Multiple sequence alignment - TraesCS3B01G482700

Loading Multiple Alignment...

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 TraesCS3B01G482700 chr3B 100.000 2681 0 0 1 2681 729721463 729718783 0.000000e+00 4951
1 TraesCS3B01G482700 chr3B 85.382 301 36 8 287 582 812336550 812336847 3.350000e-79 305
2 TraesCS3B01G482700 chr3A 88.185 1515 108 23 285 1759 687101871 687100388 0.000000e+00 1740
3 TraesCS3B01G482700 chr4B 94.158 736 33 7 1950 2681 5921509 5922238 0.000000e+00 1112
4 TraesCS3B01G482700 chr4B 90.323 248 23 1 39 286 286177903 286177657 9.260000e-85 324
5 TraesCS3B01G482700 chr4B 81.597 288 44 8 1 286 519804709 519804429 2.080000e-56 230
6 TraesCS3B01G482700 chr2B 92.192 730 49 4 1915 2643 769969230 769969952 0.000000e+00 1026
7 TraesCS3B01G482700 chr2B 85.763 295 32 9 292 582 775835472 775835760 1.210000e-78 303
8 TraesCS3B01G482700 chr3D 91.929 731 40 2 1140 1870 550256046 550255335 0.000000e+00 1005
9 TraesCS3B01G482700 chr3D 86.379 881 65 19 285 1134 550268469 550267613 0.000000e+00 911
10 TraesCS3B01G482700 chr3D 98.485 66 1 0 1849 1914 550253981 550253916 1.690000e-22 117
11 TraesCS3B01G482700 chr7D 85.934 782 81 18 1906 2681 59395563 59396321 0.000000e+00 808
12 TraesCS3B01G482700 chr7D 89.595 519 48 5 2087 2602 18138381 18137866 0.000000e+00 654
13 TraesCS3B01G482700 chr7D 89.858 493 44 4 2134 2625 436112896 436112409 1.750000e-176 628
14 TraesCS3B01G482700 chr7D 90.000 250 20 5 39 286 89828269 89828023 4.310000e-83 318
15 TraesCS3B01G482700 chr7D 89.558 249 23 3 39 286 89828703 89828949 2.000000e-81 313
16 TraesCS3B01G482700 chr7D 85.667 300 34 9 285 582 41696792 41696500 9.320000e-80 307
17 TraesCS3B01G482700 chr7D 85.050 301 36 8 285 582 479018465 479018759 5.610000e-77 298
18 TraesCS3B01G482700 chr7D 85.714 161 19 3 1926 2085 18138694 18138537 1.650000e-37 167
19 TraesCS3B01G482700 chr5D 85.332 784 73 22 1923 2681 522050089 522049323 0.000000e+00 773
20 TraesCS3B01G482700 chr5D 85.156 768 81 20 1922 2681 268878692 268877950 0.000000e+00 756
21 TraesCS3B01G482700 chr5D 85.908 589 49 8 2094 2681 268693229 268692674 4.940000e-167 597
22 TraesCS3B01G482700 chr1A 86.028 637 73 12 1914 2545 460327310 460327935 0.000000e+00 669
23 TraesCS3B01G482700 chr6A 87.202 461 41 9 2224 2681 613634740 613634295 2.380000e-140 508
24 TraesCS3B01G482700 chr1D 87.000 300 33 5 285 582 442153519 442153814 1.540000e-87 333
25 TraesCS3B01G482700 chr1D 89.200 250 22 4 39 286 296896337 296896091 9.320000e-80 307
26 TraesCS3B01G482700 chr1D 88.933 253 21 4 39 286 467509858 467510108 3.350000e-79 305
27 TraesCS3B01G482700 chr7A 85.855 304 36 6 281 582 165445161 165445459 1.550000e-82 316
28 TraesCS3B01G482700 chr7A 84.971 173 23 3 1913 2085 728014233 728014064 3.550000e-39 172
29 TraesCS3B01G482700 chr5A 89.370 254 24 3 40 292 412113857 412114108 1.550000e-82 316
30 TraesCS3B01G482700 chr2D 89.157 249 24 3 39 286 68730047 68729801 9.320000e-80 307
31 TraesCS3B01G482700 chr2D 85.235 298 38 5 287 582 64628413 64628120 4.340000e-78 302
32 TraesCS3B01G482700 chr4D 87.549 257 26 6 39 292 272996606 272996353 2.610000e-75 292
33 TraesCS3B01G482700 chr6B 84.385 301 38 7 285 582 683549469 683549763 1.210000e-73 287
34 TraesCS3B01G482700 chr6D 87.352 253 23 6 39 284 456121248 456120998 5.650000e-72 281
35 TraesCS3B01G482700 chrUn 83.660 306 39 10 285 582 320341296 320341598 7.310000e-71 278
36 TraesCS3B01G482700 chr4A 84.242 165 25 1 1921 2085 426003432 426003595 2.760000e-35 159
37 TraesCS3B01G482700 chr2A 81.053 190 21 9 98 284 603735391 603735214 1.290000e-28 137


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 TraesCS3B01G482700 chr3B 729718783 729721463 2680 True 4951.0 4951 100.0000 1 2681 1 chr3B.!!$R1 2680
1 TraesCS3B01G482700 chr3A 687100388 687101871 1483 True 1740.0 1740 88.1850 285 1759 1 chr3A.!!$R1 1474
2 TraesCS3B01G482700 chr4B 5921509 5922238 729 False 1112.0 1112 94.1580 1950 2681 1 chr4B.!!$F1 731
3 TraesCS3B01G482700 chr2B 769969230 769969952 722 False 1026.0 1026 92.1920 1915 2643 1 chr2B.!!$F1 728
4 TraesCS3B01G482700 chr3D 550267613 550268469 856 True 911.0 911 86.3790 285 1134 1 chr3D.!!$R1 849
5 TraesCS3B01G482700 chr3D 550253916 550256046 2130 True 561.0 1005 95.2070 1140 1914 2 chr3D.!!$R2 774
6 TraesCS3B01G482700 chr7D 59395563 59396321 758 False 808.0 808 85.9340 1906 2681 1 chr7D.!!$F1 775
7 TraesCS3B01G482700 chr7D 18137866 18138694 828 True 410.5 654 87.6545 1926 2602 2 chr7D.!!$R4 676
8 TraesCS3B01G482700 chr5D 522049323 522050089 766 True 773.0 773 85.3320 1923 2681 1 chr5D.!!$R3 758
9 TraesCS3B01G482700 chr5D 268877950 268878692 742 True 756.0 756 85.1560 1922 2681 1 chr5D.!!$R2 759
10 TraesCS3B01G482700 chr5D 268692674 268693229 555 True 597.0 597 85.9080 2094 2681 1 chr5D.!!$R1 587
11 TraesCS3B01G482700 chr1A 460327310 460327935 625 False 669.0 669 86.0280 1914 2545 1 chr1A.!!$F1 631

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
173 174 0.175989 GGCCAACCGTCAACCAAAAA 59.824 50.0 0.0 0.0 0.0 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 3409 0.040067 CGCGATGATCAGATCCGACA 60.04 55.0 0.0 0.0 0.0 4.35 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 4.143333 CAGCCATGCAGCTTGGGC 62.143 66.667 24.96 18.92 42.61 5.36
27 28 3.145551 CCATGCAGCTTGGGCCTC 61.146 66.667 17.99 0.00 39.73 4.70
28 29 3.145551 CATGCAGCTTGGGCCTCC 61.146 66.667 4.53 0.00 39.73 4.30
29 30 4.453892 ATGCAGCTTGGGCCTCCC 62.454 66.667 4.53 0.00 45.71 4.30
55 56 2.079049 CGACTTTTCGGCCTACTGC 58.921 57.895 0.00 0.00 41.89 4.40
56 57 0.389948 CGACTTTTCGGCCTACTGCT 60.390 55.000 0.00 0.00 41.89 4.24
64 65 2.859992 GGCCTACTGCTGACCAAAG 58.140 57.895 0.00 0.00 40.92 2.77
65 66 0.324943 GGCCTACTGCTGACCAAAGA 59.675 55.000 0.00 0.00 40.92 2.52
66 67 1.677217 GGCCTACTGCTGACCAAAGAG 60.677 57.143 0.00 0.00 40.92 2.85
67 68 1.002544 GCCTACTGCTGACCAAAGAGT 59.997 52.381 0.00 0.00 36.87 3.24
68 69 2.233922 GCCTACTGCTGACCAAAGAGTA 59.766 50.000 0.00 0.00 36.87 2.59
69 70 3.851098 CCTACTGCTGACCAAAGAGTAC 58.149 50.000 0.00 0.00 0.00 2.73
70 71 3.511934 CCTACTGCTGACCAAAGAGTACT 59.488 47.826 0.00 0.00 0.00 2.73
71 72 4.021016 CCTACTGCTGACCAAAGAGTACTT 60.021 45.833 0.00 0.00 38.05 2.24
72 73 4.423625 ACTGCTGACCAAAGAGTACTTT 57.576 40.909 0.00 0.00 45.75 2.66
73 74 4.781934 ACTGCTGACCAAAGAGTACTTTT 58.218 39.130 0.00 0.00 43.41 2.27
74 75 4.816925 ACTGCTGACCAAAGAGTACTTTTC 59.183 41.667 0.00 0.00 43.41 2.29
75 76 3.807622 TGCTGACCAAAGAGTACTTTTCG 59.192 43.478 0.00 0.00 43.41 3.46
76 77 3.186613 GCTGACCAAAGAGTACTTTTCGG 59.813 47.826 1.62 1.62 43.41 4.30
77 78 3.135994 TGACCAAAGAGTACTTTTCGGC 58.864 45.455 3.07 0.00 43.41 5.54
78 79 2.483106 GACCAAAGAGTACTTTTCGGCC 59.517 50.000 3.07 0.00 43.41 6.13
79 80 2.105993 ACCAAAGAGTACTTTTCGGCCT 59.894 45.455 3.07 0.00 43.41 5.19
80 81 2.484264 CCAAAGAGTACTTTTCGGCCTG 59.516 50.000 0.00 0.00 43.41 4.85
81 82 3.399330 CAAAGAGTACTTTTCGGCCTGA 58.601 45.455 0.00 0.00 43.41 3.86
82 83 2.745515 AGAGTACTTTTCGGCCTGAC 57.254 50.000 0.00 0.00 0.00 3.51
83 84 1.067776 AGAGTACTTTTCGGCCTGACG 60.068 52.381 0.00 0.00 0.00 4.35
84 85 0.669625 AGTACTTTTCGGCCTGACGC 60.670 55.000 0.00 0.00 0.00 5.19
85 86 0.669625 GTACTTTTCGGCCTGACGCT 60.670 55.000 0.00 0.00 37.74 5.07
86 87 0.669318 TACTTTTCGGCCTGACGCTG 60.669 55.000 0.00 0.00 46.15 5.18
87 88 2.668212 TTTTCGGCCTGACGCTGG 60.668 61.111 0.00 0.00 44.74 4.85
93 94 3.294493 GCCTGACGCTGGCCAAAA 61.294 61.111 7.01 0.00 41.62 2.44
94 95 2.855514 GCCTGACGCTGGCCAAAAA 61.856 57.895 7.01 0.00 41.62 1.94
95 96 1.286880 CCTGACGCTGGCCAAAAAG 59.713 57.895 7.01 0.33 0.00 2.27
96 97 1.286880 CTGACGCTGGCCAAAAAGG 59.713 57.895 7.01 0.00 41.84 3.11
115 116 2.973420 CCTTTTCGGCCTAGCTACG 58.027 57.895 0.00 0.00 0.00 3.51
116 117 0.529992 CCTTTTCGGCCTAGCTACGG 60.530 60.000 0.00 4.07 0.00 4.02
117 118 0.458669 CTTTTCGGCCTAGCTACGGA 59.541 55.000 0.00 1.39 0.00 4.69
118 119 1.068741 CTTTTCGGCCTAGCTACGGAT 59.931 52.381 0.00 0.00 0.00 4.18
119 120 0.672342 TTTCGGCCTAGCTACGGATC 59.328 55.000 0.00 0.00 0.00 3.36
120 121 0.178998 TTCGGCCTAGCTACGGATCT 60.179 55.000 0.00 0.00 0.00 2.75
121 122 0.605860 TCGGCCTAGCTACGGATCTC 60.606 60.000 0.00 0.00 0.00 2.75
122 123 0.606944 CGGCCTAGCTACGGATCTCT 60.607 60.000 0.00 0.00 0.00 3.10
123 124 1.623163 GGCCTAGCTACGGATCTCTT 58.377 55.000 11.96 0.00 0.00 2.85
124 125 1.542472 GGCCTAGCTACGGATCTCTTC 59.458 57.143 11.96 0.00 0.00 2.87
125 126 1.198178 GCCTAGCTACGGATCTCTTCG 59.802 57.143 11.96 0.00 0.00 3.79
126 127 1.807742 CCTAGCTACGGATCTCTTCGG 59.192 57.143 3.82 0.00 0.00 4.30
127 128 1.198178 CTAGCTACGGATCTCTTCGGC 59.802 57.143 0.00 0.00 0.00 5.54
128 129 1.007154 GCTACGGATCTCTTCGGCC 60.007 63.158 0.00 0.00 0.00 6.13
129 130 1.735376 GCTACGGATCTCTTCGGCCA 61.735 60.000 2.24 0.00 0.00 5.36
130 131 0.744874 CTACGGATCTCTTCGGCCAA 59.255 55.000 2.24 0.00 0.00 4.52
131 132 1.341531 CTACGGATCTCTTCGGCCAAT 59.658 52.381 2.24 0.00 0.00 3.16
132 133 0.179073 ACGGATCTCTTCGGCCAATG 60.179 55.000 2.24 0.00 0.00 2.82
133 134 1.502163 CGGATCTCTTCGGCCAATGC 61.502 60.000 2.24 0.00 0.00 3.56
134 135 1.502163 GGATCTCTTCGGCCAATGCG 61.502 60.000 2.24 0.00 38.85 4.73
135 136 0.811616 GATCTCTTCGGCCAATGCGT 60.812 55.000 2.24 0.00 38.85 5.24
136 137 1.091771 ATCTCTTCGGCCAATGCGTG 61.092 55.000 2.24 0.00 38.85 5.34
144 145 2.745884 CCAATGCGTGGCCGAAGA 60.746 61.111 0.00 0.00 41.72 2.87
145 146 2.753966 CCAATGCGTGGCCGAAGAG 61.754 63.158 0.00 0.00 41.72 2.85
146 147 2.034879 CAATGCGTGGCCGAAGAGT 61.035 57.895 0.00 0.00 35.63 3.24
147 148 1.741770 AATGCGTGGCCGAAGAGTC 60.742 57.895 0.00 0.00 35.63 3.36
148 149 3.665675 ATGCGTGGCCGAAGAGTCC 62.666 63.158 0.00 0.00 35.63 3.85
149 150 4.070552 GCGTGGCCGAAGAGTCCT 62.071 66.667 0.00 0.00 35.63 3.85
150 151 2.657237 CGTGGCCGAAGAGTCCTT 59.343 61.111 0.00 0.00 35.63 3.36
151 152 1.004918 CGTGGCCGAAGAGTCCTTT 60.005 57.895 0.00 0.00 35.63 3.11
152 153 0.602905 CGTGGCCGAAGAGTCCTTTT 60.603 55.000 0.00 0.00 35.63 2.27
153 154 1.157585 GTGGCCGAAGAGTCCTTTTC 58.842 55.000 0.00 0.00 31.62 2.29
154 155 0.320421 TGGCCGAAGAGTCCTTTTCG 60.320 55.000 11.71 11.71 44.17 3.46
157 158 2.457080 CGAAGAGTCCTTTTCGGCC 58.543 57.895 11.02 0.00 41.69 6.13
158 159 0.320421 CGAAGAGTCCTTTTCGGCCA 60.320 55.000 2.24 0.00 41.69 5.36
159 160 1.876416 CGAAGAGTCCTTTTCGGCCAA 60.876 52.381 2.24 0.00 41.69 4.52
160 161 1.535896 GAAGAGTCCTTTTCGGCCAAC 59.464 52.381 2.24 0.00 31.62 3.77
161 162 0.250770 AGAGTCCTTTTCGGCCAACC 60.251 55.000 2.24 0.00 0.00 3.77
171 172 3.527641 GGCCAACCGTCAACCAAA 58.472 55.556 0.00 0.00 0.00 3.28
172 173 1.817209 GGCCAACCGTCAACCAAAA 59.183 52.632 0.00 0.00 0.00 2.44
173 174 0.175989 GGCCAACCGTCAACCAAAAA 59.824 50.000 0.00 0.00 0.00 1.94
174 175 1.282817 GCCAACCGTCAACCAAAAAC 58.717 50.000 0.00 0.00 0.00 2.43
175 176 1.404315 GCCAACCGTCAACCAAAAACA 60.404 47.619 0.00 0.00 0.00 2.83
176 177 2.263945 CCAACCGTCAACCAAAAACAC 58.736 47.619 0.00 0.00 0.00 3.32
177 178 2.263945 CAACCGTCAACCAAAAACACC 58.736 47.619 0.00 0.00 0.00 4.16
178 179 1.546961 ACCGTCAACCAAAAACACCA 58.453 45.000 0.00 0.00 0.00 4.17
179 180 2.104170 ACCGTCAACCAAAAACACCAT 58.896 42.857 0.00 0.00 0.00 3.55
180 181 2.100087 ACCGTCAACCAAAAACACCATC 59.900 45.455 0.00 0.00 0.00 3.51
181 182 2.360801 CCGTCAACCAAAAACACCATCT 59.639 45.455 0.00 0.00 0.00 2.90
182 183 3.181480 CCGTCAACCAAAAACACCATCTT 60.181 43.478 0.00 0.00 0.00 2.40
183 184 4.041723 CGTCAACCAAAAACACCATCTTC 58.958 43.478 0.00 0.00 0.00 2.87
184 185 4.041723 GTCAACCAAAAACACCATCTTCG 58.958 43.478 0.00 0.00 0.00 3.79
185 186 3.067461 TCAACCAAAAACACCATCTTCGG 59.933 43.478 0.00 0.00 0.00 4.30
186 187 1.339929 ACCAAAAACACCATCTTCGGC 59.660 47.619 0.00 0.00 0.00 5.54
187 188 1.336795 CCAAAAACACCATCTTCGGCC 60.337 52.381 0.00 0.00 0.00 6.13
188 189 0.966179 AAAAACACCATCTTCGGCCC 59.034 50.000 0.00 0.00 0.00 5.80
189 190 0.178975 AAAACACCATCTTCGGCCCA 60.179 50.000 0.00 0.00 0.00 5.36
190 191 0.893727 AAACACCATCTTCGGCCCAC 60.894 55.000 0.00 0.00 0.00 4.61
191 192 2.063015 AACACCATCTTCGGCCCACA 62.063 55.000 0.00 0.00 0.00 4.17
192 193 1.077501 CACCATCTTCGGCCCACAT 60.078 57.895 0.00 0.00 0.00 3.21
193 194 1.077501 ACCATCTTCGGCCCACATG 60.078 57.895 0.00 0.00 0.00 3.21
194 195 1.224315 CCATCTTCGGCCCACATGA 59.776 57.895 0.00 0.00 0.00 3.07
195 196 0.816825 CCATCTTCGGCCCACATGAG 60.817 60.000 0.00 0.00 0.00 2.90
196 197 0.816825 CATCTTCGGCCCACATGAGG 60.817 60.000 0.00 0.00 0.00 3.86
203 204 4.838152 CCCACATGAGGCCGACGG 62.838 72.222 10.29 10.29 0.00 4.79
204 205 4.838152 CCACATGAGGCCGACGGG 62.838 72.222 17.22 0.00 0.00 5.28
205 206 4.838152 CACATGAGGCCGACGGGG 62.838 72.222 17.22 0.00 39.58 5.73
207 208 4.530857 CATGAGGCCGACGGGGTC 62.531 72.222 17.22 0.00 42.41 4.46
210 211 2.836360 GAGGCCGACGGGGTCATA 60.836 66.667 17.22 0.00 45.54 2.15
211 212 2.122989 AGGCCGACGGGGTCATAT 60.123 61.111 17.22 0.00 45.54 1.78
212 213 1.755393 GAGGCCGACGGGGTCATATT 61.755 60.000 17.22 0.00 45.54 1.28
213 214 1.147600 GGCCGACGGGGTCATATTT 59.852 57.895 17.22 0.00 41.38 1.40
214 215 0.464916 GGCCGACGGGGTCATATTTT 60.465 55.000 17.22 0.00 41.38 1.82
215 216 1.385528 GCCGACGGGGTCATATTTTT 58.614 50.000 17.22 0.00 38.44 1.94
216 217 1.064952 GCCGACGGGGTCATATTTTTG 59.935 52.381 17.22 0.00 38.44 2.44
217 218 1.064952 CCGACGGGGTCATATTTTTGC 59.935 52.381 5.81 0.00 32.09 3.68
218 219 2.014128 CGACGGGGTCATATTTTTGCT 58.986 47.619 0.00 0.00 32.09 3.91
219 220 2.422127 CGACGGGGTCATATTTTTGCTT 59.578 45.455 0.00 0.00 32.09 3.91
220 221 3.119637 CGACGGGGTCATATTTTTGCTTT 60.120 43.478 0.00 0.00 32.09 3.51
221 222 4.617298 CGACGGGGTCATATTTTTGCTTTT 60.617 41.667 0.00 0.00 32.09 2.27
222 223 5.222079 ACGGGGTCATATTTTTGCTTTTT 57.778 34.783 0.00 0.00 0.00 1.94
242 243 5.968528 TTTTTGCATCGGGTGTTATAGTT 57.031 34.783 0.00 0.00 0.00 2.24
243 244 5.968528 TTTTGCATCGGGTGTTATAGTTT 57.031 34.783 0.00 0.00 0.00 2.66
244 245 5.554822 TTTGCATCGGGTGTTATAGTTTC 57.445 39.130 0.00 0.00 0.00 2.78
245 246 3.537580 TGCATCGGGTGTTATAGTTTCC 58.462 45.455 0.00 0.00 0.00 3.13
246 247 3.055021 TGCATCGGGTGTTATAGTTTCCA 60.055 43.478 0.00 0.00 0.00 3.53
247 248 3.942748 GCATCGGGTGTTATAGTTTCCAA 59.057 43.478 0.00 0.00 0.00 3.53
248 249 4.396790 GCATCGGGTGTTATAGTTTCCAAA 59.603 41.667 0.00 0.00 0.00 3.28
249 250 5.067283 GCATCGGGTGTTATAGTTTCCAAAT 59.933 40.000 0.00 0.00 0.00 2.32
250 251 6.405397 GCATCGGGTGTTATAGTTTCCAAATT 60.405 38.462 0.00 0.00 0.00 1.82
251 252 7.543756 CATCGGGTGTTATAGTTTCCAAATTT 58.456 34.615 0.00 0.00 0.00 1.82
252 253 6.915349 TCGGGTGTTATAGTTTCCAAATTTG 58.085 36.000 11.40 11.40 0.00 2.32
253 254 5.575218 CGGGTGTTATAGTTTCCAAATTTGC 59.425 40.000 12.92 0.00 0.00 3.68
254 255 6.571537 CGGGTGTTATAGTTTCCAAATTTGCT 60.572 38.462 12.92 6.94 0.00 3.91
255 256 7.362229 CGGGTGTTATAGTTTCCAAATTTGCTA 60.362 37.037 12.92 8.87 0.00 3.49
256 257 8.474831 GGGTGTTATAGTTTCCAAATTTGCTAT 58.525 33.333 12.92 14.69 0.00 2.97
321 322 5.521735 CACCAATTTCCAAAACAATGTTCGA 59.478 36.000 0.00 0.00 0.00 3.71
322 323 6.036517 CACCAATTTCCAAAACAATGTTCGAA 59.963 34.615 0.00 0.00 0.00 3.71
487 491 9.739276 AGTGTTCAGGAATTAGAATAATGTTCA 57.261 29.630 0.00 0.00 0.00 3.18
488 492 9.774742 GTGTTCAGGAATTAGAATAATGTTCAC 57.225 33.333 0.00 0.00 0.00 3.18
489 493 8.664798 TGTTCAGGAATTAGAATAATGTTCACG 58.335 33.333 0.00 0.00 0.00 4.35
490 494 8.879759 GTTCAGGAATTAGAATAATGTTCACGA 58.120 33.333 0.00 0.00 0.00 4.35
491 495 9.613428 TTCAGGAATTAGAATAATGTTCACGAT 57.387 29.630 0.00 0.00 0.00 3.73
492 496 9.613428 TCAGGAATTAGAATAATGTTCACGATT 57.387 29.630 0.00 0.00 0.00 3.34
549 553 6.260714 TCATGATTTCACGGAATTGATAGTGG 59.739 38.462 0.00 0.00 35.50 4.00
682 714 4.076394 GGATCTAGTATCCAAGCTCTCGT 58.924 47.826 13.35 0.00 38.09 4.18
700 732 6.189677 TCTCGTCAAGACAAAACAAAATGT 57.810 33.333 0.72 0.00 0.00 2.71
703 735 7.908082 TCTCGTCAAGACAAAACAAAATGTTAG 59.092 33.333 0.72 0.00 40.14 2.34
705 737 7.694784 TCGTCAAGACAAAACAAAATGTTAGAC 59.305 33.333 0.72 0.00 40.14 2.59
712 744 2.419667 ACAAAATGTTAGACCGGGTCG 58.580 47.619 20.87 6.46 37.67 4.79
808 841 2.092968 TGCAAGCGGATGGAAATAGACT 60.093 45.455 0.00 0.00 0.00 3.24
809 842 2.945668 GCAAGCGGATGGAAATAGACTT 59.054 45.455 0.00 0.00 0.00 3.01
827 860 1.920574 CTTGTGATCACGAAGGCTACG 59.079 52.381 20.54 1.87 0.00 3.51
863 896 2.028766 CTATTGCCGTGCGTGCTCTG 62.029 60.000 0.00 0.00 0.00 3.35
896 929 3.536917 CCCATCGTCCTAGGCGCA 61.537 66.667 10.83 9.37 0.00 6.09
919 953 1.451207 AAATCGGCCGCTACATGCA 60.451 52.632 23.51 0.00 43.06 3.96
991 1028 4.701651 CACAATCCTCTACATCCTTGCAAA 59.298 41.667 0.00 0.00 0.00 3.68
1026 1063 0.859232 CTCGAACAAGAACCACCACG 59.141 55.000 0.00 0.00 0.00 4.94
1048 1085 1.601903 CTCTCCTCATCTTCGTCCTCG 59.398 57.143 0.00 0.00 38.55 4.63
1090 1127 1.315257 ATCGTCCACAAATGCTGCCC 61.315 55.000 0.00 0.00 0.00 5.36
1138 1175 3.589542 CCCCACCACCACCACCAT 61.590 66.667 0.00 0.00 0.00 3.55
1170 1210 1.080974 CGTGGTACCACAGTCGGTC 60.081 63.158 37.40 14.30 46.47 4.79
1266 1306 0.818040 GCGTGTTCCAGACAAACCCT 60.818 55.000 0.00 0.00 40.65 4.34
1279 1319 2.337879 AAACCCTGTCAAGCTCGCCA 62.338 55.000 0.00 0.00 0.00 5.69
1301 1341 4.695231 CGCCGTCGACCTCAACGT 62.695 66.667 10.58 0.00 37.19 3.99
1341 1381 4.295119 ACGCGCGTGAAGGAGGTT 62.295 61.111 37.37 5.31 0.00 3.50
1714 1754 1.881925 GCAATGTGTGGTGCCTAGTCA 60.882 52.381 0.00 0.00 34.58 3.41
1762 1802 4.952335 GGACAGCCTAGTACTTTACTGGTA 59.048 45.833 17.74 0.00 39.81 3.25
1763 1803 5.163571 GGACAGCCTAGTACTTTACTGGTAC 60.164 48.000 17.74 11.04 39.81 3.34
1764 1804 4.708909 ACAGCCTAGTACTTTACTGGTACC 59.291 45.833 17.74 4.43 40.01 3.34
1765 1805 4.954826 CAGCCTAGTACTTTACTGGTACCT 59.045 45.833 14.36 0.00 40.01 3.08
1766 1806 5.421374 CAGCCTAGTACTTTACTGGTACCTT 59.579 44.000 14.36 2.42 40.01 3.50
1767 1807 5.421374 AGCCTAGTACTTTACTGGTACCTTG 59.579 44.000 14.36 8.64 40.01 3.61
1768 1808 5.420104 GCCTAGTACTTTACTGGTACCTTGA 59.580 44.000 14.36 0.00 40.01 3.02
1769 1809 6.405619 GCCTAGTACTTTACTGGTACCTTGAG 60.406 46.154 14.36 4.71 40.01 3.02
1770 1810 6.662663 CCTAGTACTTTACTGGTACCTTGAGT 59.337 42.308 14.36 10.93 40.01 3.41
1771 1811 6.587206 AGTACTTTACTGGTACCTTGAGTC 57.413 41.667 14.36 5.13 40.01 3.36
1772 1812 4.886496 ACTTTACTGGTACCTTGAGTCC 57.114 45.455 14.36 0.00 0.00 3.85
1773 1813 4.490706 ACTTTACTGGTACCTTGAGTCCT 58.509 43.478 14.36 0.00 0.00 3.85
1774 1814 4.906060 ACTTTACTGGTACCTTGAGTCCTT 59.094 41.667 14.36 0.00 0.00 3.36
1775 1815 4.884668 TTACTGGTACCTTGAGTCCTTG 57.115 45.455 14.36 0.00 0.00 3.61
1838 1878 7.923414 AAATTAGACTAGTCCAATGACAACC 57.077 36.000 19.38 0.00 44.33 3.77
1839 1879 6.875972 ATTAGACTAGTCCAATGACAACCT 57.124 37.500 19.38 0.00 44.33 3.50
1916 3331 9.200817 CCTTCTTTATCCCAGAAATAAATTGGA 57.799 33.333 0.00 0.00 33.76 3.53
1919 3334 7.832187 TCTTTATCCCAGAAATAAATTGGACGT 59.168 33.333 0.00 0.00 33.76 4.34
1959 3374 3.181497 CGAATGTTTCCAATTCATCCGCT 60.181 43.478 0.00 0.00 0.00 5.52
1994 3409 1.144936 GATTAGCGCCCTGACAGCT 59.855 57.895 2.29 0.00 44.24 4.24
2014 3429 0.039978 GTCGGATCTGATCATCGCGT 60.040 55.000 18.64 0.00 0.00 6.01
2131 3702 0.028770 TTCAACGCTTTCCTGCAACG 59.971 50.000 0.00 0.00 0.00 4.10
2203 3775 4.124351 CTAACGTCGGGCGCTCCA 62.124 66.667 7.64 0.00 46.11 3.86
2348 3926 2.962859 AGACCCCAGTTGCAGAAAAAT 58.037 42.857 0.00 0.00 0.00 1.82
2369 3947 6.515272 AATAAACCTTCAGCAACGAATCAT 57.485 33.333 0.00 0.00 0.00 2.45
2370 3948 4.853924 AAACCTTCAGCAACGAATCATT 57.146 36.364 0.00 0.00 0.00 2.57
2517 4096 4.879197 TGAGCTTCAGAGAAGATCACAA 57.121 40.909 20.01 2.32 37.71 3.33
2545 4124 3.132289 CCTACGGAAACTATGAGCCTCAA 59.868 47.826 0.00 0.00 0.00 3.02
2552 4131 6.030228 GGAAACTATGAGCCTCAAAAATTCG 58.970 40.000 0.00 0.00 0.00 3.34
2575 4154 5.119279 CGGAAATAATACAAGAGATCCTGCG 59.881 44.000 0.00 0.00 0.00 5.18
2625 4205 9.906660 TTACCAGTGCAGAAATTATGTAAAAAG 57.093 29.630 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.143333 GCCCAAGCTGCATGGCTG 62.143 66.667 18.01 7.06 42.24 4.85
10 11 3.145551 GAGGCCCAAGCTGCATGG 61.146 66.667 16.61 16.61 39.73 3.66
11 12 3.145551 GGAGGCCCAAGCTGCATG 61.146 66.667 0.00 0.00 39.73 4.06
12 13 4.453892 GGGAGGCCCAAGCTGCAT 62.454 66.667 0.00 0.00 44.65 3.96
15 16 4.351054 AACGGGAGGCCCAAGCTG 62.351 66.667 0.00 0.00 45.83 4.24
16 17 4.035102 GAACGGGAGGCCCAAGCT 62.035 66.667 0.00 0.00 45.83 3.74
17 18 4.344865 TGAACGGGAGGCCCAAGC 62.345 66.667 0.00 0.00 45.83 4.01
18 19 2.359975 GTGAACGGGAGGCCCAAG 60.360 66.667 0.00 0.00 45.83 3.61
19 20 3.172106 TGTGAACGGGAGGCCCAA 61.172 61.111 0.00 0.00 45.83 4.12
20 21 3.948719 GTGTGAACGGGAGGCCCA 61.949 66.667 0.00 0.00 45.83 5.36
22 23 3.998672 TCGTGTGAACGGGAGGCC 61.999 66.667 0.00 0.00 0.00 5.19
23 24 2.710724 AAGTCGTGTGAACGGGAGGC 62.711 60.000 0.00 0.00 0.00 4.70
24 25 0.249741 AAAGTCGTGTGAACGGGAGG 60.250 55.000 0.00 0.00 0.00 4.30
25 26 1.525619 GAAAAGTCGTGTGAACGGGAG 59.474 52.381 0.00 0.00 0.00 4.30
26 27 1.574134 GAAAAGTCGTGTGAACGGGA 58.426 50.000 0.00 0.00 0.00 5.14
27 28 0.231279 CGAAAAGTCGTGTGAACGGG 59.769 55.000 0.00 0.00 42.53 5.28
28 29 0.231279 CCGAAAAGTCGTGTGAACGG 59.769 55.000 0.00 0.00 46.21 4.44
29 30 0.382636 GCCGAAAAGTCGTGTGAACG 60.383 55.000 0.00 0.00 46.21 3.95
30 31 0.041576 GGCCGAAAAGTCGTGTGAAC 60.042 55.000 0.00 0.00 46.21 3.18
31 32 0.179067 AGGCCGAAAAGTCGTGTGAA 60.179 50.000 0.00 0.00 46.21 3.18
32 33 0.675083 TAGGCCGAAAAGTCGTGTGA 59.325 50.000 0.00 0.00 46.21 3.58
33 34 0.788391 GTAGGCCGAAAAGTCGTGTG 59.212 55.000 0.00 0.00 46.21 3.82
34 35 0.677842 AGTAGGCCGAAAAGTCGTGT 59.322 50.000 0.00 0.00 46.21 4.49
35 36 1.068474 CAGTAGGCCGAAAAGTCGTG 58.932 55.000 0.00 0.00 46.21 4.35
36 37 0.669625 GCAGTAGGCCGAAAAGTCGT 60.670 55.000 0.00 0.00 46.21 4.34
37 38 0.389948 AGCAGTAGGCCGAAAAGTCG 60.390 55.000 0.00 0.00 46.50 4.18
38 39 1.079503 CAGCAGTAGGCCGAAAAGTC 58.920 55.000 0.00 0.00 46.50 3.01
39 40 0.685097 TCAGCAGTAGGCCGAAAAGT 59.315 50.000 0.00 0.00 46.50 2.66
40 41 1.079503 GTCAGCAGTAGGCCGAAAAG 58.920 55.000 0.00 0.00 46.50 2.27
41 42 0.321298 GGTCAGCAGTAGGCCGAAAA 60.321 55.000 0.00 0.00 46.50 2.29
42 43 1.295423 GGTCAGCAGTAGGCCGAAA 59.705 57.895 0.00 0.00 46.50 3.46
43 44 1.476845 TTGGTCAGCAGTAGGCCGAA 61.477 55.000 0.00 0.00 46.50 4.30
44 45 1.476845 TTTGGTCAGCAGTAGGCCGA 61.477 55.000 0.00 0.00 46.50 5.54
45 46 1.003839 TTTGGTCAGCAGTAGGCCG 60.004 57.895 0.00 0.00 46.50 6.13
46 47 0.324943 TCTTTGGTCAGCAGTAGGCC 59.675 55.000 0.00 0.00 46.50 5.19
47 48 1.002544 ACTCTTTGGTCAGCAGTAGGC 59.997 52.381 0.00 0.00 45.30 3.93
48 49 3.511934 AGTACTCTTTGGTCAGCAGTAGG 59.488 47.826 0.00 0.00 0.00 3.18
49 50 4.792521 AGTACTCTTTGGTCAGCAGTAG 57.207 45.455 0.00 0.00 0.00 2.57
50 51 5.546621 AAAGTACTCTTTGGTCAGCAGTA 57.453 39.130 0.00 0.00 41.62 2.74
51 52 4.423625 AAAGTACTCTTTGGTCAGCAGT 57.576 40.909 0.00 0.00 41.62 4.40
52 53 4.084328 CGAAAAGTACTCTTTGGTCAGCAG 60.084 45.833 0.00 0.00 42.26 4.24
53 54 3.807622 CGAAAAGTACTCTTTGGTCAGCA 59.192 43.478 0.00 0.00 42.26 4.41
54 55 3.186613 CCGAAAAGTACTCTTTGGTCAGC 59.813 47.826 7.02 0.00 42.26 4.26
55 56 3.186613 GCCGAAAAGTACTCTTTGGTCAG 59.813 47.826 15.39 0.00 42.26 3.51
56 57 3.135994 GCCGAAAAGTACTCTTTGGTCA 58.864 45.455 15.39 0.00 42.26 4.02
57 58 2.483106 GGCCGAAAAGTACTCTTTGGTC 59.517 50.000 15.39 10.25 42.26 4.02
58 59 2.105993 AGGCCGAAAAGTACTCTTTGGT 59.894 45.455 15.39 0.00 42.26 3.67
59 60 2.484264 CAGGCCGAAAAGTACTCTTTGG 59.516 50.000 10.53 10.53 42.26 3.28
60 61 3.186613 GTCAGGCCGAAAAGTACTCTTTG 59.813 47.826 0.00 0.00 42.26 2.77
61 62 3.400255 GTCAGGCCGAAAAGTACTCTTT 58.600 45.455 0.00 0.00 44.59 2.52
62 63 2.609737 CGTCAGGCCGAAAAGTACTCTT 60.610 50.000 0.00 0.00 35.14 2.85
63 64 1.067776 CGTCAGGCCGAAAAGTACTCT 60.068 52.381 0.00 0.00 0.00 3.24
64 65 1.347320 CGTCAGGCCGAAAAGTACTC 58.653 55.000 0.00 0.00 0.00 2.59
65 66 0.669625 GCGTCAGGCCGAAAAGTACT 60.670 55.000 0.00 0.00 34.80 2.73
66 67 0.669625 AGCGTCAGGCCGAAAAGTAC 60.670 55.000 0.00 0.00 45.17 2.73
67 68 0.669318 CAGCGTCAGGCCGAAAAGTA 60.669 55.000 0.00 0.00 45.17 2.24
68 69 1.961277 CAGCGTCAGGCCGAAAAGT 60.961 57.895 0.00 0.00 45.17 2.66
69 70 2.680913 CCAGCGTCAGGCCGAAAAG 61.681 63.158 0.00 0.00 45.17 2.27
70 71 2.668212 CCAGCGTCAGGCCGAAAA 60.668 61.111 0.00 0.00 45.17 2.29
77 78 1.286880 CTTTTTGGCCAGCGTCAGG 59.713 57.895 5.11 0.00 0.00 3.86
78 79 1.286880 CCTTTTTGGCCAGCGTCAG 59.713 57.895 5.11 0.00 0.00 3.51
79 80 3.442441 CCTTTTTGGCCAGCGTCA 58.558 55.556 5.11 0.00 0.00 4.35
97 98 0.529992 CCGTAGCTAGGCCGAAAAGG 60.530 60.000 7.95 0.00 44.97 3.11
98 99 0.458669 TCCGTAGCTAGGCCGAAAAG 59.541 55.000 7.95 0.00 0.00 2.27
99 100 1.068127 GATCCGTAGCTAGGCCGAAAA 59.932 52.381 7.95 0.00 0.00 2.29
100 101 0.672342 GATCCGTAGCTAGGCCGAAA 59.328 55.000 7.95 0.00 0.00 3.46
101 102 0.178998 AGATCCGTAGCTAGGCCGAA 60.179 55.000 7.95 0.00 0.00 4.30
102 103 0.605860 GAGATCCGTAGCTAGGCCGA 60.606 60.000 7.95 1.71 0.00 5.54
103 104 0.606944 AGAGATCCGTAGCTAGGCCG 60.607 60.000 7.95 1.60 0.00 6.13
104 105 1.542472 GAAGAGATCCGTAGCTAGGCC 59.458 57.143 7.95 0.00 0.00 5.19
105 106 1.198178 CGAAGAGATCCGTAGCTAGGC 59.802 57.143 7.95 0.00 0.00 3.93
106 107 1.807742 CCGAAGAGATCCGTAGCTAGG 59.192 57.143 6.46 6.46 0.00 3.02
107 108 1.198178 GCCGAAGAGATCCGTAGCTAG 59.802 57.143 0.00 0.00 0.00 3.42
108 109 1.236628 GCCGAAGAGATCCGTAGCTA 58.763 55.000 0.00 0.00 0.00 3.32
109 110 1.457009 GGCCGAAGAGATCCGTAGCT 61.457 60.000 0.00 0.00 0.00 3.32
110 111 1.007154 GGCCGAAGAGATCCGTAGC 60.007 63.158 0.00 0.00 0.00 3.58
111 112 0.744874 TTGGCCGAAGAGATCCGTAG 59.255 55.000 0.00 0.00 0.00 3.51
112 113 1.068588 CATTGGCCGAAGAGATCCGTA 59.931 52.381 0.00 0.00 0.00 4.02
113 114 0.179073 CATTGGCCGAAGAGATCCGT 60.179 55.000 0.00 0.00 0.00 4.69
114 115 1.502163 GCATTGGCCGAAGAGATCCG 61.502 60.000 0.00 0.00 0.00 4.18
115 116 1.502163 CGCATTGGCCGAAGAGATCC 61.502 60.000 0.00 0.00 36.38 3.36
116 117 0.811616 ACGCATTGGCCGAAGAGATC 60.812 55.000 5.92 0.00 36.38 2.75
117 118 1.091771 CACGCATTGGCCGAAGAGAT 61.092 55.000 5.92 0.00 36.38 2.75
118 119 1.741401 CACGCATTGGCCGAAGAGA 60.741 57.895 5.92 0.00 36.38 3.10
119 120 2.753966 CCACGCATTGGCCGAAGAG 61.754 63.158 0.00 0.00 39.07 2.85
120 121 2.745884 CCACGCATTGGCCGAAGA 60.746 61.111 0.00 0.00 39.07 2.87
128 129 1.970917 GACTCTTCGGCCACGCATTG 61.971 60.000 2.24 0.00 40.69 2.82
129 130 1.741770 GACTCTTCGGCCACGCATT 60.742 57.895 2.24 0.00 40.69 3.56
130 131 2.125512 GACTCTTCGGCCACGCAT 60.126 61.111 2.24 0.00 40.69 4.73
131 132 4.373116 GGACTCTTCGGCCACGCA 62.373 66.667 2.24 0.00 40.69 5.24
132 133 3.591254 AAGGACTCTTCGGCCACGC 62.591 63.158 2.24 0.00 40.69 5.34
133 134 0.602905 AAAAGGACTCTTCGGCCACG 60.603 55.000 2.24 0.00 42.74 4.94
134 135 1.157585 GAAAAGGACTCTTCGGCCAC 58.842 55.000 2.24 0.00 31.82 5.01
135 136 0.320421 CGAAAAGGACTCTTCGGCCA 60.320 55.000 2.24 0.00 40.52 5.36
136 137 2.457080 CGAAAAGGACTCTTCGGCC 58.543 57.895 0.05 0.00 40.52 6.13
154 155 0.175989 TTTTTGGTTGACGGTTGGCC 59.824 50.000 0.00 0.00 0.00 5.36
155 156 1.282817 GTTTTTGGTTGACGGTTGGC 58.717 50.000 0.00 0.00 0.00 4.52
156 157 2.263945 GTGTTTTTGGTTGACGGTTGG 58.736 47.619 0.00 0.00 0.00 3.77
157 158 2.263945 GGTGTTTTTGGTTGACGGTTG 58.736 47.619 0.00 0.00 0.00 3.77
158 159 1.893801 TGGTGTTTTTGGTTGACGGTT 59.106 42.857 0.00 0.00 0.00 4.44
159 160 1.546961 TGGTGTTTTTGGTTGACGGT 58.453 45.000 0.00 0.00 0.00 4.83
160 161 2.360801 AGATGGTGTTTTTGGTTGACGG 59.639 45.455 0.00 0.00 0.00 4.79
161 162 3.708563 AGATGGTGTTTTTGGTTGACG 57.291 42.857 0.00 0.00 0.00 4.35
162 163 4.041723 CGAAGATGGTGTTTTTGGTTGAC 58.958 43.478 0.00 0.00 0.00 3.18
163 164 3.067461 CCGAAGATGGTGTTTTTGGTTGA 59.933 43.478 0.00 0.00 0.00 3.18
164 165 3.380142 CCGAAGATGGTGTTTTTGGTTG 58.620 45.455 0.00 0.00 0.00 3.77
165 166 2.223947 GCCGAAGATGGTGTTTTTGGTT 60.224 45.455 0.00 0.00 0.00 3.67
166 167 1.339929 GCCGAAGATGGTGTTTTTGGT 59.660 47.619 0.00 0.00 0.00 3.67
167 168 1.336795 GGCCGAAGATGGTGTTTTTGG 60.337 52.381 0.00 0.00 0.00 3.28
168 169 1.336795 GGGCCGAAGATGGTGTTTTTG 60.337 52.381 0.00 0.00 0.00 2.44
169 170 0.966179 GGGCCGAAGATGGTGTTTTT 59.034 50.000 0.00 0.00 0.00 1.94
170 171 0.178975 TGGGCCGAAGATGGTGTTTT 60.179 50.000 0.00 0.00 0.00 2.43
171 172 0.893727 GTGGGCCGAAGATGGTGTTT 60.894 55.000 0.00 0.00 0.00 2.83
172 173 1.303317 GTGGGCCGAAGATGGTGTT 60.303 57.895 0.00 0.00 0.00 3.32
173 174 1.852157 ATGTGGGCCGAAGATGGTGT 61.852 55.000 0.00 0.00 0.00 4.16
174 175 1.077501 ATGTGGGCCGAAGATGGTG 60.078 57.895 0.00 0.00 0.00 4.17
175 176 1.077501 CATGTGGGCCGAAGATGGT 60.078 57.895 0.00 0.00 0.00 3.55
176 177 0.816825 CTCATGTGGGCCGAAGATGG 60.817 60.000 12.53 2.71 0.00 3.51
177 178 0.816825 CCTCATGTGGGCCGAAGATG 60.817 60.000 5.87 7.64 0.00 2.90
178 179 1.528824 CCTCATGTGGGCCGAAGAT 59.471 57.895 5.87 0.00 0.00 2.40
179 180 2.989639 CCTCATGTGGGCCGAAGA 59.010 61.111 5.87 0.00 0.00 2.87
180 181 2.825836 GCCTCATGTGGGCCGAAG 60.826 66.667 15.39 0.00 43.49 3.79
186 187 4.838152 CCGTCGGCCTCATGTGGG 62.838 72.222 15.39 9.19 0.00 4.61
187 188 4.838152 CCCGTCGGCCTCATGTGG 62.838 72.222 5.50 9.54 0.00 4.17
188 189 4.838152 CCCCGTCGGCCTCATGTG 62.838 72.222 5.50 0.00 0.00 3.21
190 191 4.530857 GACCCCGTCGGCCTCATG 62.531 72.222 5.50 0.00 33.26 3.07
191 192 2.939760 TATGACCCCGTCGGCCTCAT 62.940 60.000 19.94 19.94 34.95 2.90
192 193 2.939760 ATATGACCCCGTCGGCCTCA 62.940 60.000 5.50 8.64 34.95 3.86
193 194 1.755393 AATATGACCCCGTCGGCCTC 61.755 60.000 5.50 2.49 34.95 4.70
194 195 1.342672 AAATATGACCCCGTCGGCCT 61.343 55.000 5.50 0.00 34.95 5.19
195 196 0.464916 AAAATATGACCCCGTCGGCC 60.465 55.000 5.50 0.00 34.95 6.13
196 197 1.064952 CAAAAATATGACCCCGTCGGC 59.935 52.381 5.50 0.00 34.95 5.54
197 198 1.064952 GCAAAAATATGACCCCGTCGG 59.935 52.381 3.60 3.60 34.95 4.79
198 199 2.014128 AGCAAAAATATGACCCCGTCG 58.986 47.619 0.00 0.00 34.95 5.12
199 200 4.450082 AAAGCAAAAATATGACCCCGTC 57.550 40.909 0.00 0.00 0.00 4.79
200 201 4.882842 AAAAGCAAAAATATGACCCCGT 57.117 36.364 0.00 0.00 0.00 5.28
220 221 5.968528 AACTATAACACCCGATGCAAAAA 57.031 34.783 0.00 0.00 0.00 1.94
221 222 5.106078 GGAAACTATAACACCCGATGCAAAA 60.106 40.000 0.00 0.00 0.00 2.44
222 223 4.396790 GGAAACTATAACACCCGATGCAAA 59.603 41.667 0.00 0.00 0.00 3.68
223 224 3.942748 GGAAACTATAACACCCGATGCAA 59.057 43.478 0.00 0.00 0.00 4.08
224 225 3.055021 TGGAAACTATAACACCCGATGCA 60.055 43.478 0.00 0.00 0.00 3.96
225 226 3.537580 TGGAAACTATAACACCCGATGC 58.462 45.455 0.00 0.00 0.00 3.91
226 227 6.693315 ATTTGGAAACTATAACACCCGATG 57.307 37.500 0.00 0.00 0.00 3.84
227 228 7.543756 CAAATTTGGAAACTATAACACCCGAT 58.456 34.615 10.49 0.00 0.00 4.18
228 229 6.570764 GCAAATTTGGAAACTATAACACCCGA 60.571 38.462 19.47 0.00 0.00 5.14
229 230 5.575218 GCAAATTTGGAAACTATAACACCCG 59.425 40.000 19.47 0.00 0.00 5.28
230 231 6.697395 AGCAAATTTGGAAACTATAACACCC 58.303 36.000 19.47 0.00 0.00 4.61
290 291 5.749462 TGTTTTGGAAATTGGTGGAACAAT 58.251 33.333 0.00 0.00 44.16 2.71
328 329 6.480524 TTTCTTGAATCGTCGAACATTCAT 57.519 33.333 16.95 0.00 38.51 2.57
329 330 5.915812 TTTCTTGAATCGTCGAACATTCA 57.084 34.783 13.72 13.72 37.26 2.57
368 370 8.768957 TTCAGAACAATGTTCAAAAATTGTGA 57.231 26.923 25.63 15.40 44.24 3.58
447 451 7.455641 TCCTGAACACTTTTACAAACTTTCA 57.544 32.000 0.00 0.00 0.00 2.69
448 452 8.926715 ATTCCTGAACACTTTTACAAACTTTC 57.073 30.769 0.00 0.00 0.00 2.62
481 485 7.481483 CGTGAACATATTTGAAATCGTGAACAT 59.519 33.333 9.33 0.00 0.00 2.71
482 486 6.794636 CGTGAACATATTTGAAATCGTGAACA 59.205 34.615 9.33 6.61 0.00 3.18
483 487 7.012943 TCGTGAACATATTTGAAATCGTGAAC 58.987 34.615 9.33 4.11 0.00 3.18
484 488 7.095397 ACTCGTGAACATATTTGAAATCGTGAA 60.095 33.333 9.33 0.00 0.00 3.18
485 489 6.367695 ACTCGTGAACATATTTGAAATCGTGA 59.632 34.615 9.33 0.00 0.00 4.35
486 490 6.534059 ACTCGTGAACATATTTGAAATCGTG 58.466 36.000 0.00 0.00 0.00 4.35
487 491 6.721571 ACTCGTGAACATATTTGAAATCGT 57.278 33.333 0.00 0.00 0.00 3.73
488 492 9.536558 TTAAACTCGTGAACATATTTGAAATCG 57.463 29.630 0.00 0.00 0.00 3.34
521 525 5.956068 TCAATTCCGTGAAATCATGAACA 57.044 34.783 0.00 0.00 34.90 3.18
537 541 7.085116 CCGAGATACACTACCACTATCAATTC 58.915 42.308 0.00 0.00 0.00 2.17
549 553 1.475280 TGCACCACCGAGATACACTAC 59.525 52.381 0.00 0.00 0.00 2.73
682 714 6.970043 CGGTCTAACATTTTGTTTTGTCTTGA 59.030 34.615 0.00 0.00 41.45 3.02
700 732 1.843368 ATGTCTTCGACCCGGTCTAA 58.157 50.000 15.70 9.95 0.00 2.10
703 735 1.076332 CAAATGTCTTCGACCCGGTC 58.924 55.000 7.59 7.59 0.00 4.79
705 737 0.953471 TGCAAATGTCTTCGACCCGG 60.953 55.000 0.00 0.00 0.00 5.73
712 744 8.006027 GCAAATTCTAAACTTGCAAATGTCTTC 58.994 33.333 0.00 0.00 43.89 2.87
792 825 3.531538 TCACAAGTCTATTTCCATCCGC 58.468 45.455 0.00 0.00 0.00 5.54
794 827 5.235186 CGTGATCACAAGTCTATTTCCATCC 59.765 44.000 24.93 0.00 0.00 3.51
808 841 1.403647 CCGTAGCCTTCGTGATCACAA 60.404 52.381 24.93 16.20 0.00 3.33
809 842 0.172578 CCGTAGCCTTCGTGATCACA 59.827 55.000 24.93 9.94 0.00 3.58
851 884 2.472232 TACAGGTCAGAGCACGCACG 62.472 60.000 1.66 0.00 0.00 5.34
852 885 0.108615 ATACAGGTCAGAGCACGCAC 60.109 55.000 1.66 0.00 0.00 5.34
853 886 0.108662 CATACAGGTCAGAGCACGCA 60.109 55.000 1.66 0.00 0.00 5.24
854 887 0.173481 TCATACAGGTCAGAGCACGC 59.827 55.000 1.66 0.00 0.00 5.34
896 929 1.029408 TGTAGCGGCCGATTTGCATT 61.029 50.000 33.48 5.22 0.00 3.56
919 953 0.413037 TTTGGGACCTTGCCATGGAT 59.587 50.000 18.40 0.00 37.82 3.41
931 965 5.240844 ACTGCAAACTTGTACTATTTGGGAC 59.759 40.000 14.66 4.10 34.55 4.46
991 1028 2.989909 TCGAGATGCCATTGTTGTGAT 58.010 42.857 0.00 0.00 0.00 3.06
1026 1063 2.616842 GAGGACGAAGATGAGGAGAGAC 59.383 54.545 0.00 0.00 0.00 3.36
1063 1100 3.250744 CATTTGTGGACGATGTAGACGT 58.749 45.455 0.00 0.00 46.58 4.34
1157 1197 2.959372 CTGCGACCGACTGTGGTA 59.041 61.111 2.58 0.00 44.01 3.25
1266 1306 4.704833 GCCCTGGCGAGCTTGACA 62.705 66.667 9.79 9.79 0.00 3.58
1404 1444 4.501714 GCCGCCGATGACACCGTA 62.502 66.667 0.00 0.00 0.00 4.02
1473 1513 0.457853 GAGTCACGGTCGCATTGCTA 60.458 55.000 7.12 0.00 0.00 3.49
1595 1635 2.317609 GCAACAAGCTCCTTCGCGA 61.318 57.895 3.71 3.71 41.15 5.87
1714 1754 7.551617 CCCTAATTCGTGGAAACTACTGTAAAT 59.448 37.037 0.00 0.00 0.00 1.40
1762 1802 0.398318 GCTGGTCAAGGACTCAAGGT 59.602 55.000 0.00 0.00 32.47 3.50
1763 1803 0.397941 TGCTGGTCAAGGACTCAAGG 59.602 55.000 0.00 0.00 32.47 3.61
1764 1804 1.071385 ACTGCTGGTCAAGGACTCAAG 59.929 52.381 0.00 0.00 32.47 3.02
1765 1805 1.131638 ACTGCTGGTCAAGGACTCAA 58.868 50.000 0.00 0.00 32.47 3.02
1766 1806 2.009681 TACTGCTGGTCAAGGACTCA 57.990 50.000 0.00 0.00 32.47 3.41
1767 1807 3.618690 ATTACTGCTGGTCAAGGACTC 57.381 47.619 0.00 0.00 32.47 3.36
1768 1808 5.700402 ATTATTACTGCTGGTCAAGGACT 57.300 39.130 0.00 0.00 32.47 3.85
1769 1809 6.555315 CAAATTATTACTGCTGGTCAAGGAC 58.445 40.000 0.00 0.00 0.00 3.85
1770 1810 5.125417 GCAAATTATTACTGCTGGTCAAGGA 59.875 40.000 0.00 0.00 33.20 3.36
1771 1811 5.105797 TGCAAATTATTACTGCTGGTCAAGG 60.106 40.000 3.71 0.00 37.00 3.61
1772 1812 5.953183 TGCAAATTATTACTGCTGGTCAAG 58.047 37.500 3.71 0.00 37.00 3.02
1773 1813 5.973899 TGCAAATTATTACTGCTGGTCAA 57.026 34.783 3.71 0.00 37.00 3.18
1774 1814 5.476599 ACTTGCAAATTATTACTGCTGGTCA 59.523 36.000 0.00 0.00 37.00 4.02
1775 1815 5.954335 ACTTGCAAATTATTACTGCTGGTC 58.046 37.500 0.00 0.00 37.00 4.02
1816 1856 6.875972 AGGTTGTCATTGGACTAGTCTAAT 57.124 37.500 24.32 24.32 44.61 1.73
1817 1857 6.952358 ACTAGGTTGTCATTGGACTAGTCTAA 59.048 38.462 22.11 22.11 44.61 2.10
1818 1858 6.491383 ACTAGGTTGTCATTGGACTAGTCTA 58.509 40.000 21.88 14.08 44.61 2.59
1819 1859 5.334421 ACTAGGTTGTCATTGGACTAGTCT 58.666 41.667 21.88 0.00 44.61 3.24
1820 1860 5.662674 ACTAGGTTGTCATTGGACTAGTC 57.337 43.478 14.87 14.87 44.61 2.59
1959 3374 2.309528 ATCGAACGGAGCTTTATGCA 57.690 45.000 0.00 0.00 45.94 3.96
1994 3409 0.040067 CGCGATGATCAGATCCGACA 60.040 55.000 0.00 0.00 0.00 4.35
2014 3429 2.566570 TAAGAGGTGGTCACGCGCA 61.567 57.895 5.73 0.00 0.00 6.09
2348 3926 5.957842 AATGATTCGTTGCTGAAGGTTTA 57.042 34.783 0.00 0.00 0.00 2.01
2552 4131 6.473397 CGCAGGATCTCTTGTATTATTTCC 57.527 41.667 0.00 0.00 0.00 3.13
2575 4154 2.816087 TCATGCAAAGAGACTTGAAGCC 59.184 45.455 0.00 0.00 0.00 4.35
2625 4205 7.663081 TGGATCTGCTGTAGGATTTATTCATTC 59.337 37.037 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.