Multiple sequence alignment - TraesCS7B01G075400

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 TraesCS7B01G075400 chr7B 100.000 3515 0 0 1 3515 84699982 84703496 0.000000e+00 6492
1 TraesCS7B01G075400 chr7B 89.718 2869 217 27 718 3514 84650993 84653855 0.000000e+00 3592
2 TraesCS7B01G075400 chr7B 89.248 1916 156 20 622 2493 84765888 84763979 0.000000e+00 2351
3 TraesCS7B01G075400 chr7A 91.263 2930 204 19 622 3515 126195420 126198333 0.000000e+00 3945
4 TraesCS7B01G075400 chr7A 89.781 1918 147 18 622 2493 126368044 126366130 0.000000e+00 2410
5 TraesCS7B01G075400 chr7A 89.181 1867 141 20 667 2494 126190976 126192820 0.000000e+00 2272
6 TraesCS7B01G075400 chr7A 94.030 134 8 0 8 141 717306722 717306855 1.650000e-48 204
7 TraesCS7B01G075400 chr7D 92.972 1736 116 6 1063 2794 123462138 123463871 0.000000e+00 2525
8 TraesCS7B01G075400 chr7D 88.774 1933 156 20 622 2494 123491118 123489187 0.000000e+00 2311
9 TraesCS7B01G075400 chr7D 90.115 1649 136 8 871 2494 123455069 123456715 0.000000e+00 2117
10 TraesCS7B01G075400 chr7D 87.117 1110 136 6 1386 2494 123484830 123483727 0.000000e+00 1251
11 TraesCS7B01G075400 chr7D 89.533 707 48 10 377 1065 123460638 123461336 0.000000e+00 872
12 TraesCS7B01G075400 chr7D 80.991 989 141 26 2563 3515 20958940 20959917 0.000000e+00 741
13 TraesCS7B01G075400 chr7D 80.652 982 145 24 2569 3515 497570704 497569733 0.000000e+00 719
14 TraesCS7B01G075400 chr2D 80.655 977 146 24 2573 3515 314051471 314052438 0.000000e+00 717
15 TraesCS7B01G075400 chr1A 80.225 976 147 27 2573 3512 560369031 560369996 0.000000e+00 691
16 TraesCS7B01G075400 chr3A 80.102 980 149 24 2571 3515 724303070 724302102 0.000000e+00 688
17 TraesCS7B01G075400 chr3A 95.455 220 8 2 162 380 714360554 714360772 2.010000e-92 350
18 TraesCS7B01G075400 chr3A 95.041 121 6 0 21 141 479776534 479776414 1.290000e-44 191
19 TraesCS7B01G075400 chr1B 80.164 978 146 26 2573 3515 670795988 670796952 0.000000e+00 688
20 TraesCS7B01G075400 chr1B 95.455 220 10 0 161 380 654508629 654508410 5.580000e-93 351
21 TraesCS7B01G075400 chr1B 93.103 232 15 1 150 380 22663551 22663782 4.350000e-89 339
22 TraesCS7B01G075400 chr1B 92.029 138 11 0 8 145 656519350 656519213 9.960000e-46 195
23 TraesCS7B01G075400 chr2A 79.959 978 151 24 2573 3515 733698442 733697475 0.000000e+00 678
24 TraesCS7B01G075400 chr6D 80.595 907 135 21 2642 3515 329886084 329886982 0.000000e+00 662
25 TraesCS7B01G075400 chr5B 79.243 978 156 24 2572 3515 54550675 54551639 3.830000e-179 638
26 TraesCS7B01G075400 chr5B 95.455 220 10 0 161 380 711813881 711813662 5.580000e-93 351
27 TraesCS7B01G075400 chr5B 95.000 220 11 0 161 380 711820070 711819851 2.600000e-91 346
28 TraesCS7B01G075400 chr5B 90.769 130 12 0 16 145 264880160 264880031 1.300000e-39 174
29 TraesCS7B01G075400 chr3B 79.103 981 156 30 2573 3515 32728298 32727329 6.400000e-177 630
30 TraesCS7B01G075400 chr3B 95.556 225 10 0 156 380 813188292 813188516 9.280000e-96 361
31 TraesCS7B01G075400 chr4B 78.528 978 157 30 2572 3515 16068952 16067994 8.400000e-166 593
32 TraesCS7B01G075400 chr4B 81.250 560 75 13 2573 3105 536849086 536848530 3.240000e-115 425
33 TraesCS7B01G075400 chr5A 83.333 414 55 10 2573 2979 23936809 23937215 1.540000e-98 370
34 TraesCS7B01G075400 chr5A 92.797 236 17 0 160 395 549412665 549412430 3.360000e-90 342
35 TraesCS7B01G075400 chr4A 95.434 219 10 0 162 380 642447270 642447488 2.010000e-92 350
36 TraesCS7B01G075400 chr2B 95.434 219 10 0 162 380 782101587 782101369 2.010000e-92 350
37 TraesCS7B01G075400 chr1D 96.032 126 5 0 16 141 411747941 411747816 4.600000e-49 206
38 TraesCS7B01G075400 chrUn 90.647 139 12 1 10 147 76006633 76006495 2.150000e-42 183
39 TraesCS7B01G075400 chr5D 89.041 146 12 2 1 146 374710662 374710521 1.000000e-40 178
40 TraesCS7B01G075400 chr4D 91.935 124 10 0 16 139 278325716 278325839 1.300000e-39 174
41 TraesCS7B01G075400 chr3D 89.552 134 13 1 8 141 47133112 47133244 6.030000e-38 169


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 TraesCS7B01G075400 chr7B 84699982 84703496 3514 False 6492.0 6492 100.000000 1 3515 1 chr7B.!!$F2 3514
1 TraesCS7B01G075400 chr7B 84650993 84653855 2862 False 3592.0 3592 89.718000 718 3514 1 chr7B.!!$F1 2796
2 TraesCS7B01G075400 chr7B 84763979 84765888 1909 True 2351.0 2351 89.248000 622 2493 1 chr7B.!!$R1 1871
3 TraesCS7B01G075400 chr7A 126190976 126198333 7357 False 3108.5 3945 90.222000 622 3515 2 chr7A.!!$F2 2893
4 TraesCS7B01G075400 chr7A 126366130 126368044 1914 True 2410.0 2410 89.781000 622 2493 1 chr7A.!!$R1 1871
5 TraesCS7B01G075400 chr7D 123489187 123491118 1931 True 2311.0 2311 88.774000 622 2494 1 chr7D.!!$R2 1872
6 TraesCS7B01G075400 chr7D 123455069 123463871 8802 False 1838.0 2525 90.873333 377 2794 3 chr7D.!!$F2 2417
7 TraesCS7B01G075400 chr7D 123483727 123484830 1103 True 1251.0 1251 87.117000 1386 2494 1 chr7D.!!$R1 1108
8 TraesCS7B01G075400 chr7D 20958940 20959917 977 False 741.0 741 80.991000 2563 3515 1 chr7D.!!$F1 952
9 TraesCS7B01G075400 chr7D 497569733 497570704 971 True 719.0 719 80.652000 2569 3515 1 chr7D.!!$R3 946
10 TraesCS7B01G075400 chr2D 314051471 314052438 967 False 717.0 717 80.655000 2573 3515 1 chr2D.!!$F1 942
11 TraesCS7B01G075400 chr1A 560369031 560369996 965 False 691.0 691 80.225000 2573 3512 1 chr1A.!!$F1 939
12 TraesCS7B01G075400 chr3A 724302102 724303070 968 True 688.0 688 80.102000 2571 3515 1 chr3A.!!$R2 944
13 TraesCS7B01G075400 chr1B 670795988 670796952 964 False 688.0 688 80.164000 2573 3515 1 chr1B.!!$F2 942
14 TraesCS7B01G075400 chr2A 733697475 733698442 967 True 678.0 678 79.959000 2573 3515 1 chr2A.!!$R1 942
15 TraesCS7B01G075400 chr6D 329886084 329886982 898 False 662.0 662 80.595000 2642 3515 1 chr6D.!!$F1 873
16 TraesCS7B01G075400 chr5B 54550675 54551639 964 False 638.0 638 79.243000 2572 3515 1 chr5B.!!$F1 943
17 TraesCS7B01G075400 chr3B 32727329 32728298 969 True 630.0 630 79.103000 2573 3515 1 chr3B.!!$R1 942
18 TraesCS7B01G075400 chr4B 16067994 16068952 958 True 593.0 593 78.528000 2572 3515 1 chr4B.!!$R1 943
19 TraesCS7B01G075400 chr4B 536848530 536849086 556 True 425.0 425 81.250000 2573 3105 1 chr4B.!!$R2 532

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
574 5775 0.179234 TCTTTGTGGTTGTGCGAGGA 59.821 50.0 0.00 0.0 0.0 3.71 F
1461 12000 0.395311 ATCTCAAGGTCCCGCGTCTA 60.395 55.0 4.92 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2441 12981 1.211212 TGATCAGATCCAGCAGGTTGG 59.789 52.381 8.00 0.0 39.70 3.77 R
2850 13409 0.179000 GATGAGGGCACGGTTCATCT 59.821 55.000 8.95 0.0 42.36 2.90 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
22 23 5.437191 ACCAAACAGGAGGAACTTATAGG 57.563 43.478 0.00 0.00 41.55 2.57
24 25 4.473559 CCAAACAGGAGGAACTTATAGGGA 59.526 45.833 0.00 0.00 41.55 4.20
26 27 4.628661 ACAGGAGGAACTTATAGGGACT 57.371 45.455 0.00 0.00 41.55 3.85
28 29 6.101274 ACAGGAGGAACTTATAGGGACTTA 57.899 41.667 0.00 0.00 41.55 2.24
29 30 6.694611 ACAGGAGGAACTTATAGGGACTTAT 58.305 40.000 0.00 0.00 41.55 1.73
30 31 7.834046 ACAGGAGGAACTTATAGGGACTTATA 58.166 38.462 0.00 0.00 41.55 0.98
31 32 7.951245 ACAGGAGGAACTTATAGGGACTTATAG 59.049 40.741 0.00 0.00 41.55 1.31
34 35 8.586744 GGAGGAACTTATAGGGACTTATAGTTG 58.413 40.741 0.00 0.00 41.55 3.16
35 36 9.145442 GAGGAACTTATAGGGACTTATAGTTGT 57.855 37.037 0.00 0.00 41.55 3.32
46 47 9.448587 AGGGACTTATAGTTGTAATATGGTCTT 57.551 33.333 0.00 0.00 27.25 3.01
77 78 9.856162 AAACTTATAAGTCCTAGAAACCAAACA 57.144 29.630 18.28 0.00 38.57 2.83
78 79 9.503399 AACTTATAAGTCCTAGAAACCAAACAG 57.497 33.333 18.28 0.00 38.57 3.16
79 80 8.101419 ACTTATAAGTCCTAGAAACCAAACAGG 58.899 37.037 12.50 0.00 37.95 4.00
93 94 5.959618 CCAAACAGGTAGGGACTTTTTAG 57.040 43.478 0.00 0.00 41.75 1.85
95 96 4.652679 AACAGGTAGGGACTTTTTAGGG 57.347 45.455 0.00 0.00 41.75 3.53
96 97 3.878086 ACAGGTAGGGACTTTTTAGGGA 58.122 45.455 0.00 0.00 41.75 4.20
98 99 3.844804 CAGGTAGGGACTTTTTAGGGACT 59.155 47.826 0.00 0.00 41.75 3.85
99 100 4.288887 CAGGTAGGGACTTTTTAGGGACTT 59.711 45.833 0.00 0.00 39.49 3.01
100 101 4.288887 AGGTAGGGACTTTTTAGGGACTTG 59.711 45.833 0.00 0.00 39.49 3.16
101 102 3.808834 AGGGACTTTTTAGGGACTTGG 57.191 47.619 0.00 0.00 34.75 3.61
102 103 2.378886 AGGGACTTTTTAGGGACTTGGG 59.621 50.000 0.00 0.00 34.75 4.12
103 104 2.377531 GGGACTTTTTAGGGACTTGGGA 59.622 50.000 0.00 0.00 41.75 4.37
104 105 3.418995 GGACTTTTTAGGGACTTGGGAC 58.581 50.000 0.00 0.00 41.75 4.46
105 106 3.074094 GGACTTTTTAGGGACTTGGGACT 59.926 47.826 0.00 0.00 41.75 3.85
106 107 4.072839 GACTTTTTAGGGACTTGGGACTG 58.927 47.826 0.00 0.00 41.75 3.51
107 108 3.720002 ACTTTTTAGGGACTTGGGACTGA 59.280 43.478 0.00 0.00 41.75 3.41
109 110 4.799715 TTTTAGGGACTTGGGACTGAAA 57.200 40.909 0.00 0.00 41.75 2.69
110 111 4.799715 TTTAGGGACTTGGGACTGAAAA 57.200 40.909 0.00 0.00 41.75 2.29
136 137 5.801380 GTCCTAGGACTTATGAACCAAACA 58.199 41.667 31.12 0.00 41.57 2.83
137 138 5.875359 GTCCTAGGACTTATGAACCAAACAG 59.125 44.000 31.12 0.00 41.57 3.16
138 139 5.045869 TCCTAGGACTTATGAACCAAACAGG 60.046 44.000 7.62 0.00 45.67 4.00
141 142 2.159382 ACTTATGAACCAAACAGGGCG 58.841 47.619 0.00 0.00 43.89 6.13
142 143 2.159382 CTTATGAACCAAACAGGGCGT 58.841 47.619 0.00 0.00 43.89 5.68
144 145 2.279935 ATGAACCAAACAGGGCGTAA 57.720 45.000 0.00 0.00 43.89 3.18
145 146 2.054232 TGAACCAAACAGGGCGTAAA 57.946 45.000 0.00 0.00 43.89 2.01
147 148 2.099427 TGAACCAAACAGGGCGTAAAAC 59.901 45.455 0.00 0.00 43.89 2.43
148 149 2.061509 ACCAAACAGGGCGTAAAACT 57.938 45.000 0.00 0.00 43.89 2.66
149 150 2.380941 ACCAAACAGGGCGTAAAACTT 58.619 42.857 0.00 0.00 43.89 2.66
150 151 2.100087 ACCAAACAGGGCGTAAAACTTG 59.900 45.455 0.00 0.00 43.89 3.16
151 152 2.100087 CCAAACAGGGCGTAAAACTTGT 59.900 45.455 0.00 0.00 0.00 3.16
170 171 6.347859 CTTGTAAAGTCAAGTACTCCCTCT 57.652 41.667 0.00 0.00 39.70 3.69
171 172 5.723672 TGTAAAGTCAAGTACTCCCTCTG 57.276 43.478 0.00 0.00 37.50 3.35
172 173 5.145564 TGTAAAGTCAAGTACTCCCTCTGT 58.854 41.667 0.00 0.00 37.50 3.41
174 175 3.818295 AGTCAAGTACTCCCTCTGTCT 57.182 47.619 0.00 0.00 30.33 3.41
175 176 3.692690 AGTCAAGTACTCCCTCTGTCTC 58.307 50.000 0.00 0.00 30.33 3.36
176 177 3.074687 AGTCAAGTACTCCCTCTGTCTCA 59.925 47.826 0.00 0.00 30.33 3.27
178 179 3.074687 TCAAGTACTCCCTCTGTCTCAGT 59.925 47.826 0.00 0.00 32.61 3.41
179 180 3.818295 AGTACTCCCTCTGTCTCAGTT 57.182 47.619 0.00 0.00 32.61 3.16
180 181 4.120946 AGTACTCCCTCTGTCTCAGTTT 57.879 45.455 0.00 0.00 32.61 2.66
181 182 5.258216 AGTACTCCCTCTGTCTCAGTTTA 57.742 43.478 0.00 0.00 32.61 2.01
183 184 3.845860 ACTCCCTCTGTCTCAGTTTACA 58.154 45.455 0.00 0.00 32.61 2.41
184 185 4.223953 ACTCCCTCTGTCTCAGTTTACAA 58.776 43.478 0.00 0.00 32.61 2.41
185 186 4.282195 ACTCCCTCTGTCTCAGTTTACAAG 59.718 45.833 0.00 0.00 32.61 3.16
186 187 4.223953 TCCCTCTGTCTCAGTTTACAAGT 58.776 43.478 0.00 0.00 32.61 3.16
187 188 4.281182 TCCCTCTGTCTCAGTTTACAAGTC 59.719 45.833 0.00 0.00 32.61 3.01
189 190 4.282195 CCTCTGTCTCAGTTTACAAGTCCT 59.718 45.833 0.00 0.00 32.61 3.85
191 192 6.349777 CCTCTGTCTCAGTTTACAAGTCCTAG 60.350 46.154 0.00 0.00 32.61 3.02
193 194 4.021368 TGTCTCAGTTTACAAGTCCTAGGC 60.021 45.833 2.96 0.00 0.00 3.93
194 195 3.192844 TCTCAGTTTACAAGTCCTAGGCG 59.807 47.826 2.96 0.00 0.00 5.52
195 196 2.895404 TCAGTTTACAAGTCCTAGGCGT 59.105 45.455 2.96 1.00 0.00 5.68
196 197 4.081406 TCAGTTTACAAGTCCTAGGCGTA 58.919 43.478 2.96 0.00 0.00 4.42
197 198 4.708421 TCAGTTTACAAGTCCTAGGCGTAT 59.292 41.667 2.96 0.00 0.00 3.06
199 200 5.975939 CAGTTTACAAGTCCTAGGCGTATAC 59.024 44.000 2.96 8.10 0.00 1.47
201 202 3.309600 ACAAGTCCTAGGCGTATACCT 57.690 47.619 2.96 0.00 44.31 3.08
202 203 4.443978 ACAAGTCCTAGGCGTATACCTA 57.556 45.455 2.96 0.00 41.50 3.08
209 210 1.046204 AGGCGTATACCTAGGTTGCC 58.954 55.000 27.06 27.06 38.67 4.52
210 211 0.754472 GGCGTATACCTAGGTTGCCA 59.246 55.000 28.35 12.18 40.66 4.92
211 212 1.139455 GGCGTATACCTAGGTTGCCAA 59.861 52.381 28.35 11.86 40.66 4.52
212 213 2.224450 GGCGTATACCTAGGTTGCCAAT 60.224 50.000 28.35 17.01 40.66 3.16
213 214 3.473625 GCGTATACCTAGGTTGCCAATT 58.526 45.455 22.11 0.00 0.00 2.32
214 215 3.881089 GCGTATACCTAGGTTGCCAATTT 59.119 43.478 22.11 0.00 0.00 1.82
215 216 5.058490 GCGTATACCTAGGTTGCCAATTTA 58.942 41.667 22.11 0.00 0.00 1.40
216 217 5.528320 GCGTATACCTAGGTTGCCAATTTAA 59.472 40.000 22.11 0.00 0.00 1.52
219 220 7.442969 CGTATACCTAGGTTGCCAATTTAATCA 59.557 37.037 22.11 0.00 0.00 2.57
220 221 5.914898 ACCTAGGTTGCCAATTTAATCAC 57.085 39.130 9.21 0.00 0.00 3.06
221 222 4.709886 ACCTAGGTTGCCAATTTAATCACC 59.290 41.667 9.21 0.00 0.00 4.02
224 225 4.941713 AGGTTGCCAATTTAATCACCCTA 58.058 39.130 0.00 0.00 0.00 3.53
225 226 5.337788 AGGTTGCCAATTTAATCACCCTAA 58.662 37.500 0.00 0.00 0.00 2.69
227 228 7.129425 AGGTTGCCAATTTAATCACCCTAATA 58.871 34.615 0.00 0.00 0.00 0.98
228 229 7.789349 AGGTTGCCAATTTAATCACCCTAATAT 59.211 33.333 0.00 0.00 0.00 1.28
229 230 9.084533 GGTTGCCAATTTAATCACCCTAATATA 57.915 33.333 0.00 0.00 0.00 0.86
329 330 9.920946 ATATGACTTGTATTAGGTTGGTCAAAT 57.079 29.630 0.00 0.00 36.16 2.32
330 331 8.650143 ATGACTTGTATTAGGTTGGTCAAATT 57.350 30.769 0.00 0.00 36.16 1.82
331 332 9.747898 ATGACTTGTATTAGGTTGGTCAAATTA 57.252 29.630 0.00 0.00 36.16 1.40
332 333 9.575868 TGACTTGTATTAGGTTGGTCAAATTAA 57.424 29.630 0.00 0.00 30.81 1.40
335 336 8.618702 TTGTATTAGGTTGGTCAAATTAACGA 57.381 30.769 0.00 0.00 0.00 3.85
336 337 8.795842 TGTATTAGGTTGGTCAAATTAACGAT 57.204 30.769 0.00 0.00 0.00 3.73
337 338 8.885722 TGTATTAGGTTGGTCAAATTAACGATC 58.114 33.333 0.00 0.00 0.00 3.69
338 339 9.106070 GTATTAGGTTGGTCAAATTAACGATCT 57.894 33.333 0.00 0.00 0.00 2.75
341 342 6.113411 AGGTTGGTCAAATTAACGATCTAGG 58.887 40.000 0.00 0.00 0.00 3.02
342 343 5.296035 GGTTGGTCAAATTAACGATCTAGGG 59.704 44.000 0.00 0.00 0.00 3.53
343 344 5.031066 TGGTCAAATTAACGATCTAGGGG 57.969 43.478 0.00 0.00 0.00 4.79
344 345 4.472108 TGGTCAAATTAACGATCTAGGGGT 59.528 41.667 0.00 0.00 0.00 4.95
348 349 3.930634 ATTAACGATCTAGGGGTACGC 57.069 47.619 0.29 0.29 43.76 4.42
358 359 4.814294 GGGTACGCTCACGCCCTG 62.814 72.222 2.05 0.00 45.53 4.45
359 360 4.065281 GGTACGCTCACGCCCTGT 62.065 66.667 0.00 0.00 45.53 4.00
360 361 2.703798 GGTACGCTCACGCCCTGTA 61.704 63.158 0.00 0.00 45.53 2.74
361 362 1.213537 GTACGCTCACGCCCTGTAA 59.786 57.895 0.00 0.00 45.53 2.41
362 363 0.388907 GTACGCTCACGCCCTGTAAA 60.389 55.000 0.00 0.00 45.53 2.01
364 365 1.374252 CGCTCACGCCCTGTAAACT 60.374 57.895 0.00 0.00 0.00 2.66
366 367 0.320421 GCTCACGCCCTGTAAACTGA 60.320 55.000 0.00 0.00 0.00 3.41
367 368 1.714794 CTCACGCCCTGTAAACTGAG 58.285 55.000 0.00 0.00 0.00 3.35
368 369 1.272490 CTCACGCCCTGTAAACTGAGA 59.728 52.381 0.00 0.00 0.00 3.27
370 371 1.272490 CACGCCCTGTAAACTGAGAGA 59.728 52.381 0.00 0.00 0.00 3.10
371 372 1.546476 ACGCCCTGTAAACTGAGAGAG 59.454 52.381 0.00 0.00 0.00 3.20
372 373 1.819288 CGCCCTGTAAACTGAGAGAGA 59.181 52.381 0.00 0.00 0.00 3.10
373 374 2.159310 CGCCCTGTAAACTGAGAGAGAG 60.159 54.545 0.00 0.00 0.00 3.20
375 376 2.763448 CCCTGTAAACTGAGAGAGAGGG 59.237 54.545 0.00 0.00 33.23 4.30
376 377 3.564571 CCCTGTAAACTGAGAGAGAGGGA 60.565 52.174 8.74 0.00 41.40 4.20
377 378 3.699038 CCTGTAAACTGAGAGAGAGGGAG 59.301 52.174 0.00 0.00 0.00 4.30
378 379 4.340617 CTGTAAACTGAGAGAGAGGGAGT 58.659 47.826 0.00 0.00 0.00 3.85
379 380 5.502079 CTGTAAACTGAGAGAGAGGGAGTA 58.498 45.833 0.00 0.00 0.00 2.59
380 381 5.888901 TGTAAACTGAGAGAGAGGGAGTAA 58.111 41.667 0.00 0.00 0.00 2.24
388 5582 4.884247 AGAGAGAGGGAGTAAAACGTTTG 58.116 43.478 15.46 0.00 0.00 2.93
390 5584 4.377897 AGAGAGGGAGTAAAACGTTTGTG 58.622 43.478 15.46 0.00 0.00 3.33
416 5610 8.079211 ACTCTTTGTAGGTCTAGCATTATTGA 57.921 34.615 0.00 0.00 0.00 2.57
423 5617 4.513442 GGTCTAGCATTATTGACCACACA 58.487 43.478 6.18 0.00 45.87 3.72
424 5618 4.572389 GGTCTAGCATTATTGACCACACAG 59.428 45.833 6.18 0.00 45.87 3.66
425 5619 4.034510 GTCTAGCATTATTGACCACACAGC 59.965 45.833 0.00 0.00 0.00 4.40
426 5620 2.794103 AGCATTATTGACCACACAGCA 58.206 42.857 0.00 0.00 0.00 4.41
428 5622 3.192001 AGCATTATTGACCACACAGCAAG 59.808 43.478 0.00 0.00 0.00 4.01
429 5623 3.674138 GCATTATTGACCACACAGCAAGG 60.674 47.826 0.00 0.00 0.00 3.61
437 5638 3.052082 CACAGCAAGGGACGCCTG 61.052 66.667 0.00 0.00 0.00 4.85
442 5643 2.358737 CAAGGGACGCCTGTGGAC 60.359 66.667 0.00 0.00 0.00 4.02
449 5650 0.238289 GACGCCTGTGGACACAAATG 59.762 55.000 6.60 1.91 41.33 2.32
459 5660 1.135689 GGACACAAATGCCACGTCATC 60.136 52.381 0.00 0.00 0.00 2.92
469 5670 1.227234 CACGTCATCCCATGCGCTA 60.227 57.895 9.73 0.00 34.66 4.26
481 5682 2.414481 CCATGCGCTAAGATATGTGCTC 59.586 50.000 9.73 0.00 40.02 4.26
508 5709 1.202371 GGACGACAGTCACTGTTCACA 60.202 52.381 12.92 0.00 45.44 3.58
509 5710 2.545952 GGACGACAGTCACTGTTCACAT 60.546 50.000 12.92 0.00 45.44 3.21
516 5717 5.811562 ACAGTCACTGTTCACATGGAATGC 61.812 45.833 3.98 0.00 45.42 3.56
563 5764 6.095432 TGTATCATTTGGGTTTCTTTGTGG 57.905 37.500 0.00 0.00 0.00 4.17
564 5765 5.600484 TGTATCATTTGGGTTTCTTTGTGGT 59.400 36.000 0.00 0.00 0.00 4.16
565 5766 5.628797 ATCATTTGGGTTTCTTTGTGGTT 57.371 34.783 0.00 0.00 0.00 3.67
568 5769 3.601443 TTGGGTTTCTTTGTGGTTGTG 57.399 42.857 0.00 0.00 0.00 3.33
574 5775 0.179234 TCTTTGTGGTTGTGCGAGGA 59.821 50.000 0.00 0.00 0.00 3.71
608 5813 2.342179 GTGCTAGAGGTGAAAGACAGC 58.658 52.381 0.00 0.00 46.00 4.40
697 5902 1.475034 GCCTTCACTTGTGTGTCCTCA 60.475 52.381 0.46 0.00 44.14 3.86
713 5918 1.067212 CCTCAGTACCATCGGTGCTAC 59.933 57.143 3.31 0.00 46.43 3.58
721 5927 7.679500 AGTACCATCGGTGCTACCTAGCTAA 62.679 48.000 1.55 0.00 46.31 3.09
918 6152 4.884164 CCTTCTTTTAAGACATGGGGCTAG 59.116 45.833 0.00 0.00 34.13 3.42
926 6160 0.916358 ACATGGGGCTAGCAGAACCT 60.916 55.000 18.24 0.92 0.00 3.50
946 6180 2.982130 GACAGCCCCAGACATCGT 59.018 61.111 0.00 0.00 0.00 3.73
1028 6280 3.133365 AAGGAGCACCAAACGGGCT 62.133 57.895 2.07 0.00 42.05 5.19
1034 6286 2.115266 ACCAAACGGGCTGGGAAG 59.885 61.111 0.00 0.00 42.05 3.46
1206 7283 2.180769 CCGACCATCGACTTCGCA 59.819 61.111 0.00 0.00 43.74 5.10
1209 7286 1.443872 GACCATCGACTTCGCACGT 60.444 57.895 0.00 0.00 39.60 4.49
1461 12000 0.395311 ATCTCAAGGTCCCGCGTCTA 60.395 55.000 4.92 0.00 0.00 2.59
1554 12093 4.719369 GCCGACGACAACGAGCCT 62.719 66.667 0.00 0.00 42.66 4.58
1832 12371 3.284449 GAACACCACCACCGCCAC 61.284 66.667 0.00 0.00 0.00 5.01
1944 12484 4.838486 CAGGTCGTCGAGCTCGGC 62.838 72.222 33.98 32.14 38.40 5.54
2049 12589 2.637383 GGACCTCGAGGAGCGTGTT 61.637 63.158 37.69 13.78 41.80 3.32
2076 12616 1.752358 GCGGGATGCTGATCAGAGGA 61.752 60.000 27.04 9.34 41.73 3.71
2388 12928 2.093711 GGAGAGAAGGAGGAAAGCACTC 60.094 54.545 0.00 0.00 0.00 3.51
2473 13013 3.059051 GGATCTGATCAAGCATTTCGAGC 60.059 47.826 18.64 0.00 0.00 5.03
2524 13064 5.856455 CAGAAGGACGCGTAAAATGAATTTT 59.144 36.000 13.97 6.29 42.21 1.82
2605 13155 3.631250 TGAAGGCTCAAGAAAAACCAGT 58.369 40.909 0.00 0.00 0.00 4.00
2640 13191 1.168714 GCCATCAACCAGTCAGGAAC 58.831 55.000 0.00 0.00 41.22 3.62
2682 13233 9.720769 TTACAACCAACTAGGAATAGAAAAGAG 57.279 33.333 0.00 0.00 41.22 2.85
2818 13373 7.502561 AGTGAACTTAAACCAATAGAGCAAACT 59.497 33.333 0.00 0.00 0.00 2.66
2980 13540 1.133025 CGCCGAAAGATGGAAATGCTT 59.867 47.619 0.00 0.00 0.00 3.91
3062 13644 2.244651 ACGAAAGTCCACACAGCGC 61.245 57.895 0.00 0.00 44.19 5.92
3132 13714 6.419413 GTCACTGAACAAACAAACAAACAGAA 59.581 34.615 0.00 0.00 0.00 3.02
3134 13716 7.043059 TCACTGAACAAACAAACAAACAGAAAC 60.043 33.333 0.00 0.00 0.00 2.78
3226 13826 3.384467 ACATTGCTACTGCCAACAAAAGT 59.616 39.130 0.00 0.00 38.71 2.66
3236 13836 1.410932 CCAACAAAAGTGAGGACCCCA 60.411 52.381 0.00 0.00 0.00 4.96
3252 13852 1.321943 CCAATCCCCTCCCTACCCT 59.678 63.158 0.00 0.00 0.00 4.34
3263 13863 1.079825 TCCCTACCCTAGGCAAAGACA 59.920 52.381 2.05 0.00 44.86 3.41
3276 13876 2.415090 GCAAAGACATCGAGCAAGCAAT 60.415 45.455 0.00 0.00 0.00 3.56
3298 13898 4.323417 TCACAGATTGGCTAACGAACAAT 58.677 39.130 0.00 0.00 37.52 2.71
3327 13929 6.243216 AGGAATGCGGACCTAAACTAATTA 57.757 37.500 0.00 0.00 34.47 1.40
3329 13931 7.114095 AGGAATGCGGACCTAAACTAATTAAA 58.886 34.615 0.00 0.00 34.47 1.52
3376 13979 1.944024 TCGCCGATGAAACAACAAACT 59.056 42.857 0.00 0.00 0.00 2.66
3412 14015 0.983378 GCACCCCTACACTCTCCCAT 60.983 60.000 0.00 0.00 0.00 4.00
3424 14027 1.210204 TCTCCCATCTTGCCCAAGCT 61.210 55.000 3.18 0.00 40.80 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.227527 CCCTATAAGTTCCTCCTGTTTGGT 59.772 45.833 0.00 0.00 37.07 3.67
1 2 4.473559 TCCCTATAAGTTCCTCCTGTTTGG 59.526 45.833 0.00 0.00 37.10 3.28
4 5 4.961585 AGTCCCTATAAGTTCCTCCTGTT 58.038 43.478 0.00 0.00 0.00 3.16
5 6 4.628661 AGTCCCTATAAGTTCCTCCTGT 57.371 45.455 0.00 0.00 0.00 4.00
7 8 8.071235 ACTATAAGTCCCTATAAGTTCCTCCT 57.929 38.462 0.00 0.00 0.00 3.69
8 9 8.586744 CAACTATAAGTCCCTATAAGTTCCTCC 58.413 40.741 0.00 0.00 0.00 4.30
9 10 9.145442 ACAACTATAAGTCCCTATAAGTTCCTC 57.855 37.037 0.00 0.00 0.00 3.71
20 21 9.448587 AAGACCATATTACAACTATAAGTCCCT 57.551 33.333 0.00 0.00 0.00 4.20
52 53 9.503399 CTGTTTGGTTTCTAGGACTTATAAGTT 57.497 33.333 18.96 7.26 39.88 2.66
54 55 8.494016 CCTGTTTGGTTTCTAGGACTTATAAG 57.506 38.462 11.05 11.05 0.00 1.73
71 72 4.765339 CCTAAAAAGTCCCTACCTGTTTGG 59.235 45.833 0.00 0.00 42.93 3.28
74 75 4.042560 GTCCCTAAAAAGTCCCTACCTGTT 59.957 45.833 0.00 0.00 0.00 3.16
75 76 3.586174 GTCCCTAAAAAGTCCCTACCTGT 59.414 47.826 0.00 0.00 0.00 4.00
76 77 3.844804 AGTCCCTAAAAAGTCCCTACCTG 59.155 47.826 0.00 0.00 0.00 4.00
77 78 4.157668 AGTCCCTAAAAAGTCCCTACCT 57.842 45.455 0.00 0.00 0.00 3.08
78 79 4.567116 CCAAGTCCCTAAAAAGTCCCTACC 60.567 50.000 0.00 0.00 0.00 3.18
79 80 4.567116 CCCAAGTCCCTAAAAAGTCCCTAC 60.567 50.000 0.00 0.00 0.00 3.18
80 81 3.590182 CCCAAGTCCCTAAAAAGTCCCTA 59.410 47.826 0.00 0.00 0.00 3.53
82 83 2.377531 TCCCAAGTCCCTAAAAAGTCCC 59.622 50.000 0.00 0.00 0.00 4.46
84 85 4.072839 CAGTCCCAAGTCCCTAAAAAGTC 58.927 47.826 0.00 0.00 0.00 3.01
86 87 4.367039 TCAGTCCCAAGTCCCTAAAAAG 57.633 45.455 0.00 0.00 0.00 2.27
87 88 4.799715 TTCAGTCCCAAGTCCCTAAAAA 57.200 40.909 0.00 0.00 0.00 1.94
88 89 4.799715 TTTCAGTCCCAAGTCCCTAAAA 57.200 40.909 0.00 0.00 0.00 1.52
89 90 4.799715 TTTTCAGTCCCAAGTCCCTAAA 57.200 40.909 0.00 0.00 0.00 1.85
113 114 5.801380 TGTTTGGTTCATAAGTCCTAGGAC 58.199 41.667 31.29 31.29 44.86 3.85
114 115 5.045869 CCTGTTTGGTTCATAAGTCCTAGGA 60.046 44.000 7.62 7.62 0.00 2.94
116 117 5.186198 CCCTGTTTGGTTCATAAGTCCTAG 58.814 45.833 0.00 0.00 0.00 3.02
117 118 4.566907 GCCCTGTTTGGTTCATAAGTCCTA 60.567 45.833 0.00 0.00 0.00 2.94
118 119 3.814316 GCCCTGTTTGGTTCATAAGTCCT 60.814 47.826 0.00 0.00 0.00 3.85
119 120 2.492088 GCCCTGTTTGGTTCATAAGTCC 59.508 50.000 0.00 0.00 0.00 3.85
120 121 2.161609 CGCCCTGTTTGGTTCATAAGTC 59.838 50.000 0.00 0.00 0.00 3.01
121 122 2.159382 CGCCCTGTTTGGTTCATAAGT 58.841 47.619 0.00 0.00 0.00 2.24
122 123 2.159382 ACGCCCTGTTTGGTTCATAAG 58.841 47.619 0.00 0.00 0.00 1.73
123 124 2.279935 ACGCCCTGTTTGGTTCATAA 57.720 45.000 0.00 0.00 0.00 1.90
124 125 3.420300 TTACGCCCTGTTTGGTTCATA 57.580 42.857 0.00 0.00 0.00 2.15
126 127 2.054232 TTTACGCCCTGTTTGGTTCA 57.946 45.000 0.00 0.00 0.00 3.18
127 128 2.359848 AGTTTTACGCCCTGTTTGGTTC 59.640 45.455 0.00 0.00 0.00 3.62
129 130 2.061509 AGTTTTACGCCCTGTTTGGT 57.938 45.000 0.00 0.00 0.00 3.67
130 131 2.100087 ACAAGTTTTACGCCCTGTTTGG 59.900 45.455 0.00 0.00 0.00 3.28
131 132 3.430333 ACAAGTTTTACGCCCTGTTTG 57.570 42.857 0.00 0.00 0.00 2.93
133 134 4.641541 ACTTTACAAGTTTTACGCCCTGTT 59.358 37.500 0.00 0.00 39.04 3.16
134 135 4.201657 ACTTTACAAGTTTTACGCCCTGT 58.798 39.130 0.00 0.00 39.04 4.00
135 136 4.273969 TGACTTTACAAGTTTTACGCCCTG 59.726 41.667 0.00 0.00 43.03 4.45
136 137 4.453751 TGACTTTACAAGTTTTACGCCCT 58.546 39.130 0.00 0.00 43.03 5.19
137 138 4.816786 TGACTTTACAAGTTTTACGCCC 57.183 40.909 0.00 0.00 43.03 6.13
148 149 5.601313 ACAGAGGGAGTACTTGACTTTACAA 59.399 40.000 0.00 0.00 39.06 2.41
149 150 5.145564 ACAGAGGGAGTACTTGACTTTACA 58.854 41.667 0.00 0.00 39.06 2.41
150 151 5.477637 AGACAGAGGGAGTACTTGACTTTAC 59.522 44.000 0.00 0.00 39.06 2.01
151 152 5.642165 AGACAGAGGGAGTACTTGACTTTA 58.358 41.667 0.00 0.00 39.06 1.85
155 156 3.422796 TGAGACAGAGGGAGTACTTGAC 58.577 50.000 0.00 0.00 0.00 3.18
156 157 3.074687 ACTGAGACAGAGGGAGTACTTGA 59.925 47.826 0.00 0.00 35.18 3.02
157 158 3.426615 ACTGAGACAGAGGGAGTACTTG 58.573 50.000 0.00 0.00 35.18 3.16
158 159 3.818295 ACTGAGACAGAGGGAGTACTT 57.182 47.619 0.00 0.00 35.18 2.24
159 160 3.818295 AACTGAGACAGAGGGAGTACT 57.182 47.619 0.00 0.00 35.18 2.73
161 162 4.994282 TGTAAACTGAGACAGAGGGAGTA 58.006 43.478 5.76 0.00 35.18 2.59
162 163 3.845860 TGTAAACTGAGACAGAGGGAGT 58.154 45.455 5.76 0.00 35.18 3.85
163 164 4.282195 ACTTGTAAACTGAGACAGAGGGAG 59.718 45.833 5.76 0.00 35.18 4.30
164 165 4.223953 ACTTGTAAACTGAGACAGAGGGA 58.776 43.478 5.76 0.00 35.18 4.20
165 166 4.561105 GACTTGTAAACTGAGACAGAGGG 58.439 47.826 5.76 0.00 35.18 4.30
166 167 4.282195 AGGACTTGTAAACTGAGACAGAGG 59.718 45.833 5.76 0.00 35.18 3.69
168 169 5.477291 CCTAGGACTTGTAAACTGAGACAGA 59.523 44.000 1.05 0.00 35.18 3.41
170 171 4.021368 GCCTAGGACTTGTAAACTGAGACA 60.021 45.833 14.75 0.00 0.00 3.41
171 172 4.496360 GCCTAGGACTTGTAAACTGAGAC 58.504 47.826 14.75 0.00 0.00 3.36
172 173 3.192844 CGCCTAGGACTTGTAAACTGAGA 59.807 47.826 14.75 0.00 0.00 3.27
174 175 2.895404 ACGCCTAGGACTTGTAAACTGA 59.105 45.455 14.75 0.00 0.00 3.41
175 176 3.314541 ACGCCTAGGACTTGTAAACTG 57.685 47.619 14.75 0.00 0.00 3.16
176 177 5.068329 GGTATACGCCTAGGACTTGTAAACT 59.932 44.000 14.75 0.00 0.00 2.66
178 179 5.203528 AGGTATACGCCTAGGACTTGTAAA 58.796 41.667 14.75 0.00 37.04 2.01
179 180 4.796606 AGGTATACGCCTAGGACTTGTAA 58.203 43.478 14.75 0.00 37.04 2.41
180 181 4.443978 AGGTATACGCCTAGGACTTGTA 57.556 45.455 14.75 9.37 37.04 2.41
181 182 3.309600 AGGTATACGCCTAGGACTTGT 57.690 47.619 14.75 7.29 37.04 3.16
189 190 2.242043 GGCAACCTAGGTATACGCCTA 58.758 52.381 26.05 0.00 39.94 3.93
191 192 0.754472 TGGCAACCTAGGTATACGCC 59.246 55.000 26.36 26.36 38.56 5.68
193 194 7.442969 TGATTAAATTGGCAACCTAGGTATACG 59.557 37.037 16.67 5.52 0.00 3.06
194 195 8.565416 GTGATTAAATTGGCAACCTAGGTATAC 58.435 37.037 16.67 8.74 0.00 1.47
195 196 7.722285 GGTGATTAAATTGGCAACCTAGGTATA 59.278 37.037 16.67 0.00 0.00 1.47
196 197 6.549736 GGTGATTAAATTGGCAACCTAGGTAT 59.450 38.462 16.67 0.83 0.00 2.73
197 198 5.889289 GGTGATTAAATTGGCAACCTAGGTA 59.111 40.000 16.67 0.00 0.00 3.08
199 200 4.099419 GGGTGATTAAATTGGCAACCTAGG 59.901 45.833 7.41 7.41 35.26 3.02
201 202 4.941713 AGGGTGATTAAATTGGCAACCTA 58.058 39.130 0.00 0.00 46.13 3.08
202 203 3.790126 AGGGTGATTAAATTGGCAACCT 58.210 40.909 0.00 0.00 43.35 3.50
203 204 5.669164 TTAGGGTGATTAAATTGGCAACC 57.331 39.130 0.00 0.00 38.39 3.77
304 305 9.747898 AATTTGACCAACCTAATACAAGTCATA 57.252 29.630 0.00 0.00 33.21 2.15
305 306 8.650143 AATTTGACCAACCTAATACAAGTCAT 57.350 30.769 0.00 0.00 33.21 3.06
306 307 9.575868 TTAATTTGACCAACCTAATACAAGTCA 57.424 29.630 0.00 0.00 0.00 3.41
307 308 9.836076 GTTAATTTGACCAACCTAATACAAGTC 57.164 33.333 0.00 0.00 0.00 3.01
308 309 8.508875 CGTTAATTTGACCAACCTAATACAAGT 58.491 33.333 0.00 0.00 0.00 3.16
309 310 8.723311 TCGTTAATTTGACCAACCTAATACAAG 58.277 33.333 0.00 0.00 0.00 3.16
311 312 8.795842 ATCGTTAATTTGACCAACCTAATACA 57.204 30.769 0.00 0.00 0.00 2.29
314 315 9.326413 CTAGATCGTTAATTTGACCAACCTAAT 57.674 33.333 0.00 0.00 0.00 1.73
315 316 7.767198 CCTAGATCGTTAATTTGACCAACCTAA 59.233 37.037 0.00 0.00 0.00 2.69
316 317 7.270047 CCTAGATCGTTAATTTGACCAACCTA 58.730 38.462 0.00 0.00 0.00 3.08
317 318 6.113411 CCTAGATCGTTAATTTGACCAACCT 58.887 40.000 0.00 0.00 0.00 3.50
318 319 5.296035 CCCTAGATCGTTAATTTGACCAACC 59.704 44.000 0.00 0.00 0.00 3.77
319 320 5.296035 CCCCTAGATCGTTAATTTGACCAAC 59.704 44.000 0.00 0.00 0.00 3.77
320 321 5.045432 ACCCCTAGATCGTTAATTTGACCAA 60.045 40.000 0.00 0.00 0.00 3.67
322 323 5.032327 ACCCCTAGATCGTTAATTTGACC 57.968 43.478 0.00 0.00 0.00 4.02
323 324 5.689068 CGTACCCCTAGATCGTTAATTTGAC 59.311 44.000 0.00 0.00 0.00 3.18
324 325 5.737063 GCGTACCCCTAGATCGTTAATTTGA 60.737 44.000 0.00 0.00 0.00 2.69
325 326 4.446719 GCGTACCCCTAGATCGTTAATTTG 59.553 45.833 0.00 0.00 0.00 2.32
326 327 4.343239 AGCGTACCCCTAGATCGTTAATTT 59.657 41.667 0.00 0.00 0.00 1.82
327 328 3.893813 AGCGTACCCCTAGATCGTTAATT 59.106 43.478 0.00 0.00 0.00 1.40
328 329 3.494332 AGCGTACCCCTAGATCGTTAAT 58.506 45.455 0.00 0.00 0.00 1.40
329 330 2.880890 GAGCGTACCCCTAGATCGTTAA 59.119 50.000 0.00 0.00 0.00 2.01
330 331 2.158769 TGAGCGTACCCCTAGATCGTTA 60.159 50.000 0.00 0.00 0.00 3.18
331 332 1.316651 GAGCGTACCCCTAGATCGTT 58.683 55.000 0.00 0.00 0.00 3.85
332 333 0.182061 TGAGCGTACCCCTAGATCGT 59.818 55.000 0.00 0.00 0.00 3.73
335 336 2.716814 CGTGAGCGTACCCCTAGAT 58.283 57.895 0.00 0.00 0.00 1.98
336 337 4.230603 CGTGAGCGTACCCCTAGA 57.769 61.111 0.00 0.00 0.00 2.43
348 349 1.272490 TCTCAGTTTACAGGGCGTGAG 59.728 52.381 14.98 0.00 34.06 3.51
351 352 1.546476 CTCTCTCAGTTTACAGGGCGT 59.454 52.381 0.00 0.00 0.00 5.68
352 353 1.819288 TCTCTCTCAGTTTACAGGGCG 59.181 52.381 0.00 0.00 0.00 6.13
353 354 2.167487 CCTCTCTCTCAGTTTACAGGGC 59.833 54.545 0.00 0.00 0.00 5.19
355 356 3.699038 CTCCCTCTCTCTCAGTTTACAGG 59.301 52.174 0.00 0.00 0.00 4.00
357 358 4.390129 ACTCCCTCTCTCTCAGTTTACA 57.610 45.455 0.00 0.00 0.00 2.41
358 359 6.837471 TTTACTCCCTCTCTCTCAGTTTAC 57.163 41.667 0.00 0.00 0.00 2.01
359 360 6.072064 CGTTTTACTCCCTCTCTCTCAGTTTA 60.072 42.308 0.00 0.00 0.00 2.01
360 361 5.279056 CGTTTTACTCCCTCTCTCTCAGTTT 60.279 44.000 0.00 0.00 0.00 2.66
361 362 4.218852 CGTTTTACTCCCTCTCTCTCAGTT 59.781 45.833 0.00 0.00 0.00 3.16
362 363 3.759618 CGTTTTACTCCCTCTCTCTCAGT 59.240 47.826 0.00 0.00 0.00 3.41
364 365 3.764218 ACGTTTTACTCCCTCTCTCTCA 58.236 45.455 0.00 0.00 0.00 3.27
366 367 4.344390 ACAAACGTTTTACTCCCTCTCTCT 59.656 41.667 11.66 0.00 0.00 3.10
367 368 4.448060 CACAAACGTTTTACTCCCTCTCTC 59.552 45.833 11.66 0.00 0.00 3.20
368 369 4.100498 TCACAAACGTTTTACTCCCTCTCT 59.900 41.667 11.66 0.00 0.00 3.10
370 371 4.124970 GTCACAAACGTTTTACTCCCTCT 58.875 43.478 11.66 0.00 0.00 3.69
371 372 4.124970 AGTCACAAACGTTTTACTCCCTC 58.875 43.478 11.66 0.00 0.00 4.30
372 373 4.124970 GAGTCACAAACGTTTTACTCCCT 58.875 43.478 24.32 12.67 0.00 4.20
373 374 4.124970 AGAGTCACAAACGTTTTACTCCC 58.875 43.478 27.77 15.49 35.13 4.30
375 376 6.540205 ACAAAGAGTCACAAACGTTTTACTC 58.460 36.000 25.93 25.93 34.85 2.59
376 377 6.490566 ACAAAGAGTCACAAACGTTTTACT 57.509 33.333 11.66 14.57 0.00 2.24
377 378 6.903479 CCTACAAAGAGTCACAAACGTTTTAC 59.097 38.462 11.66 10.02 0.00 2.01
378 379 6.594937 ACCTACAAAGAGTCACAAACGTTTTA 59.405 34.615 11.66 0.00 0.00 1.52
379 380 5.413523 ACCTACAAAGAGTCACAAACGTTTT 59.586 36.000 11.66 0.00 0.00 2.43
380 381 4.939439 ACCTACAAAGAGTCACAAACGTTT 59.061 37.500 7.96 7.96 0.00 3.60
388 5582 4.785511 TGCTAGACCTACAAAGAGTCAC 57.214 45.455 0.00 0.00 32.82 3.67
390 5584 8.198109 TCAATAATGCTAGACCTACAAAGAGTC 58.802 37.037 0.00 0.00 0.00 3.36
416 5610 2.111043 CGTCCCTTGCTGTGTGGT 59.889 61.111 0.00 0.00 0.00 4.16
419 5613 3.560251 AGGCGTCCCTTGCTGTGT 61.560 61.111 0.00 0.00 38.74 3.72
420 5614 3.052082 CAGGCGTCCCTTGCTGTG 61.052 66.667 0.00 0.00 40.33 3.66
421 5615 3.560251 ACAGGCGTCCCTTGCTGT 61.560 61.111 0.00 0.00 40.33 4.40
422 5616 3.052082 CACAGGCGTCCCTTGCTG 61.052 66.667 0.00 0.00 40.33 4.41
423 5617 4.335647 CCACAGGCGTCCCTTGCT 62.336 66.667 0.00 0.00 40.33 3.91
424 5618 4.329545 TCCACAGGCGTCCCTTGC 62.330 66.667 0.00 0.00 40.33 4.01
425 5619 2.358737 GTCCACAGGCGTCCCTTG 60.359 66.667 0.00 0.00 40.33 3.61
426 5620 2.847234 TGTCCACAGGCGTCCCTT 60.847 61.111 0.00 0.00 40.33 3.95
428 5622 2.951475 TTTGTGTCCACAGGCGTCCC 62.951 60.000 0.00 0.00 42.94 4.46
429 5623 0.889186 ATTTGTGTCCACAGGCGTCC 60.889 55.000 0.00 0.00 42.94 4.79
437 5638 0.040425 GACGTGGCATTTGTGTCCAC 60.040 55.000 0.00 10.14 45.02 4.02
442 5643 0.171007 GGGATGACGTGGCATTTGTG 59.829 55.000 0.00 0.00 0.00 3.33
449 5650 3.576356 CGCATGGGATGACGTGGC 61.576 66.667 3.11 0.00 0.00 5.01
459 5660 1.466167 GCACATATCTTAGCGCATGGG 59.534 52.381 11.47 5.47 0.00 4.00
469 5670 1.606480 CCGATGGCGAGCACATATCTT 60.606 52.381 0.00 0.00 40.82 2.40
481 5682 2.579787 GACTGTCGTCCGATGGCG 60.580 66.667 0.00 0.00 33.98 5.69
522 5723 6.460781 TGATACATACCAGACGACAGTTTTT 58.539 36.000 0.00 0.00 0.00 1.94
531 5732 4.703897 ACCCAAATGATACATACCAGACG 58.296 43.478 0.00 0.00 0.00 4.18
563 5764 2.029290 TCCTAGAACTTCCTCGCACAAC 60.029 50.000 0.00 0.00 0.00 3.32
564 5765 2.231478 CTCCTAGAACTTCCTCGCACAA 59.769 50.000 0.00 0.00 0.00 3.33
565 5766 1.819288 CTCCTAGAACTTCCTCGCACA 59.181 52.381 0.00 0.00 0.00 4.57
568 5769 1.064357 CGTCTCCTAGAACTTCCTCGC 59.936 57.143 0.00 0.00 0.00 5.03
574 5775 3.942748 CTCTAGCACGTCTCCTAGAACTT 59.057 47.826 14.49 0.00 39.46 2.66
608 5813 1.139308 CGTCTCAGCAGCTCTCCAG 59.861 63.158 0.00 0.00 0.00 3.86
721 5927 0.465460 TTTGCTTGTCGAGGCTTGGT 60.465 50.000 0.97 0.00 0.00 3.67
926 6160 3.315142 GATGTCTGGGGCTGTCGCA 62.315 63.158 0.00 0.00 38.10 5.10
946 6180 7.704271 AGATAGTTCGATACTGATTCGTTTGA 58.296 34.615 9.58 0.00 37.73 2.69
953 6191 9.005777 GGTAAGAGAGATAGTTCGATACTGATT 57.994 37.037 9.58 0.00 37.73 2.57
1206 7283 4.078516 GGCAGGCCGGACTTACGT 62.079 66.667 7.41 0.00 0.00 3.57
1281 7358 0.167470 GGATCTTGTCGACGTCGTCA 59.833 55.000 34.40 31.66 40.80 4.35
1563 12102 3.465403 CTCCTCTCCACGCCAGGG 61.465 72.222 0.00 0.00 0.00 4.45
1832 12371 2.098680 GAGACTCGTCGGCGTCAG 59.901 66.667 10.18 2.21 39.49 3.51
2000 12540 2.183300 GCACATCCTCGCCGTACA 59.817 61.111 0.00 0.00 0.00 2.90
2179 12719 2.803155 AAGTGCGGCCATGTCACGAT 62.803 55.000 2.24 0.00 35.97 3.73
2332 12872 1.354705 CCCATCCATGATGCTCCTGAT 59.645 52.381 0.00 0.00 38.59 2.90
2388 12928 1.938657 TTGCCTTCTCCGAGAGAGCG 61.939 60.000 13.91 0.00 42.90 5.03
2441 12981 1.211212 TGATCAGATCCAGCAGGTTGG 59.789 52.381 8.00 0.00 39.70 3.77
2524 13064 1.273606 GTGCTCTGTAAGACTCTGGCA 59.726 52.381 0.00 0.00 38.67 4.92
2605 13155 7.395772 TGGTTGATGGCTATGTTAATTCAAAGA 59.604 33.333 0.00 0.00 0.00 2.52
2619 13170 1.951209 TCCTGACTGGTTGATGGCTA 58.049 50.000 0.00 0.00 37.07 3.93
2640 13191 2.080693 TGTAATGGCGGCTTTGTGTAG 58.919 47.619 18.73 0.00 0.00 2.74
2781 13336 5.751990 GGTTTAAGTTCACTCGAAAGACTCA 59.248 40.000 0.00 0.00 35.39 3.41
2818 13373 1.293498 GCTCAGCCCGAAGTTCTCA 59.707 57.895 0.56 0.00 0.00 3.27
2850 13409 0.179000 GATGAGGGCACGGTTCATCT 59.821 55.000 8.95 0.00 42.36 2.90
2980 13540 1.302431 CGTGCCCAGAACCATGTCA 60.302 57.895 0.00 0.00 0.00 3.58
3062 13644 2.148916 TCGTGCTTGTAACAGTGAGG 57.851 50.000 0.00 0.00 0.00 3.86
3205 13803 3.737266 CACTTTTGTTGGCAGTAGCAATG 59.263 43.478 0.00 0.00 44.61 2.82
3206 13804 3.636300 TCACTTTTGTTGGCAGTAGCAAT 59.364 39.130 0.00 0.00 44.61 3.56
3226 13826 1.307866 GAGGGGATTGGGGTCCTCA 60.308 63.158 0.00 0.00 41.50 3.86
3236 13836 0.875311 CCTAGGGTAGGGAGGGGATT 59.125 60.000 0.00 0.00 42.42 3.01
3252 13852 2.621338 CTTGCTCGATGTCTTTGCCTA 58.379 47.619 0.00 0.00 0.00 3.93
3263 13863 2.391616 TCTGTGATTGCTTGCTCGAT 57.608 45.000 0.00 0.00 0.00 3.59
3276 13876 3.394674 TGTTCGTTAGCCAATCTGTGA 57.605 42.857 0.00 0.00 0.00 3.58
3298 13898 2.286365 AGGTCCGCATTCCTTTTGAA 57.714 45.000 0.00 0.00 37.38 2.69
3329 13931 2.645802 TGGAGCGTGGTTACTTGTTTT 58.354 42.857 0.00 0.00 0.00 2.43
3336 13938 1.092348 GGGATTTGGAGCGTGGTTAC 58.908 55.000 0.00 0.00 0.00 2.50
3337 13939 0.988832 AGGGATTTGGAGCGTGGTTA 59.011 50.000 0.00 0.00 0.00 2.85
3376 13979 2.425592 CTGAGCGGTGGTGGTTGA 59.574 61.111 0.00 0.00 0.00 3.18
3424 14027 1.434188 TCTCCTTCTTGAAGGTGCCA 58.566 50.000 23.78 8.37 40.81 4.92
3466 14069 4.290722 AGAAATCCCTTGTTGAGACTGGAT 59.709 41.667 0.00 0.00 33.64 3.41


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

AutoCloner maintained by Alex Coulton.