Multiple sequence alignment - TraesCS5B01G205000

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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 TraesCS5B01G205000 chr5B 100.000 2552 0 0 1 2552 373220732 373223283 0.000000e+00 4713.0
1 TraesCS5B01G205000 chr6A 97.036 2227 56 2 222 2439 184710729 184712954 0.000000e+00 3738.0
2 TraesCS5B01G205000 chr6A 80.332 422 61 15 237 651 119336771 119336365 1.480000e-77 300.0
3 TraesCS5B01G205000 chr6A 85.333 75 11 0 142 216 553081172 553081098 7.570000e-11 78.7
4 TraesCS5B01G205000 chr2B 96.989 2225 50 3 222 2437 408291811 408289595 0.000000e+00 3722.0
5 TraesCS5B01G205000 chr2B 96.659 1317 34 2 1130 2437 772543527 772544842 0.000000e+00 2180.0
6 TraesCS5B01G205000 chr2B 91.743 109 7 2 2331 2438 429459272 429459379 1.580000e-32 150.0
7 TraesCS5B01G205000 chr2B 91.346 104 9 0 2335 2438 5491283 5491180 2.650000e-30 143.0
8 TraesCS5B01G205000 chr2A 96.900 2226 59 3 222 2438 768555453 768553229 0.000000e+00 3720.0
9 TraesCS5B01G205000 chr2A 86.842 76 10 0 140 215 384972319 384972244 4.520000e-13 86.1
10 TraesCS5B01G205000 chr7D 95.376 2206 88 9 220 2415 106623668 106625869 0.000000e+00 3496.0
11 TraesCS5B01G205000 chr7D 90.882 340 31 0 530 869 627406938 627406599 8.320000e-125 457.0
12 TraesCS5B01G205000 chr7D 94.595 74 4 0 142 215 159740965 159740892 5.770000e-22 115.0
13 TraesCS5B01G205000 chr5A 89.062 1737 143 14 727 2437 666310952 666312667 0.000000e+00 2111.0
14 TraesCS5B01G205000 chr5A 89.076 119 9 2 19 137 417252421 417252307 7.360000e-31 145.0
15 TraesCS5B01G205000 chr2D 94.048 1361 63 8 296 1647 559820742 559819391 0.000000e+00 2049.0
16 TraesCS5B01G205000 chr2D 94.667 75 4 0 142 216 562579396 562579470 1.600000e-22 117.0
17 TraesCS5B01G205000 chr2D 88.158 76 9 0 141 216 39170752 39170677 9.720000e-15 91.6
18 TraesCS5B01G205000 chr6B 91.213 1468 94 18 986 2437 21463821 21462373 0.000000e+00 1964.0
19 TraesCS5B01G205000 chr4D 95.554 1147 46 4 1290 2435 401371413 401372555 0.000000e+00 1831.0
20 TraesCS5B01G205000 chr7B 91.680 1214 93 7 1229 2437 482023683 482024893 0.000000e+00 1676.0
21 TraesCS5B01G205000 chr3B 91.382 1172 88 8 1272 2438 32936182 32937345 0.000000e+00 1592.0
22 TraesCS5B01G205000 chr5D 94.828 116 6 0 2437 2552 333057909 333057794 5.610000e-42 182.0
23 TraesCS5B01G205000 chr5D 93.333 75 5 0 142 216 333057971 333057897 7.460000e-21 111.0
24 TraesCS5B01G205000 chr1D 94.828 116 6 0 2437 2552 402299964 402299849 5.610000e-42 182.0
25 TraesCS5B01G205000 chr1D 86.667 75 10 0 142 216 60949673 60949599 1.630000e-12 84.2
26 TraesCS5B01G205000 chr1D 87.500 72 9 0 142 213 402298635 402298706 1.630000e-12 84.2
27 TraesCS5B01G205000 chr1A 94.828 116 6 0 2437 2552 321881040 321881155 5.610000e-42 182.0
28 TraesCS5B01G205000 chr1A 93.103 116 8 0 2437 2552 574333728 574333613 1.210000e-38 171.0
29 TraesCS5B01G205000 chr1A 88.750 80 9 0 134 213 321882385 321882306 5.810000e-17 99.0
30 TraesCS5B01G205000 chr1A 96.970 33 0 1 138 169 531316320 531316352 1.000000e-03 54.7
31 TraesCS5B01G205000 chr3D 92.241 116 8 1 2437 2552 351947117 351947003 2.030000e-36 163.0
32 TraesCS5B01G205000 chr3D 88.158 76 7 2 142 216 7127585 7127511 3.500000e-14 89.8
33 TraesCS5B01G205000 chr3D 87.500 72 9 0 142 213 351945797 351945868 1.630000e-12 84.2
34 TraesCS5B01G205000 chr3D 100.000 28 0 0 142 169 565000749 565000776 5.000000e-03 52.8
35 TraesCS5B01G205000 chr4A 94.595 74 4 0 143 216 718496612 718496539 5.770000e-22 115.0
36 TraesCS5B01G205000 chr4B 93.333 75 5 0 142 216 536120879 536120953 7.460000e-21 111.0
37 TraesCS5B01G205000 chr4B 86.842 76 9 1 140 215 536121982 536121908 1.630000e-12 84.2


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 TraesCS5B01G205000 chr5B 373220732 373223283 2551 False 4713 4713 100.000 1 2552 1 chr5B.!!$F1 2551
1 TraesCS5B01G205000 chr6A 184710729 184712954 2225 False 3738 3738 97.036 222 2439 1 chr6A.!!$F1 2217
2 TraesCS5B01G205000 chr2B 408289595 408291811 2216 True 3722 3722 96.989 222 2437 1 chr2B.!!$R2 2215
3 TraesCS5B01G205000 chr2B 772543527 772544842 1315 False 2180 2180 96.659 1130 2437 1 chr2B.!!$F2 1307
4 TraesCS5B01G205000 chr2A 768553229 768555453 2224 True 3720 3720 96.900 222 2438 1 chr2A.!!$R2 2216
5 TraesCS5B01G205000 chr7D 106623668 106625869 2201 False 3496 3496 95.376 220 2415 1 chr7D.!!$F1 2195
6 TraesCS5B01G205000 chr5A 666310952 666312667 1715 False 2111 2111 89.062 727 2437 1 chr5A.!!$F1 1710
7 TraesCS5B01G205000 chr2D 559819391 559820742 1351 True 2049 2049 94.048 296 1647 1 chr2D.!!$R2 1351
8 TraesCS5B01G205000 chr6B 21462373 21463821 1448 True 1964 1964 91.213 986 2437 1 chr6B.!!$R1 1451
9 TraesCS5B01G205000 chr4D 401371413 401372555 1142 False 1831 1831 95.554 1290 2435 1 chr4D.!!$F1 1145
10 TraesCS5B01G205000 chr7B 482023683 482024893 1210 False 1676 1676 91.680 1229 2437 1 chr7B.!!$F1 1208
11 TraesCS5B01G205000 chr3B 32936182 32937345 1163 False 1592 1592 91.382 1272 2438 1 chr3B.!!$F1 1166

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
129 130 0.02877 TTTACGTGCTGTGCTGCAAC 59.971 50.0 2.77 0.0 45.12 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 1780 0.035458 CCAGAAAGCTCTCAACCCGT 59.965 55.0 0.0 0.0 0.0 5.28 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
17 18 4.337060 GTTGACAAACGGGCGGCC 62.337 66.667 20.04 20.04 0.00 6.13
18 19 4.877619 TTGACAAACGGGCGGCCA 62.878 61.111 29.19 2.80 0.00 5.36
65 66 2.728817 CCGTGACCTCGGGCTATC 59.271 66.667 2.85 0.00 45.88 2.08
66 67 2.331805 CGTGACCTCGGGCTATCG 59.668 66.667 0.00 0.00 0.00 2.92
67 68 2.027751 GTGACCTCGGGCTATCGC 59.972 66.667 0.00 0.00 0.00 4.58
68 69 2.123854 TGACCTCGGGCTATCGCT 60.124 61.111 0.00 0.00 36.09 4.93
69 70 2.336809 GACCTCGGGCTATCGCTG 59.663 66.667 0.00 0.00 36.09 5.18
70 71 3.214250 GACCTCGGGCTATCGCTGG 62.214 68.421 0.00 0.00 36.09 4.85
71 72 4.671569 CCTCGGGCTATCGCTGGC 62.672 72.222 0.00 0.00 36.09 4.85
72 73 3.610669 CTCGGGCTATCGCTGGCT 61.611 66.667 0.00 0.00 36.09 4.75
73 74 3.565910 CTCGGGCTATCGCTGGCTC 62.566 68.421 0.00 0.00 36.09 4.70
74 75 3.610669 CGGGCTATCGCTGGCTCT 61.611 66.667 0.00 0.00 36.09 4.09
75 76 2.030262 GGGCTATCGCTGGCTCTG 59.970 66.667 0.00 0.00 36.09 3.35
76 77 2.664518 GGCTATCGCTGGCTCTGC 60.665 66.667 0.00 0.00 36.09 4.26
82 83 4.748679 CGCTGGCTCTGCGTTTGC 62.749 66.667 14.96 0.00 44.43 3.68
92 93 4.268655 GCGTTTGCATCCGATTCG 57.731 55.556 9.44 0.00 42.15 3.34
93 94 1.297598 GCGTTTGCATCCGATTCGG 60.298 57.895 19.16 19.16 44.69 4.30
94 95 1.977594 GCGTTTGCATCCGATTCGGT 61.978 55.000 23.64 9.40 44.09 4.69
95 96 2.657477 GCGTTTGCATCCGATTCGGTA 61.657 52.381 23.64 11.68 44.09 4.02
96 97 4.720111 GCGTTTGCATCCGATTCGGTAC 62.720 54.545 23.64 14.66 44.09 3.34
121 122 4.640805 CGTACAAATCTTTACGTGCTGT 57.359 40.909 0.00 0.00 37.02 4.40
122 123 4.382831 CGTACAAATCTTTACGTGCTGTG 58.617 43.478 0.00 0.00 37.02 3.66
123 124 3.268013 ACAAATCTTTACGTGCTGTGC 57.732 42.857 0.00 0.00 0.00 4.57
124 125 2.878406 ACAAATCTTTACGTGCTGTGCT 59.122 40.909 0.00 0.00 0.00 4.40
125 126 3.228749 CAAATCTTTACGTGCTGTGCTG 58.771 45.455 0.00 0.00 0.00 4.41
126 127 0.798776 ATCTTTACGTGCTGTGCTGC 59.201 50.000 0.00 0.00 0.00 5.25
127 128 0.531753 TCTTTACGTGCTGTGCTGCA 60.532 50.000 0.00 0.00 41.05 4.41
128 129 0.307453 CTTTACGTGCTGTGCTGCAA 59.693 50.000 2.77 0.00 45.12 4.08
129 130 0.028770 TTTACGTGCTGTGCTGCAAC 59.971 50.000 2.77 0.00 45.12 4.17
130 131 1.092345 TTACGTGCTGTGCTGCAACA 61.092 50.000 2.77 4.31 45.12 3.33
139 140 2.358957 TGTGCTGCAACAGATATGACC 58.641 47.619 2.77 0.00 32.44 4.02
140 141 1.328680 GTGCTGCAACAGATATGACCG 59.671 52.381 2.77 0.00 32.44 4.79
141 142 0.940126 GCTGCAACAGATATGACCGG 59.060 55.000 0.00 0.00 32.44 5.28
142 143 1.473257 GCTGCAACAGATATGACCGGA 60.473 52.381 9.46 0.00 32.44 5.14
143 144 2.477825 CTGCAACAGATATGACCGGAG 58.522 52.381 9.46 0.00 32.44 4.63
144 145 1.831106 TGCAACAGATATGACCGGAGT 59.169 47.619 9.46 0.00 0.00 3.85
145 146 2.205074 GCAACAGATATGACCGGAGTG 58.795 52.381 9.46 0.00 0.00 3.51
146 147 2.159099 GCAACAGATATGACCGGAGTGA 60.159 50.000 9.46 0.00 0.00 3.41
147 148 3.678806 GCAACAGATATGACCGGAGTGAA 60.679 47.826 9.46 0.00 0.00 3.18
148 149 4.115516 CAACAGATATGACCGGAGTGAAG 58.884 47.826 9.46 0.00 0.00 3.02
149 150 3.366396 ACAGATATGACCGGAGTGAAGT 58.634 45.455 9.46 0.00 0.00 3.01
150 151 3.381908 ACAGATATGACCGGAGTGAAGTC 59.618 47.826 9.46 0.00 0.00 3.01
151 152 3.634448 CAGATATGACCGGAGTGAAGTCT 59.366 47.826 9.46 0.00 0.00 3.24
152 153 4.822350 CAGATATGACCGGAGTGAAGTCTA 59.178 45.833 9.46 0.00 0.00 2.59
153 154 5.475220 CAGATATGACCGGAGTGAAGTCTAT 59.525 44.000 9.46 0.00 0.00 1.98
154 155 6.015856 CAGATATGACCGGAGTGAAGTCTATT 60.016 42.308 9.46 0.00 0.00 1.73
155 156 6.551601 AGATATGACCGGAGTGAAGTCTATTT 59.448 38.462 9.46 0.00 0.00 1.40
156 157 4.884668 TGACCGGAGTGAAGTCTATTTT 57.115 40.909 9.46 0.00 0.00 1.82
157 158 5.988310 TGACCGGAGTGAAGTCTATTTTA 57.012 39.130 9.46 0.00 0.00 1.52
158 159 6.349243 TGACCGGAGTGAAGTCTATTTTAA 57.651 37.500 9.46 0.00 0.00 1.52
159 160 6.761312 TGACCGGAGTGAAGTCTATTTTAAA 58.239 36.000 9.46 0.00 0.00 1.52
160 161 6.647895 TGACCGGAGTGAAGTCTATTTTAAAC 59.352 38.462 9.46 0.00 0.00 2.01
161 162 5.936372 ACCGGAGTGAAGTCTATTTTAAACC 59.064 40.000 9.46 0.00 0.00 3.27
162 163 6.171213 CCGGAGTGAAGTCTATTTTAAACCT 58.829 40.000 0.00 0.00 0.00 3.50
163 164 6.653740 CCGGAGTGAAGTCTATTTTAAACCTT 59.346 38.462 0.00 0.00 0.00 3.50
164 165 7.360946 CCGGAGTGAAGTCTATTTTAAACCTTG 60.361 40.741 0.00 0.00 0.00 3.61
165 166 7.386848 CGGAGTGAAGTCTATTTTAAACCTTGA 59.613 37.037 0.00 0.00 0.00 3.02
166 167 9.063615 GGAGTGAAGTCTATTTTAAACCTTGAA 57.936 33.333 0.00 0.00 0.00 2.69
180 181 9.515226 TTTAAACCTTGAATTCATACAGCTAGT 57.485 29.630 9.40 0.00 0.00 2.57
181 182 7.617041 AAACCTTGAATTCATACAGCTAGTC 57.383 36.000 9.40 0.00 0.00 2.59
182 183 5.352284 ACCTTGAATTCATACAGCTAGTCG 58.648 41.667 9.40 0.00 0.00 4.18
183 184 4.747108 CCTTGAATTCATACAGCTAGTCGG 59.253 45.833 9.40 0.00 0.00 4.79
184 185 4.322080 TGAATTCATACAGCTAGTCGGG 57.678 45.455 3.38 0.00 0.00 5.14
185 186 3.958147 TGAATTCATACAGCTAGTCGGGA 59.042 43.478 3.38 0.00 0.00 5.14
186 187 4.588951 TGAATTCATACAGCTAGTCGGGAT 59.411 41.667 3.38 0.00 0.00 3.85
187 188 4.792521 ATTCATACAGCTAGTCGGGATC 57.207 45.455 0.00 0.00 0.00 3.36
188 189 3.223674 TCATACAGCTAGTCGGGATCA 57.776 47.619 0.00 0.00 0.00 2.92
189 190 3.562182 TCATACAGCTAGTCGGGATCAA 58.438 45.455 0.00 0.00 0.00 2.57
190 191 3.958147 TCATACAGCTAGTCGGGATCAAA 59.042 43.478 0.00 0.00 0.00 2.69
191 192 2.674796 ACAGCTAGTCGGGATCAAAC 57.325 50.000 0.00 0.00 0.00 2.93
192 193 1.207329 ACAGCTAGTCGGGATCAAACC 59.793 52.381 0.00 0.00 0.00 3.27
193 194 0.831307 AGCTAGTCGGGATCAAACCC 59.169 55.000 0.00 0.00 45.92 4.11
203 204 4.042271 GGGATCAAACCCTAACCTTTCA 57.958 45.455 0.00 0.00 45.90 2.69
204 205 4.412843 GGGATCAAACCCTAACCTTTCAA 58.587 43.478 0.00 0.00 45.90 2.69
205 206 5.023452 GGGATCAAACCCTAACCTTTCAAT 58.977 41.667 0.00 0.00 45.90 2.57
206 207 5.127194 GGGATCAAACCCTAACCTTTCAATC 59.873 44.000 0.00 0.00 45.90 2.67
207 208 5.127194 GGATCAAACCCTAACCTTTCAATCC 59.873 44.000 0.00 0.00 0.00 3.01
208 209 4.412843 TCAAACCCTAACCTTTCAATCCC 58.587 43.478 0.00 0.00 0.00 3.85
209 210 4.107311 TCAAACCCTAACCTTTCAATCCCT 59.893 41.667 0.00 0.00 0.00 4.20
210 211 3.739401 ACCCTAACCTTTCAATCCCTG 57.261 47.619 0.00 0.00 0.00 4.45
211 212 3.265489 ACCCTAACCTTTCAATCCCTGA 58.735 45.455 0.00 0.00 0.00 3.86
212 213 3.660669 ACCCTAACCTTTCAATCCCTGAA 59.339 43.478 0.00 0.00 42.48 3.02
535 536 2.418910 CGCTCTCCCACGTCCTCAT 61.419 63.158 0.00 0.00 0.00 2.90
688 689 1.296715 GTCGTGGAGACCAAGGCAT 59.703 57.895 3.74 0.00 43.95 4.40
849 850 1.532868 GCGTCAACATCTGCTTCTGTT 59.467 47.619 0.00 0.00 36.04 3.16
998 999 0.100503 GCAAAGAGCACCGTTGTTGT 59.899 50.000 6.64 0.00 44.79 3.32
1187 1196 1.529244 GAGCTGTGTTGTGGGCCTT 60.529 57.895 4.53 0.00 0.00 4.35
1311 1329 0.178992 CAAGTGAGGGTTGGCAGGAA 60.179 55.000 0.00 0.00 0.00 3.36
1325 1343 4.752879 GGAAGTGCTACCGCGGCA 62.753 66.667 28.58 15.64 39.65 5.69
1410 1428 0.465097 CTGCTTGGCTCCATGGTAGG 60.465 60.000 12.58 4.75 0.00 3.18
1446 1464 1.775039 CTTATGGGCATCGTGCGGTG 61.775 60.000 0.00 0.00 46.21 4.94
1539 1557 0.107945 GGCGTCCTCTGAGCTCATTT 60.108 55.000 18.63 0.00 0.00 2.32
1679 1697 2.079925 GGGCATCTGTTGTCTCTGTTC 58.920 52.381 0.00 0.00 0.00 3.18
1720 1738 0.390866 CCGAGCTGATGTTGCAGTCT 60.391 55.000 0.00 0.00 38.17 3.24
1742 1760 2.485124 GCTCTGGCTAATCAGACTGCAT 60.485 50.000 0.00 0.00 38.70 3.96
1762 1780 1.253593 TGTTGCAAGGTTGTGTGGCA 61.254 50.000 0.00 0.00 0.00 4.92
1824 1842 0.617820 AGACTATCCCTTGTGCCGGT 60.618 55.000 1.90 0.00 0.00 5.28
1962 1980 2.369001 GGTGCCTACCTCCCCTCT 59.631 66.667 0.00 0.00 43.97 3.69
1979 1997 4.030913 CCCTCTTATGGTGTCTTCCACTA 58.969 47.826 0.00 0.00 43.94 2.74
2296 2326 1.080974 GTGGACCGTCTACGTGGTG 60.081 63.158 0.00 0.00 38.99 4.17
2381 2412 7.321908 GTTTTCCTAAATTAACCGGGCAATTA 58.678 34.615 6.32 0.00 0.00 1.40
2455 2486 3.388552 AAATCCCTGAAATCTGGACCC 57.611 47.619 7.82 0.00 37.15 4.46
2456 2487 2.293598 ATCCCTGAAATCTGGACCCT 57.706 50.000 7.82 0.00 37.15 4.34
2457 2488 2.961536 TCCCTGAAATCTGGACCCTA 57.038 50.000 7.82 0.00 37.15 3.53
2458 2489 3.438131 TCCCTGAAATCTGGACCCTAT 57.562 47.619 7.82 0.00 37.15 2.57
2459 2490 4.569676 TCCCTGAAATCTGGACCCTATA 57.430 45.455 7.82 0.00 37.15 1.31
2460 2491 4.232091 TCCCTGAAATCTGGACCCTATAC 58.768 47.826 7.82 0.00 37.15 1.47
2461 2492 4.077982 TCCCTGAAATCTGGACCCTATACT 60.078 45.833 7.82 0.00 37.15 2.12
2462 2493 4.660771 CCCTGAAATCTGGACCCTATACTT 59.339 45.833 7.82 0.00 37.15 2.24
2463 2494 5.844516 CCCTGAAATCTGGACCCTATACTTA 59.155 44.000 7.82 0.00 37.15 2.24
2464 2495 6.502158 CCCTGAAATCTGGACCCTATACTTAT 59.498 42.308 7.82 0.00 37.15 1.73
2465 2496 7.678598 CCCTGAAATCTGGACCCTATACTTATA 59.321 40.741 7.82 0.00 37.15 0.98
2466 2497 8.754080 CCTGAAATCTGGACCCTATACTTATAG 58.246 40.741 0.31 0.00 37.15 1.31
2467 2498 9.535170 CTGAAATCTGGACCCTATACTTATAGA 57.465 37.037 5.04 0.00 38.30 1.98
2470 2501 9.495382 AAATCTGGACCCTATACTTATAGATCC 57.505 37.037 14.19 14.19 38.30 3.36
2471 2502 6.982899 TCTGGACCCTATACTTATAGATCCC 58.017 44.000 16.45 10.05 38.30 3.85
2472 2503 5.763355 TGGACCCTATACTTATAGATCCCG 58.237 45.833 16.45 0.00 38.30 5.14
2473 2504 5.139001 GGACCCTATACTTATAGATCCCGG 58.861 50.000 0.00 0.00 38.30 5.73
2474 2505 5.340695 GGACCCTATACTTATAGATCCCGGT 60.341 48.000 0.00 3.63 38.30 5.28
2475 2506 5.764432 ACCCTATACTTATAGATCCCGGTC 58.236 45.833 0.00 0.00 38.30 4.79
2476 2507 5.495436 ACCCTATACTTATAGATCCCGGTCT 59.505 44.000 0.00 0.00 38.30 3.85
2477 2508 6.680197 ACCCTATACTTATAGATCCCGGTCTA 59.320 42.308 0.00 1.90 38.30 2.59
2478 2509 7.353058 ACCCTATACTTATAGATCCCGGTCTAT 59.647 40.741 16.41 16.41 42.50 1.98
2479 2510 8.226112 CCCTATACTTATAGATCCCGGTCTATT 58.774 40.741 17.16 5.33 40.79 1.73
2480 2511 9.643735 CCTATACTTATAGATCCCGGTCTATTT 57.356 37.037 17.16 7.49 40.79 1.40
2485 2516 8.591940 ACTTATAGATCCCGGTCTATTTTAACC 58.408 37.037 17.16 0.00 40.79 2.85
2486 2517 4.701651 AGATCCCGGTCTATTTTAACCC 57.298 45.455 0.00 0.00 31.49 4.11
2487 2518 4.304659 AGATCCCGGTCTATTTTAACCCT 58.695 43.478 0.00 0.00 31.49 4.34
2488 2519 3.918294 TCCCGGTCTATTTTAACCCTG 57.082 47.619 0.00 0.00 31.49 4.45
2489 2520 2.506644 TCCCGGTCTATTTTAACCCTGG 59.493 50.000 0.00 0.00 31.49 4.45
2490 2521 2.506644 CCCGGTCTATTTTAACCCTGGA 59.493 50.000 0.00 0.00 31.49 3.86
2491 2522 3.137728 CCCGGTCTATTTTAACCCTGGAT 59.862 47.826 0.00 0.00 31.49 3.41
2492 2523 4.386711 CCGGTCTATTTTAACCCTGGATC 58.613 47.826 0.00 0.00 31.49 3.36
2493 2524 4.386711 CGGTCTATTTTAACCCTGGATCC 58.613 47.826 4.20 4.20 31.49 3.36
2494 2525 4.386711 GGTCTATTTTAACCCTGGATCCG 58.613 47.826 7.39 1.76 0.00 4.18
2495 2526 4.386711 GTCTATTTTAACCCTGGATCCGG 58.613 47.826 14.26 14.26 0.00 5.14
2496 2527 4.042174 TCTATTTTAACCCTGGATCCGGT 58.958 43.478 19.51 12.50 0.00 5.28
2497 2528 3.750501 ATTTTAACCCTGGATCCGGTT 57.249 42.857 22.88 22.88 44.55 4.44
2498 2529 4.866327 ATTTTAACCCTGGATCCGGTTA 57.134 40.909 21.19 21.19 42.40 2.85
2499 2530 4.866327 TTTTAACCCTGGATCCGGTTAT 57.134 40.909 24.01 11.67 42.67 1.89
2500 2531 3.849563 TTAACCCTGGATCCGGTTATG 57.150 47.619 24.01 11.81 42.67 1.90
2501 2532 0.182775 AACCCTGGATCCGGTTATGC 59.817 55.000 19.33 0.00 40.62 3.14
2502 2533 1.073199 CCCTGGATCCGGTTATGCC 59.927 63.158 19.51 0.00 0.00 4.40
2503 2534 1.705002 CCCTGGATCCGGTTATGCCA 61.705 60.000 19.51 2.33 36.97 4.92
2504 2535 0.250467 CCTGGATCCGGTTATGCCAG 60.250 60.000 19.51 17.64 44.40 4.85
2505 2536 0.469917 CTGGATCCGGTTATGCCAGT 59.530 55.000 12.93 0.00 40.88 4.00
2506 2537 0.916086 TGGATCCGGTTATGCCAGTT 59.084 50.000 7.39 0.00 36.97 3.16
2507 2538 1.283613 TGGATCCGGTTATGCCAGTTT 59.716 47.619 7.39 0.00 36.97 2.66
2508 2539 1.676006 GGATCCGGTTATGCCAGTTTG 59.324 52.381 0.00 0.00 36.97 2.93
2509 2540 1.676006 GATCCGGTTATGCCAGTTTGG 59.324 52.381 0.00 0.00 41.55 3.28
2510 2541 0.402504 TCCGGTTATGCCAGTTTGGT 59.597 50.000 0.00 0.00 40.46 3.67
2511 2542 0.525761 CCGGTTATGCCAGTTTGGTG 59.474 55.000 0.00 0.00 40.46 4.17
2512 2543 1.243902 CGGTTATGCCAGTTTGGTGT 58.756 50.000 0.00 0.00 40.46 4.16
2513 2544 1.068610 CGGTTATGCCAGTTTGGTGTG 60.069 52.381 0.00 0.00 40.46 3.82
2514 2545 1.336795 GGTTATGCCAGTTTGGTGTGC 60.337 52.381 0.00 0.00 40.46 4.57
2515 2546 1.613437 GTTATGCCAGTTTGGTGTGCT 59.387 47.619 0.00 0.00 40.46 4.40
2516 2547 1.246649 TATGCCAGTTTGGTGTGCTG 58.753 50.000 0.00 0.00 40.46 4.41
2518 2549 3.447040 CCAGTTTGGTGTGCTGGG 58.553 61.111 0.00 0.00 44.36 4.45
2519 2550 1.152777 CCAGTTTGGTGTGCTGGGA 60.153 57.895 0.00 0.00 44.36 4.37
2520 2551 0.754957 CCAGTTTGGTGTGCTGGGAA 60.755 55.000 0.00 0.00 44.36 3.97
2521 2552 0.670162 CAGTTTGGTGTGCTGGGAAG 59.330 55.000 0.00 0.00 0.00 3.46
2522 2553 0.550914 AGTTTGGTGTGCTGGGAAGA 59.449 50.000 0.00 0.00 0.00 2.87
2523 2554 1.145738 AGTTTGGTGTGCTGGGAAGAT 59.854 47.619 0.00 0.00 0.00 2.40
2524 2555 2.375174 AGTTTGGTGTGCTGGGAAGATA 59.625 45.455 0.00 0.00 0.00 1.98
2525 2556 3.010584 AGTTTGGTGTGCTGGGAAGATAT 59.989 43.478 0.00 0.00 0.00 1.63
2526 2557 3.737559 TTGGTGTGCTGGGAAGATATT 57.262 42.857 0.00 0.00 0.00 1.28
2527 2558 3.003394 TGGTGTGCTGGGAAGATATTG 57.997 47.619 0.00 0.00 0.00 1.90
2528 2559 2.575735 TGGTGTGCTGGGAAGATATTGA 59.424 45.455 0.00 0.00 0.00 2.57
2529 2560 3.202818 TGGTGTGCTGGGAAGATATTGAT 59.797 43.478 0.00 0.00 0.00 2.57
2530 2561 3.817647 GGTGTGCTGGGAAGATATTGATC 59.182 47.826 0.00 0.00 0.00 2.92
2531 2562 3.817647 GTGTGCTGGGAAGATATTGATCC 59.182 47.826 0.00 0.00 31.81 3.36
2535 2566 2.115343 GGGAAGATATTGATCCCGGC 57.885 55.000 0.00 0.00 43.20 6.13
2536 2567 1.340114 GGGAAGATATTGATCCCGGCC 60.340 57.143 0.00 0.00 43.20 6.13
2537 2568 1.351017 GGAAGATATTGATCCCGGCCA 59.649 52.381 2.24 0.00 31.81 5.36
2538 2569 2.616510 GGAAGATATTGATCCCGGCCAG 60.617 54.545 2.24 0.00 31.81 4.85
2539 2570 0.987294 AGATATTGATCCCGGCCAGG 59.013 55.000 2.24 0.00 40.63 4.45
2540 2571 0.984230 GATATTGATCCCGGCCAGGA 59.016 55.000 10.99 10.99 45.00 3.86
2541 2572 0.693049 ATATTGATCCCGGCCAGGAC 59.307 55.000 10.77 5.25 45.00 3.85
2542 2573 0.399949 TATTGATCCCGGCCAGGACT 60.400 55.000 10.77 0.00 45.00 3.85
2543 2574 0.399949 ATTGATCCCGGCCAGGACTA 60.400 55.000 10.77 0.00 45.00 2.59
2544 2575 0.399949 TTGATCCCGGCCAGGACTAT 60.400 55.000 10.77 0.00 45.00 2.12
2545 2576 0.399949 TGATCCCGGCCAGGACTATT 60.400 55.000 10.77 0.00 45.00 1.73
2546 2577 0.321996 GATCCCGGCCAGGACTATTC 59.678 60.000 10.77 0.00 45.00 1.75
2547 2578 0.104934 ATCCCGGCCAGGACTATTCT 60.105 55.000 10.77 0.00 45.00 2.40
2548 2579 0.759436 TCCCGGCCAGGACTATTCTC 60.759 60.000 2.59 0.00 45.00 2.87
2549 2580 0.760945 CCCGGCCAGGACTATTCTCT 60.761 60.000 14.30 0.00 45.00 3.10
2550 2581 1.123928 CCGGCCAGGACTATTCTCTT 58.876 55.000 2.24 0.00 45.00 2.85
2551 2582 1.069358 CCGGCCAGGACTATTCTCTTC 59.931 57.143 2.24 0.00 45.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.337060 GGCCGCCCGTTTGTCAAC 62.337 66.667 0.00 0.00 0.00 3.18
49 50 2.331805 CGATAGCCCGAGGTCACG 59.668 66.667 0.00 0.00 0.00 4.35
66 67 2.862347 GATGCAAACGCAGAGCCAGC 62.862 60.000 0.00 0.00 44.13 4.85
67 68 1.136147 GATGCAAACGCAGAGCCAG 59.864 57.895 0.00 0.00 44.13 4.85
68 69 2.334946 GGATGCAAACGCAGAGCCA 61.335 57.895 0.00 0.00 44.13 4.75
69 70 2.486966 GGATGCAAACGCAGAGCC 59.513 61.111 0.00 0.00 44.13 4.70
70 71 1.709147 ATCGGATGCAAACGCAGAGC 61.709 55.000 8.35 0.00 44.13 4.09
71 72 0.729116 AATCGGATGCAAACGCAGAG 59.271 50.000 8.35 0.00 44.13 3.35
72 73 0.726827 GAATCGGATGCAAACGCAGA 59.273 50.000 8.35 0.00 44.13 4.26
73 74 0.587242 CGAATCGGATGCAAACGCAG 60.587 55.000 8.35 0.00 44.13 5.18
74 75 1.423450 CGAATCGGATGCAAACGCA 59.577 52.632 8.35 0.00 45.23 5.24
75 76 4.268655 CGAATCGGATGCAAACGC 57.731 55.556 8.35 0.00 0.00 4.84
100 101 4.382831 CACAGCACGTAAAGATTTGTACG 58.617 43.478 4.51 4.51 46.58 3.67
101 102 4.084013 AGCACAGCACGTAAAGATTTGTAC 60.084 41.667 0.00 0.00 0.00 2.90
102 103 4.062293 AGCACAGCACGTAAAGATTTGTA 58.938 39.130 0.00 0.00 0.00 2.41
103 104 2.878406 AGCACAGCACGTAAAGATTTGT 59.122 40.909 0.00 0.00 0.00 2.83
104 105 3.228749 CAGCACAGCACGTAAAGATTTG 58.771 45.455 0.00 0.00 0.00 2.32
105 106 2.350772 GCAGCACAGCACGTAAAGATTT 60.351 45.455 0.00 0.00 0.00 2.17
106 107 1.197721 GCAGCACAGCACGTAAAGATT 59.802 47.619 0.00 0.00 0.00 2.40
107 108 0.798776 GCAGCACAGCACGTAAAGAT 59.201 50.000 0.00 0.00 0.00 2.40
108 109 0.531753 TGCAGCACAGCACGTAAAGA 60.532 50.000 0.00 0.00 40.11 2.52
109 110 0.307453 TTGCAGCACAGCACGTAAAG 59.693 50.000 0.00 0.00 45.61 1.85
110 111 0.028770 GTTGCAGCACAGCACGTAAA 59.971 50.000 0.00 0.00 45.61 2.01
111 112 1.092345 TGTTGCAGCACAGCACGTAA 61.092 50.000 0.00 0.00 45.61 3.18
112 113 1.498043 CTGTTGCAGCACAGCACGTA 61.498 55.000 5.63 0.00 45.61 3.57
113 114 2.823593 TGTTGCAGCACAGCACGT 60.824 55.556 0.00 0.00 45.61 4.49
114 115 1.848932 ATCTGTTGCAGCACAGCACG 61.849 55.000 12.79 0.00 45.61 5.34
115 116 1.159285 TATCTGTTGCAGCACAGCAC 58.841 50.000 12.79 4.43 45.61 4.40
116 117 1.741145 CATATCTGTTGCAGCACAGCA 59.259 47.619 12.79 4.79 43.51 4.41
117 118 2.011947 TCATATCTGTTGCAGCACAGC 58.988 47.619 12.79 2.82 43.51 4.40
118 119 2.353889 GGTCATATCTGTTGCAGCACAG 59.646 50.000 11.61 11.61 44.96 3.66
119 120 2.358957 GGTCATATCTGTTGCAGCACA 58.641 47.619 0.00 0.00 0.00 4.57
120 121 1.328680 CGGTCATATCTGTTGCAGCAC 59.671 52.381 0.00 0.00 0.00 4.40
121 122 1.655484 CGGTCATATCTGTTGCAGCA 58.345 50.000 2.37 2.37 0.00 4.41
122 123 0.940126 CCGGTCATATCTGTTGCAGC 59.060 55.000 0.00 0.00 0.00 5.25
123 124 2.159043 ACTCCGGTCATATCTGTTGCAG 60.159 50.000 0.00 0.00 0.00 4.41
124 125 1.831106 ACTCCGGTCATATCTGTTGCA 59.169 47.619 0.00 0.00 0.00 4.08
125 126 2.159099 TCACTCCGGTCATATCTGTTGC 60.159 50.000 0.00 0.00 0.00 4.17
126 127 3.801114 TCACTCCGGTCATATCTGTTG 57.199 47.619 0.00 0.00 0.00 3.33
127 128 3.769844 ACTTCACTCCGGTCATATCTGTT 59.230 43.478 0.00 0.00 0.00 3.16
128 129 3.366396 ACTTCACTCCGGTCATATCTGT 58.634 45.455 0.00 0.00 0.00 3.41
129 130 3.634448 AGACTTCACTCCGGTCATATCTG 59.366 47.826 0.00 0.00 32.98 2.90
130 131 3.904717 AGACTTCACTCCGGTCATATCT 58.095 45.455 0.00 0.00 32.98 1.98
131 132 5.968528 ATAGACTTCACTCCGGTCATATC 57.031 43.478 0.00 0.00 32.98 1.63
132 133 6.732896 AAATAGACTTCACTCCGGTCATAT 57.267 37.500 0.00 0.00 32.98 1.78
133 134 6.540438 AAAATAGACTTCACTCCGGTCATA 57.460 37.500 0.00 0.00 32.98 2.15
134 135 5.422214 AAAATAGACTTCACTCCGGTCAT 57.578 39.130 0.00 0.00 32.98 3.06
135 136 4.884668 AAAATAGACTTCACTCCGGTCA 57.115 40.909 0.00 0.00 32.98 4.02
136 137 6.091849 GGTTTAAAATAGACTTCACTCCGGTC 59.908 42.308 0.00 0.00 0.00 4.79
137 138 5.936372 GGTTTAAAATAGACTTCACTCCGGT 59.064 40.000 0.00 0.00 0.00 5.28
138 139 6.171213 AGGTTTAAAATAGACTTCACTCCGG 58.829 40.000 0.00 0.00 0.00 5.14
139 140 7.386848 TCAAGGTTTAAAATAGACTTCACTCCG 59.613 37.037 0.00 0.00 0.00 4.63
140 141 8.617290 TCAAGGTTTAAAATAGACTTCACTCC 57.383 34.615 0.00 0.00 0.00 3.85
154 155 9.515226 ACTAGCTGTATGAATTCAAGGTTTAAA 57.485 29.630 13.09 0.00 0.00 1.52
155 156 9.162764 GACTAGCTGTATGAATTCAAGGTTTAA 57.837 33.333 13.09 0.00 0.00 1.52
156 157 7.491372 CGACTAGCTGTATGAATTCAAGGTTTA 59.509 37.037 13.09 0.00 0.00 2.01
157 158 6.313905 CGACTAGCTGTATGAATTCAAGGTTT 59.686 38.462 13.09 0.00 0.00 3.27
158 159 5.812642 CGACTAGCTGTATGAATTCAAGGTT 59.187 40.000 13.09 0.00 0.00 3.50
159 160 5.352284 CGACTAGCTGTATGAATTCAAGGT 58.648 41.667 13.09 13.21 0.00 3.50
160 161 4.747108 CCGACTAGCTGTATGAATTCAAGG 59.253 45.833 13.09 4.33 0.00 3.61
161 162 4.747108 CCCGACTAGCTGTATGAATTCAAG 59.253 45.833 13.09 6.75 0.00 3.02
162 163 4.404394 TCCCGACTAGCTGTATGAATTCAA 59.596 41.667 13.09 0.00 0.00 2.69
163 164 3.958147 TCCCGACTAGCTGTATGAATTCA 59.042 43.478 11.26 11.26 0.00 2.57
164 165 4.585955 TCCCGACTAGCTGTATGAATTC 57.414 45.455 0.00 0.00 0.00 2.17
165 166 4.588951 TGATCCCGACTAGCTGTATGAATT 59.411 41.667 0.00 0.00 0.00 2.17
166 167 4.152647 TGATCCCGACTAGCTGTATGAAT 58.847 43.478 0.00 0.00 0.00 2.57
167 168 3.562182 TGATCCCGACTAGCTGTATGAA 58.438 45.455 0.00 0.00 0.00 2.57
168 169 3.223674 TGATCCCGACTAGCTGTATGA 57.776 47.619 0.00 0.00 0.00 2.15
169 170 4.051922 GTTTGATCCCGACTAGCTGTATG 58.948 47.826 0.00 0.00 0.00 2.39
170 171 3.069729 GGTTTGATCCCGACTAGCTGTAT 59.930 47.826 0.00 0.00 0.00 2.29
171 172 2.429610 GGTTTGATCCCGACTAGCTGTA 59.570 50.000 0.00 0.00 0.00 2.74
172 173 1.207329 GGTTTGATCCCGACTAGCTGT 59.793 52.381 0.00 0.00 0.00 4.40
173 174 1.473434 GGGTTTGATCCCGACTAGCTG 60.473 57.143 0.00 0.00 37.93 4.24
174 175 0.831307 GGGTTTGATCCCGACTAGCT 59.169 55.000 0.00 0.00 37.93 3.32
175 176 3.381370 GGGTTTGATCCCGACTAGC 57.619 57.895 0.00 0.00 37.93 3.42
183 184 5.127194 GGATTGAAAGGTTAGGGTTTGATCC 59.873 44.000 0.00 0.00 0.00 3.36
184 185 5.127194 GGGATTGAAAGGTTAGGGTTTGATC 59.873 44.000 0.00 0.00 0.00 2.92
185 186 5.023452 GGGATTGAAAGGTTAGGGTTTGAT 58.977 41.667 0.00 0.00 0.00 2.57
186 187 4.107311 AGGGATTGAAAGGTTAGGGTTTGA 59.893 41.667 0.00 0.00 0.00 2.69
187 188 4.220602 CAGGGATTGAAAGGTTAGGGTTTG 59.779 45.833 0.00 0.00 0.00 2.93
188 189 4.107311 TCAGGGATTGAAAGGTTAGGGTTT 59.893 41.667 0.00 0.00 31.34 3.27
189 190 3.660669 TCAGGGATTGAAAGGTTAGGGTT 59.339 43.478 0.00 0.00 31.34 4.11
190 191 3.265489 TCAGGGATTGAAAGGTTAGGGT 58.735 45.455 0.00 0.00 31.34 4.34
191 192 4.316025 TTCAGGGATTGAAAGGTTAGGG 57.684 45.455 0.00 0.00 42.69 3.53
200 201 4.403432 GCAAGGATGATTTCAGGGATTGAA 59.597 41.667 0.00 0.00 43.92 2.69
201 202 3.956199 GCAAGGATGATTTCAGGGATTGA 59.044 43.478 0.00 0.00 0.00 2.57
202 203 3.069158 GGCAAGGATGATTTCAGGGATTG 59.931 47.826 0.00 0.00 0.00 2.67
203 204 3.303049 GGCAAGGATGATTTCAGGGATT 58.697 45.455 0.00 0.00 0.00 3.01
204 205 2.425392 GGGCAAGGATGATTTCAGGGAT 60.425 50.000 0.00 0.00 0.00 3.85
205 206 1.063717 GGGCAAGGATGATTTCAGGGA 60.064 52.381 0.00 0.00 0.00 4.20
206 207 1.406903 GGGCAAGGATGATTTCAGGG 58.593 55.000 0.00 0.00 0.00 4.45
207 208 1.027357 CGGGCAAGGATGATTTCAGG 58.973 55.000 0.00 0.00 0.00 3.86
208 209 0.383231 GCGGGCAAGGATGATTTCAG 59.617 55.000 0.00 0.00 0.00 3.02
209 210 0.034186 AGCGGGCAAGGATGATTTCA 60.034 50.000 0.00 0.00 0.00 2.69
210 211 1.876156 CTAGCGGGCAAGGATGATTTC 59.124 52.381 0.00 0.00 0.00 2.17
211 212 1.212935 ACTAGCGGGCAAGGATGATTT 59.787 47.619 0.00 0.00 0.00 2.17
212 213 0.839946 ACTAGCGGGCAAGGATGATT 59.160 50.000 0.00 0.00 0.00 2.57
213 214 0.107456 CACTAGCGGGCAAGGATGAT 59.893 55.000 0.00 0.00 0.00 2.45
214 215 1.522092 CACTAGCGGGCAAGGATGA 59.478 57.895 0.00 0.00 0.00 2.92
215 216 2.182842 GCACTAGCGGGCAAGGATG 61.183 63.158 0.00 0.00 0.00 3.51
216 217 2.190578 GCACTAGCGGGCAAGGAT 59.809 61.111 0.00 0.00 0.00 3.24
217 218 4.096003 GGCACTAGCGGGCAAGGA 62.096 66.667 3.97 0.00 43.41 3.36
219 220 3.704231 ATGGGCACTAGCGGGCAAG 62.704 63.158 10.17 0.00 43.41 4.01
220 221 3.727258 ATGGGCACTAGCGGGCAA 61.727 61.111 10.17 0.00 43.41 4.52
688 689 0.317160 CAAGTGCACGACCCTACTCA 59.683 55.000 12.01 0.00 0.00 3.41
998 999 1.220749 GTTAGCTCACGCCCCATGA 59.779 57.895 0.00 0.00 36.60 3.07
1187 1196 0.867746 GTCATTGTTGTCAGCAGCGA 59.132 50.000 0.00 0.00 0.00 4.93
1410 1428 1.457346 AAGCAAGGCATCTACAGCAC 58.543 50.000 0.00 0.00 0.00 4.40
1446 1464 0.169009 GCAACGGATCTCTGCAAACC 59.831 55.000 8.67 0.00 36.09 3.27
1586 1604 1.241165 CATGAAGCAGGAGCAACACA 58.759 50.000 0.00 0.00 45.49 3.72
1720 1738 1.134580 GCAGTCTGATTAGCCAGAGCA 60.135 52.381 3.32 0.00 43.15 4.26
1742 1760 0.108424 GCCACACAACCTTGCAACAA 60.108 50.000 0.00 0.00 0.00 2.83
1762 1780 0.035458 CCAGAAAGCTCTCAACCCGT 59.965 55.000 0.00 0.00 0.00 5.28
1824 1842 2.245159 CAGAGTGGTCTGCAACAGAA 57.755 50.000 0.00 0.00 43.89 3.02
1997 2015 1.672356 GCACCGGAGTCACAAGCAT 60.672 57.895 9.46 0.00 0.00 3.79
2175 2193 7.066163 CACTGAGCACTACCAATCATGAAATTA 59.934 37.037 0.00 0.00 0.00 1.40
2296 2326 0.885196 AGAAGCGACTCACTCTCACC 59.115 55.000 0.00 0.00 0.00 4.02
2381 2412 9.213799 GCCTCATCGATTAATTAAGAAGAAGAT 57.786 33.333 3.94 0.46 0.00 2.40
2439 2470 4.235372 AGTATAGGGTCCAGATTTCAGGG 58.765 47.826 0.00 0.00 0.00 4.45
2440 2471 5.896073 AAGTATAGGGTCCAGATTTCAGG 57.104 43.478 0.00 0.00 0.00 3.86
2441 2472 9.535170 TCTATAAGTATAGGGTCCAGATTTCAG 57.465 37.037 5.68 0.00 37.00 3.02
2444 2475 9.495382 GGATCTATAAGTATAGGGTCCAGATTT 57.505 37.037 17.14 0.00 39.10 2.17
2445 2476 8.068733 GGGATCTATAAGTATAGGGTCCAGATT 58.931 40.741 20.39 0.00 39.95 2.40
2446 2477 7.597327 GGGATCTATAAGTATAGGGTCCAGAT 58.403 42.308 20.39 5.63 39.95 2.90
2447 2478 6.353689 CGGGATCTATAAGTATAGGGTCCAGA 60.354 46.154 20.39 2.15 39.95 3.86
2448 2479 5.828859 CGGGATCTATAAGTATAGGGTCCAG 59.171 48.000 20.39 16.31 39.95 3.86
2449 2480 5.340611 CCGGGATCTATAAGTATAGGGTCCA 60.341 48.000 20.39 1.87 39.95 4.02
2450 2481 5.139001 CCGGGATCTATAAGTATAGGGTCC 58.861 50.000 15.36 15.36 38.86 4.46
2451 2482 5.764432 ACCGGGATCTATAAGTATAGGGTC 58.236 45.833 6.32 4.96 37.00 4.46
2452 2483 5.495436 AGACCGGGATCTATAAGTATAGGGT 59.505 44.000 6.32 4.78 37.00 4.34
2453 2484 6.015991 AGACCGGGATCTATAAGTATAGGG 57.984 45.833 6.32 2.13 37.00 3.53
2454 2485 9.643735 AAATAGACCGGGATCTATAAGTATAGG 57.356 37.037 13.43 0.00 40.36 2.57
2459 2490 8.591940 GGTTAAAATAGACCGGGATCTATAAGT 58.408 37.037 13.43 6.30 40.36 2.24
2460 2491 8.039538 GGGTTAAAATAGACCGGGATCTATAAG 58.960 40.741 13.43 0.00 40.36 1.73
2461 2492 7.736234 AGGGTTAAAATAGACCGGGATCTATAA 59.264 37.037 13.43 4.08 40.36 0.98
2462 2493 7.179694 CAGGGTTAAAATAGACCGGGATCTATA 59.820 40.741 13.43 0.00 40.36 1.31
2463 2494 6.013639 CAGGGTTAAAATAGACCGGGATCTAT 60.014 42.308 6.32 7.65 42.57 1.98
2464 2495 5.306160 CAGGGTTAAAATAGACCGGGATCTA 59.694 44.000 6.32 5.17 36.78 1.98
2465 2496 4.102681 CAGGGTTAAAATAGACCGGGATCT 59.897 45.833 6.32 2.48 36.78 2.75
2466 2497 4.386711 CAGGGTTAAAATAGACCGGGATC 58.613 47.826 6.32 0.00 36.78 3.36
2467 2498 3.137728 CCAGGGTTAAAATAGACCGGGAT 59.862 47.826 6.32 0.00 36.78 3.85
2468 2499 2.506644 CCAGGGTTAAAATAGACCGGGA 59.493 50.000 6.32 0.00 36.78 5.14
2469 2500 2.506644 TCCAGGGTTAAAATAGACCGGG 59.493 50.000 6.32 0.00 36.78 5.73
2470 2501 3.918294 TCCAGGGTTAAAATAGACCGG 57.082 47.619 0.00 0.00 36.78 5.28
2471 2502 4.386711 GGATCCAGGGTTAAAATAGACCG 58.613 47.826 6.95 0.00 36.78 4.79
2472 2503 4.386711 CGGATCCAGGGTTAAAATAGACC 58.613 47.826 13.41 0.00 35.14 3.85
2473 2504 4.141551 ACCGGATCCAGGGTTAAAATAGAC 60.142 45.833 21.65 0.00 30.73 2.59
2474 2505 4.042174 ACCGGATCCAGGGTTAAAATAGA 58.958 43.478 21.65 0.00 30.73 1.98
2475 2506 4.432980 ACCGGATCCAGGGTTAAAATAG 57.567 45.455 21.65 0.00 30.73 1.73
2476 2507 4.866327 AACCGGATCCAGGGTTAAAATA 57.134 40.909 19.33 0.00 44.44 1.40
2477 2508 3.750501 AACCGGATCCAGGGTTAAAAT 57.249 42.857 19.33 0.00 44.44 1.82
2483 2514 1.705997 GGCATAACCGGATCCAGGGT 61.706 60.000 21.65 18.94 38.44 4.34
2484 2515 1.073199 GGCATAACCGGATCCAGGG 59.927 63.158 21.65 14.21 0.00 4.45
2485 2516 1.836391 TGGCATAACCGGATCCAGG 59.164 57.895 9.46 16.00 43.94 4.45
2493 2524 1.068610 CACACCAAACTGGCATAACCG 60.069 52.381 0.00 0.00 42.67 4.44
2494 2525 1.336795 GCACACCAAACTGGCATAACC 60.337 52.381 0.00 0.00 42.67 2.85
2495 2526 1.613437 AGCACACCAAACTGGCATAAC 59.387 47.619 0.00 0.00 42.67 1.89
2496 2527 1.612950 CAGCACACCAAACTGGCATAA 59.387 47.619 0.00 0.00 42.67 1.90
2497 2528 1.246649 CAGCACACCAAACTGGCATA 58.753 50.000 0.00 0.00 42.67 3.14
2498 2529 1.466025 CCAGCACACCAAACTGGCAT 61.466 55.000 0.00 0.00 44.16 4.40
2499 2530 2.126596 CCAGCACACCAAACTGGCA 61.127 57.895 0.00 0.00 44.16 4.92
2500 2531 2.730094 CCAGCACACCAAACTGGC 59.270 61.111 0.00 0.00 44.16 4.85
2502 2533 0.670162 CTTCCCAGCACACCAAACTG 59.330 55.000 0.00 0.00 0.00 3.16
2503 2534 0.550914 TCTTCCCAGCACACCAAACT 59.449 50.000 0.00 0.00 0.00 2.66
2504 2535 1.620822 ATCTTCCCAGCACACCAAAC 58.379 50.000 0.00 0.00 0.00 2.93
2505 2536 3.737559 ATATCTTCCCAGCACACCAAA 57.262 42.857 0.00 0.00 0.00 3.28
2506 2537 3.010027 TCAATATCTTCCCAGCACACCAA 59.990 43.478 0.00 0.00 0.00 3.67
2507 2538 2.575735 TCAATATCTTCCCAGCACACCA 59.424 45.455 0.00 0.00 0.00 4.17
2508 2539 3.281727 TCAATATCTTCCCAGCACACC 57.718 47.619 0.00 0.00 0.00 4.16
2509 2540 3.817647 GGATCAATATCTTCCCAGCACAC 59.182 47.826 0.00 0.00 32.29 3.82
2510 2541 4.090761 GGATCAATATCTTCCCAGCACA 57.909 45.455 0.00 0.00 32.29 4.57
2516 2547 1.340114 GGCCGGGATCAATATCTTCCC 60.340 57.143 2.18 7.28 44.83 3.97
2517 2548 1.351017 TGGCCGGGATCAATATCTTCC 59.649 52.381 2.18 0.00 32.29 3.46
2518 2549 2.616510 CCTGGCCGGGATCAATATCTTC 60.617 54.545 28.28 0.00 32.29 2.87
2519 2550 1.352352 CCTGGCCGGGATCAATATCTT 59.648 52.381 28.28 0.00 32.29 2.40
2520 2551 0.987294 CCTGGCCGGGATCAATATCT 59.013 55.000 28.28 0.00 32.29 1.98
2521 2552 0.984230 TCCTGGCCGGGATCAATATC 59.016 55.000 30.65 0.00 0.00 1.63
2522 2553 0.693049 GTCCTGGCCGGGATCAATAT 59.307 55.000 36.01 0.00 37.73 1.28
2523 2554 0.399949 AGTCCTGGCCGGGATCAATA 60.400 55.000 36.01 10.31 37.73 1.90
2524 2555 0.399949 TAGTCCTGGCCGGGATCAAT 60.400 55.000 36.01 22.95 37.73 2.57
2525 2556 0.399949 ATAGTCCTGGCCGGGATCAA 60.400 55.000 36.01 23.42 37.73 2.57
2526 2557 0.399949 AATAGTCCTGGCCGGGATCA 60.400 55.000 36.01 25.63 37.73 2.92
2527 2558 0.321996 GAATAGTCCTGGCCGGGATC 59.678 60.000 36.01 26.74 37.73 3.36
2528 2559 0.104934 AGAATAGTCCTGGCCGGGAT 60.105 55.000 36.01 24.88 37.73 3.85
2529 2560 0.759436 GAGAATAGTCCTGGCCGGGA 60.759 60.000 30.65 30.65 0.00 5.14
2530 2561 0.760945 AGAGAATAGTCCTGGCCGGG 60.761 60.000 26.30 26.30 0.00 5.73
2531 2562 1.069358 GAAGAGAATAGTCCTGGCCGG 59.931 57.143 3.88 3.88 0.00 6.13
2532 2563 2.517650 GAAGAGAATAGTCCTGGCCG 57.482 55.000 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.