323 30.769 0.00 0.00 0.00 4.57
211 212 7.281999 CCAAATTGTAGAAGGCAAAAGGAAAAA 59.718 33.333 0.00 0.00 0.00 1.94
212 213 6.765512 CCAAATTGTAGAAGGCAAAAGGAAAA 59.234 34.615 0.00 0.00 0.00 2.29
213 214 6.098982 TCCAAATTGTAGAAGGCAAAAGGAAA 59.901 34.615 0.00 0.00 0.00 3.13
214 215 5.600484 TCCAAATTGTAGAAGGCAAAAGGAA 59.400 36.000 0.00 0.00 0.00 3.36
215 216 5.144100 TCCAAATTGTAGAAGGCAAAAGGA 58.856 37.500 0.00 0.00 0.00 3.36
216 217 5.467035 TCCAAATTGTAGAAGGCAAAAGG 57.533 39.130 0.00 0.00 0.00 3.11
217 218 5.349543 GCATCCAAATTGTAGAAGGCAAAAG 59.650 40.000 0.00 0.00 0.00 2.27
218 219 5.237048 GCATCCAAATTGTAGAAGGCAAAA 58.763 37.500 0.00 0.00 0.00 2.44
219 220 4.322650 GGCATCCAAATTGTAGAAGGCAAA 60.323 41.667 0.00 0.00 0.00 3.68
220 221 3.195396 GGCATCCAAATTGTAGAAGGCAA 59.805 43.478 0.00 0.00 0.00 4.52
221 222 2.760092 GGCATCCAAATTGTAGAAGGCA 59.240 45.455 0.00 0.00 0.00 4.75
222 223 2.223572 CGGCATCCAAATTGTAGAAGGC 60.224 50.000 0.00 0.00 0.00 4.35
223 224 3.016736 ACGGCATCCAAATTGTAGAAGG 58.983 45.455 0.00 0.00 0.00 3.46
224 225 4.082787 ACAACGGCATCCAAATTGTAGAAG 60.083 41.667 0.00 0.00 31.88 2.85
225 226 3.823873 ACAACGGCATCCAAATTGTAGAA 59.176 39.130 0.00 0.00 31.88 2.10
226 227 3.190327 CACAACGGCATCCAAATTGTAGA 59.810 43.478 0.00 0.00 32.39 2.59
227 228 3.190327 TCACAACGGCATCCAAATTGTAG 59.810 43.478 0.00 0.00 32.39 2.74
228 229 3.149981 TCACAACGGCATCCAAATTGTA 58.850 40.909 0.00 0.00 32.39 2.41
229 230 1.959985 TCACAACGGCATCCAAATTGT 59.040 42.857 0.00 0.00 33.86 2.71
230 231 2.721274 TCACAACGGCATCCAAATTG 57.279 45.000 0.00 0.00 0.00 2.32
231 232 3.742433 TTTCACAACGGCATCCAAATT 57.258 38.095 0.00 0.00 0.00 1.82
232 233 3.587923 CATTTCACAACGGCATCCAAAT 58.412 40.909 0.00 0.00 0.00 2.32
233 234 2.865670 GCATTTCACAACGGCATCCAAA 60.866 45.455 0.00 0.00 0.00 3.28
234 235 1.336702 GCATTTCACAACGGCATCCAA 60.337 47.619 0.00 0.00 0.00 3.53
235 236 0.243365 GCATTTCACAACGGCATCCA 59.757 50.000 0.00 0.00 0.00 3.41
236 237 0.458370 GGCATTTCACAACGGCATCC 60.458 55.000 0.00 0.00 0.00 3.51
237 238 0.243365 TGGCATTTCACAACGGCATC 59.757 50.000 0.00 0.00 0.00 3.91
238 239 0.896923 ATGGCATTTCACAACGGCAT 59.103 45.000 0.00 0.00 39.55 4.40
239 240 0.038435 CATGGCATTTCACAACGGCA 60.038 50.000 0.00 0.00 38.39 5.69
240 241 0.243365 TCATGGCATTTCACAACGGC 59.757 50.000 0.00 0.00 0.00 5.68
241 242 2.424601 AGATCATGGCATTTCACAACGG 59.575 45.455 0.00 0.00 0.00 4.44
242 243 3.127376 TCAGATCATGGCATTTCACAACG 59.873 43.478 0.00 0.00 0.00 4.10
243 244 4.707030 TCAGATCATGGCATTTCACAAC 57.293 40.909 0.00 0.00 0.00 3.32
244 245 4.768448 ACTTCAGATCATGGCATTTCACAA 59.232 37.500 0.00 0.00 0.00 3.33
245 246 4.338012 ACTTCAGATCATGGCATTTCACA 58.662 39.130 0.00 0.00 0.00 3.58
246 247 4.978083 ACTTCAGATCATGGCATTTCAC 57.022 40.909 0.00 0.00 0.00 3.18
247 248 5.477637 TCAAACTTCAGATCATGGCATTTCA 59.522 36.000 0.00 0.00 0.00 2.69
248 249 5.957798 TCAAACTTCAGATCATGGCATTTC 58.042 37.500 0.00 0.00 0.00 2.17
249 250 5.479375 ACTCAAACTTCAGATCATGGCATTT 59.521 36.000 0.00 0.00 0.00 2.32
250 251 5.014858 ACTCAAACTTCAGATCATGGCATT 58.985 37.500 0.00 0.00 0.00 3.56
251 252 4.597004 ACTCAAACTTCAGATCATGGCAT 58.403 39.130 0.00 0.00 0.00 4.40
252 253 4.025040 ACTCAAACTTCAGATCATGGCA 57.975 40.909 0.00 0.00 0.00 4.92
253 254 5.048504 TCAAACTCAAACTTCAGATCATGGC 60.049 40.000 0.00 0.00 0.00 4.40
254 255 6.349115 CCTCAAACTCAAACTTCAGATCATGG 60.349 42.308 0.00 0.00 0.00 3.66
255 256 6.609533 CCTCAAACTCAAACTTCAGATCATG 58.390 40.000 0.00 0.00 0.00 3.07
256 257 5.182760 GCCTCAAACTCAAACTTCAGATCAT 59.817 40.000 0.00 0.00 0.00 2.45
257 258 4.516698 GCCTCAAACTCAAACTTCAGATCA 59.483 41.667 0.00 0.00 0.00 2.92
258 259 4.759183 AGCCTCAAACTCAAACTTCAGATC 59.241 41.667 0.00 0.00 0.00 2.75
259 260 4.518211 CAGCCTCAAACTCAAACTTCAGAT 59.482 41.667 0.00 0.00 0.00 2.90
260 261 3.879295 CAGCCTCAAACTCAAACTTCAGA 59.121 43.478 0.00 0.00 0.00 3.27
261 262 3.629398 ACAGCCTCAAACTCAAACTTCAG 59.371 43.478 0.00 0.00 0.00 3.02
262 263 3.620488 ACAGCCTCAAACTCAAACTTCA 58.380 40.909 0.00 0.00 0.00 3.02
263 264 4.639135 AACAGCCTCAAACTCAAACTTC 57.361 40.909 0.00 0.00 0.00 3.01
264 265 6.330278 GTTTAACAGCCTCAAACTCAAACTT 58.670 36.000 0.00 0.00 31.08 2.66
265 266 5.448632 CGTTTAACAGCCTCAAACTCAAACT 60.449 40.000 0.00 0.00 31.47 2.66
266 267 4.733405 CGTTTAACAGCCTCAAACTCAAAC 59.267 41.667 0.00 0.00 31.47 2.93
267 268 4.732355 GCGTTTAACAGCCTCAAACTCAAA 60.732 41.667 0.00 0.00 31.47 2.69
268 269 3.242936 GCGTTTAACAGCCTCAAACTCAA 60.243 43.478 0.00 0.00 31.47 3.02
269 270 2.289547 GCGTTTAACAGCCTCAAACTCA 59.710 45.455 0.00 0.00 31.47 3.41
270 271 2.661979 CGCGTTTAACAGCCTCAAACTC 60.662 50.000 0.00 0.00 31.47 3.01
271 272 1.263217 CGCGTTTAACAGCCTCAAACT 59.737 47.619 0.00 0.00 31.47 2.66
272 273 1.262151 TCGCGTTTAACAGCCTCAAAC 59.738 47.619 5.77 0.00 0.00 2.93
273 274 1.584175 TCGCGTTTAACAGCCTCAAA 58.416 45.000 5.77 0.00 0.00 2.69
274 275 1.463056 CATCGCGTTTAACAGCCTCAA 59.537 47.619 5.77 0.00 0.00 3.02
275 276 1.075542 CATCGCGTTTAACAGCCTCA 58.924 50.000 5.77 0.00 0.00 3.86
276 277 0.247695 GCATCGCGTTTAACAGCCTC 60.248 55.000 5.77 0.00 0.00 4.70
277 278 0.953471 TGCATCGCGTTTAACAGCCT 60.953 50.000 5.77 0.00 0.00 4.58
278 279 0.521242 CTGCATCGCGTTTAACAGCC 60.521 55.000 5.77 0.00 0.00 4.85
279 280 0.442310 TCTGCATCGCGTTTAACAGC 59.558 50.000 5.77 0.00 0.00 4.40
280 281 4.448891 CATATCTGCATCGCGTTTAACAG 58.551 43.478 5.77 8.42 0.00 3.16
281 282 4.451379 CATATCTGCATCGCGTTTAACA 57.549 40.909 5.77 0.00 0.00 2.41
294 295 0.041488 GCTTGTCTGCGCATATCTGC 60.041 55.000 12.24 9.89 45.31 4.26
295 296 1.260825 CAGCTTGTCTGCGCATATCTG 59.739 52.381 12.24 9.05 35.78 2.90
296 297 1.137675 TCAGCTTGTCTGCGCATATCT 59.862 47.619 12.24 0.00 42.56 1.98
297 298 1.526041 CTCAGCTTGTCTGCGCATATC 59.474 52.381 12.24 5.01 42.56 1.63
298 299 1.137675 TCTCAGCTTGTCTGCGCATAT 59.862 47.619 12.24 0.00 42.56 1.78
299 300 0.532115 TCTCAGCTTGTCTGCGCATA 59.468 50.000 12.24 0.00 42.56 3.14
300 301 0.107800 ATCTCAGCTTGTCTGCGCAT 60.108 50.000 12.24 0.00 42.56 4.73
301 302 1.017701 CATCTCAGCTTGTCTGCGCA 61.018 55.000 10.98 10.98 42.56 6.09
302 303 1.703438 CCATCTCAGCTTGTCTGCGC 61.703 60.000 0.00 0.00 42.56 6.09
303 304 0.108472 TCCATCTCAGCTTGTCTGCG 60.108 55.000 0.00 0.00 42.56 5.18
304 305 1.654317 CTCCATCTCAGCTTGTCTGC 58.346 55.000 0.00 0.00 42.56 4.26
1142 1229 5.411053 AGCTTGAGATTCAGTAGCAAAGAAC 59.589 40.000 5.77 0.00 33.78 3.01
2083 4337 1.047002 TGGCCCAAAATGTCCAACTG 58.953 50.000 0.00 0.00 0.00 3.16
2126 4380 5.418209 ACGCATAACTACTAACTTGGACTCT 59.582 40.000 0.00 0.00 0.00 3.24
2367 4621 6.190346 TGGTACATGGTAAACTGGTAAACT 57.810 37.500 0.00 0.00 0.00 2.66
2449 4705 9.836864 AAATCTGTACTGTGCAAATATATGAGA 57.163 29.630 0.00 0.00 0.00 3.27
2484 4740 5.861251 GCCATGATCGTTTATTTCAACAACA 59.139 36.000 0.00 0.00 0.00 3.33
2485 4741 5.861251 TGCCATGATCGTTTATTTCAACAAC 59.139 36.000 0.00 0.00 0.00 3.32
2486 4742 6.018589 TGCCATGATCGTTTATTTCAACAA 57.981 33.333 0.00 0.00 0.00 2.83
2487 4743 5.635417 TGCCATGATCGTTTATTTCAACA 57.365 34.783 0.00 0.00 0.00 3.33
2488 4744 5.861251 TGTTGCCATGATCGTTTATTTCAAC 59.139 36.000 0.00 0.00 0.00 3.18
2489 4745 5.861251 GTGTTGCCATGATCGTTTATTTCAA 59.139 36.000 0.00 0.00 0.00 2.69
2490 4746 5.048434 TGTGTTGCCATGATCGTTTATTTCA 60.048 36.000 0.00 0.00 0.00 2.69
2491 4747 5.398169 TGTGTTGCCATGATCGTTTATTTC 58.602 37.500 0.00 0.00 0.00 2.17
2532 4789 3.565764 ATGAGGCTGCAGCTGTAATAA 57.434 42.857 35.82 16.21 41.70 1.40
2533 4790 4.635223 CTTATGAGGCTGCAGCTGTAATA 58.365 43.478 35.82 22.64 41.70 0.98
2534 4791 3.474600 CTTATGAGGCTGCAGCTGTAAT 58.525 45.455 35.82 23.61 41.70 1.89
2558 4815 2.977405 CACCAGTTCTTGTGCTTAGC 57.023 50.000 0.00 0.00 0.00 3.09
2590 4847 8.989653 ATTTAACGACAAAAAGAACCAAAGAA 57.010 26.923 0.00 0.00 0.00 2.52
2609 4866 2.094234 ACCAAGCCATGCGGAATTTAAC 60.094 45.455 0.00 0.00 0.00 2.01
2682 4942 5.536161 ACAGGTCAGCAATAACAAATGACTT 59.464 36.000 3.91 0.00 40.07 3.01
2684 4944 5.376854 ACAGGTCAGCAATAACAAATGAC 57.623 39.130 0.00 0.00 39.59 3.06
2781 6048 9.710818 ATTAACACTCTCCTCTTACAGGTATAA 57.289 33.333 0.00 0.00 43.95 0.98
2782 6049 9.352191 GATTAACACTCTCCTCTTACAGGTATA 57.648 37.037 0.00 0.00 43.95 1.47
2791 6058 5.544176 TGTTCCAGATTAACACTCTCCTCTT 59.456 40.000 0.00 0.00 32.07 2.85
2829 6329 6.493802 TCTCTTTTAGGCTACTTGTTCTCTCA 59.506 38.462 0.00 0.00 0.00 3.27
2844 6344 8.304596 GGGTTGGTTAATTTCTTCTCTTTTAGG 58.695 37.037 0.00 0.00 0.00 2.69
2873 6373 3.729698 GTACAACCGGCGGCAACC 61.730 66.667 28.71 6.65 0.00 3.77
2890 6390 1.651138 GTGAGATCTTTGCTCGACGTG 59.349 52.381 0.00 0.00 35.15 4.49
2898 6398 2.413453 GTCGGAACAGTGAGATCTTTGC 59.587 50.000 0.00 0.00 0.00 3.68
2901 6401 2.095161 GTCGTCGGAACAGTGAGATCTT 60.095 50.000 0.00 0.00 0.00 2.40
2909 6409 1.957562 CCAGAGTCGTCGGAACAGT 59.042 57.895 0.00 0.00 0.00 3.55
2920 6420 0.534652 GGGATCAGCATGCCAGAGTC 60.535 60.000 15.66 11.58 40.33 3.36
2926 6426 1.700955 AATTCTGGGATCAGCATGCC 58.299 50.000 15.66 0.00 41.02 4.40


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

AutoCloner maintained by Alex Coulton.