Multiple sequence alignment - TraesCS2A01G099600

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 TraesCS2A01G099600 chr2A 100.000 4235 0 0 1 4235 52574138 52569904 0.000000e+00 7821.0
1 TraesCS2A01G099600 chr2A 86.491 2354 297 18 869 3214 52756522 52758862 0.000000e+00 2566.0
2 TraesCS2A01G099600 chr2A 82.496 1931 295 31 678 2592 52541133 52539230 0.000000e+00 1653.0
3 TraesCS2A01G099600 chr2A 82.891 339 41 5 595 927 761277780 761278107 5.360000e-74 289.0
4 TraesCS2A01G099600 chr2A 92.632 95 5 1 783 877 52428309 52428217 7.390000e-28 135.0
5 TraesCS2A01G099600 chr2D 96.567 3350 95 10 407 3753 51160746 51157414 0.000000e+00 5531.0
6 TraesCS2A01G099600 chr2D 87.123 2353 282 16 869 3214 51253154 51255492 0.000000e+00 2647.0
7 TraesCS2A01G099600 chr2D 90.276 833 73 5 726 1554 51138033 51137205 0.000000e+00 1083.0
8 TraesCS2A01G099600 chr2D 89.139 267 19 4 3970 4226 51157122 51156856 1.470000e-84 324.0
9 TraesCS2A01G099600 chr2D 91.960 199 16 0 3773 3971 51157359 51157161 3.220000e-71 279.0
10 TraesCS2A01G099600 chr2D 83.163 196 22 5 3517 3704 51255733 51255925 7.280000e-38 169.0
11 TraesCS2A01G099600 chr2D 90.566 53 5 0 3370 3422 51130734 51130682 2.110000e-08 71.3
12 TraesCS2A01G099600 chr2B 95.193 3412 137 11 298 3697 79709785 79706389 0.000000e+00 5367.0
13 TraesCS2A01G099600 chr2B 86.619 2354 292 18 869 3214 80200438 80202776 0.000000e+00 2580.0
14 TraesCS2A01G099600 chr2B 84.899 2384 324 25 783 3146 79671967 79669600 0.000000e+00 2375.0
15 TraesCS2A01G099600 chr2B 81.622 2590 358 50 595 3133 794032148 794029626 0.000000e+00 2037.0
16 TraesCS2A01G099600 chr2B 89.032 155 17 0 1 155 79710744 79710590 4.320000e-45 193.0
17 TraesCS2A01G099600 chr2B 80.000 245 33 8 3470 3704 80202971 80203209 2.620000e-37 167.0
18 TraesCS2A01G099600 chr2B 85.593 118 14 1 3097 3211 79669606 79669489 2.070000e-23 121.0
19 TraesCS2A01G099600 chr7D 81.047 2712 459 35 509 3212 76396486 76399150 0.000000e+00 2109.0
20 TraesCS2A01G099600 chr7D 82.267 2047 328 24 1178 3212 79360862 79358839 0.000000e+00 1736.0
21 TraesCS2A01G099600 chr7A 81.577 2486 422 28 737 3212 80313655 80316114 0.000000e+00 2021.0
22 TraesCS2A01G099600 chr7A 83.022 2032 315 18 1190 3212 82155452 82153442 0.000000e+00 1814.0


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 TraesCS2A01G099600 chr2A 52569904 52574138 4234 True 7821.000000 7821 100.000000 1 4235 1 chr2A.!!$R3 4234
1 TraesCS2A01G099600 chr2A 52756522 52758862 2340 False 2566.000000 2566 86.491000 869 3214 1 chr2A.!!$F1 2345
2 TraesCS2A01G099600 chr2A 52539230 52541133 1903 True 1653.000000 1653 82.496000 678 2592 1 chr2A.!!$R2 1914
3 TraesCS2A01G099600 chr2D 51156856 51160746 3890 True 2044.666667 5531 92.555333 407 4226 3 chr2D.!!$R3 3819
4 TraesCS2A01G099600 chr2D 51253154 51255925 2771 False 1408.000000 2647 85.143000 869 3704 2 chr2D.!!$F1 2835
5 TraesCS2A01G099600 chr2D 51137205 51138033 828 True 1083.000000 1083 90.276000 726 1554 1 chr2D.!!$R2 828
6 TraesCS2A01G099600 chr2B 79706389 79710744 4355 True 2780.000000 5367 92.112500 1 3697 2 chr2B.!!$R3 3696
7 TraesCS2A01G099600 chr2B 794029626 794032148 2522 True 2037.000000 2037 81.622000 595 3133 1 chr2B.!!$R1 2538
8 TraesCS2A01G099600 chr2B 80200438 80203209 2771 False 1373.500000 2580 83.309500 869 3704 2 chr2B.!!$F1 2835
9 TraesCS2A01G099600 chr2B 79669489 79671967 2478 True 1248.000000 2375 85.246000 783 3211 2 chr2B.!!$R2 2428
10 TraesCS2A01G099600 chr7D 76396486 76399150 2664 False 2109.000000 2109 81.047000 509 3212 1 chr7D.!!$F1 2703
11 TraesCS2A01G099600 chr7D 79358839 79360862 2023 True 1736.000000 1736 82.267000 1178 3212 1 chr7D.!!$R1 2034
12 TraesCS2A01G099600 chr7A 80313655 80316114 2459 False 2021.000000 2021 81.577000 737 3212 1 chr7A.!!$F1 2475
13 TraesCS2A01G099600 chr7A 82153442 82155452 2010 True 1814.000000 1814 83.022000 1190 3212 1 chr7A.!!$R1 2022

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
276 1030 0.034574 TATGCTGCCGTTGGGTTCAT 60.035 50.000 0.00 0.0 34.97 2.57 F
287 1041 0.251916 TGGGTTCATTCGCTGGGTAG 59.748 55.000 0.00 0.0 0.00 3.18 F
288 1042 0.252197 GGGTTCATTCGCTGGGTAGT 59.748 55.000 0.00 0.0 0.00 2.73 F
1575 2358 1.269206 CGGTGCAACAACAAGCTCATT 60.269 47.619 0.98 0.0 39.98 2.57 F
2269 3075 1.465387 GTGTGGTGTTGTTCAACGACA 59.535 47.619 6.50 6.5 40.03 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2209 3015 0.034896 ATTCTGCGGACGTTGGACTT 59.965 50.000 0.00 0.00 0.00 3.01 R
2248 3054 1.465387 GTCGTTGAACAACACCACACA 59.535 47.619 16.13 0.00 41.20 3.72 R
2372 3191 4.079850 AGGCCACAGAGCTGCTCG 62.080 66.667 22.77 19.05 35.36 5.03 R
2931 3755 1.831343 CGGTTATCGTCGGGTAGTTG 58.169 55.000 0.00 0.00 0.00 3.16 R
4111 5105 0.034670 AGACAGGAGCCAATGGAAGC 60.035 55.000 2.05 0.00 0.00 3.86 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.696989 TGCGATCACCATGAATGACT 57.303 45.000 0.00 0.00 0.00 3.41
37 38 8.506437 TGAATGACTTTTGTGCTGTTAGATTAG 58.494 33.333 0.00 0.00 0.00 1.73
42 43 6.942576 ACTTTTGTGCTGTTAGATTAGTGGAT 59.057 34.615 0.00 0.00 0.00 3.41
65 66 4.837860 TGTTTTCATCTGGCCCTGTTTAAT 59.162 37.500 0.00 0.00 0.00 1.40
66 67 5.047377 TGTTTTCATCTGGCCCTGTTTAATC 60.047 40.000 0.00 0.00 0.00 1.75
68 69 3.889815 TCATCTGGCCCTGTTTAATCAG 58.110 45.455 0.00 6.57 35.45 2.90
77 78 4.627035 GCCCTGTTTAATCAGTTCAAATGC 59.373 41.667 11.63 1.36 34.02 3.56
121 122 5.376854 TGCTTGAGAAATAAAGGAGTTGC 57.623 39.130 0.00 0.00 0.00 4.17
127 128 4.265073 AGAAATAAAGGAGTTGCTGCGAT 58.735 39.130 0.00 0.00 0.00 4.58
137 138 5.525378 AGGAGTTGCTGCGATAAGAAAATAG 59.475 40.000 0.00 0.00 0.00 1.73
140 141 7.009568 AGTTGCTGCGATAAGAAAATAGAAG 57.990 36.000 0.00 0.00 0.00 2.85
161 247 4.904241 AGCAGAGCCCAGTTATTGATATC 58.096 43.478 0.00 0.00 0.00 1.63
163 249 5.072872 AGCAGAGCCCAGTTATTGATATCTT 59.927 40.000 3.98 0.00 0.00 2.40
164 250 5.180868 GCAGAGCCCAGTTATTGATATCTTG 59.819 44.000 3.98 0.00 0.00 3.02
167 253 6.100279 AGAGCCCAGTTATTGATATCTTGTGA 59.900 38.462 3.98 0.00 0.00 3.58
168 254 6.662755 AGCCCAGTTATTGATATCTTGTGAA 58.337 36.000 3.98 0.00 0.00 3.18
169 255 6.769822 AGCCCAGTTATTGATATCTTGTGAAG 59.230 38.462 3.98 0.00 0.00 3.02
184 938 4.044336 TGTGAAGCATTTTGGTCTTGTG 57.956 40.909 0.00 0.00 0.00 3.33
185 939 3.698539 TGTGAAGCATTTTGGTCTTGTGA 59.301 39.130 0.00 0.00 0.00 3.58
192 946 4.512571 GCATTTTGGTCTTGTGAAGCATTT 59.487 37.500 0.00 0.00 0.00 2.32
193 947 5.559417 GCATTTTGGTCTTGTGAAGCATTTG 60.559 40.000 0.00 0.00 0.00 2.32
194 948 3.731652 TTGGTCTTGTGAAGCATTTGG 57.268 42.857 0.00 0.00 0.00 3.28
195 949 2.942804 TGGTCTTGTGAAGCATTTGGA 58.057 42.857 0.00 0.00 0.00 3.53
196 950 2.886523 TGGTCTTGTGAAGCATTTGGAG 59.113 45.455 0.00 0.00 0.00 3.86
197 951 3.149196 GGTCTTGTGAAGCATTTGGAGA 58.851 45.455 0.00 0.00 0.00 3.71
198 952 3.760684 GGTCTTGTGAAGCATTTGGAGAT 59.239 43.478 0.00 0.00 0.00 2.75
199 953 4.943705 GGTCTTGTGAAGCATTTGGAGATA 59.056 41.667 0.00 0.00 0.00 1.98
200 954 5.415701 GGTCTTGTGAAGCATTTGGAGATAA 59.584 40.000 0.00 0.00 0.00 1.75
201 955 6.071952 GGTCTTGTGAAGCATTTGGAGATAAA 60.072 38.462 0.00 0.00 0.00 1.40
202 956 7.025963 GTCTTGTGAAGCATTTGGAGATAAAG 58.974 38.462 0.00 0.00 0.00 1.85
203 957 6.942005 TCTTGTGAAGCATTTGGAGATAAAGA 59.058 34.615 0.00 0.00 0.00 2.52
204 958 7.448161 TCTTGTGAAGCATTTGGAGATAAAGAA 59.552 33.333 0.00 0.00 0.00 2.52
205 959 7.523293 TGTGAAGCATTTGGAGATAAAGAAA 57.477 32.000 0.00 0.00 0.00 2.52
206 960 7.370383 TGTGAAGCATTTGGAGATAAAGAAAC 58.630 34.615 0.00 0.00 0.00 2.78
207 961 7.014134 TGTGAAGCATTTGGAGATAAAGAAACA 59.986 33.333 0.00 0.00 0.00 2.83
208 962 7.540055 GTGAAGCATTTGGAGATAAAGAAACAG 59.460 37.037 0.00 0.00 0.00 3.16
209 963 7.448161 TGAAGCATTTGGAGATAAAGAAACAGA 59.552 33.333 0.00 0.00 0.00 3.41
210 964 7.951347 AGCATTTGGAGATAAAGAAACAGAT 57.049 32.000 0.00 0.00 0.00 2.90
211 965 7.994194 AGCATTTGGAGATAAAGAAACAGATC 58.006 34.615 0.00 0.00 0.00 2.75
212 966 7.613022 AGCATTTGGAGATAAAGAAACAGATCA 59.387 33.333 0.00 0.00 0.00 2.92
213 967 8.246180 GCATTTGGAGATAAAGAAACAGATCAA 58.754 33.333 0.00 0.00 0.00 2.57
214 968 9.784680 CATTTGGAGATAAAGAAACAGATCAAG 57.215 33.333 0.00 0.00 0.00 3.02
215 969 9.745018 ATTTGGAGATAAAGAAACAGATCAAGA 57.255 29.630 0.00 0.00 0.00 3.02
216 970 8.553459 TTGGAGATAAAGAAACAGATCAAGAC 57.447 34.615 0.00 0.00 0.00 3.01
217 971 7.106239 TGGAGATAAAGAAACAGATCAAGACC 58.894 38.462 0.00 0.00 0.00 3.85
218 972 6.256757 GGAGATAAAGAAACAGATCAAGACCG 59.743 42.308 0.00 0.00 0.00 4.79
219 973 6.936279 AGATAAAGAAACAGATCAAGACCGA 58.064 36.000 0.00 0.00 0.00 4.69
220 974 7.560368 AGATAAAGAAACAGATCAAGACCGAT 58.440 34.615 0.00 0.00 0.00 4.18
221 975 5.869753 AAAGAAACAGATCAAGACCGATG 57.130 39.130 0.00 0.00 0.00 3.84
222 976 3.265791 AGAAACAGATCAAGACCGATGC 58.734 45.455 0.00 0.00 0.00 3.91
223 977 1.645034 AACAGATCAAGACCGATGCG 58.355 50.000 0.00 0.00 0.00 4.73
233 987 4.838152 CCGATGCGGGTCAGTGGG 62.838 72.222 0.00 0.00 44.15 4.61
239 993 3.047877 CGGGTCAGTGGGCGTTTC 61.048 66.667 0.00 0.00 0.00 2.78
240 994 2.671963 GGGTCAGTGGGCGTTTCC 60.672 66.667 0.00 0.00 0.00 3.13
253 1007 3.897325 GGCGTTTCCCTCTTTAGTTTTG 58.103 45.455 0.00 0.00 0.00 2.44
254 1008 3.317149 GGCGTTTCCCTCTTTAGTTTTGT 59.683 43.478 0.00 0.00 0.00 2.83
255 1009 4.202080 GGCGTTTCCCTCTTTAGTTTTGTT 60.202 41.667 0.00 0.00 0.00 2.83
256 1010 5.345702 GCGTTTCCCTCTTTAGTTTTGTTT 58.654 37.500 0.00 0.00 0.00 2.83
257 1011 5.808540 GCGTTTCCCTCTTTAGTTTTGTTTT 59.191 36.000 0.00 0.00 0.00 2.43
258 1012 6.974048 GCGTTTCCCTCTTTAGTTTTGTTTTA 59.026 34.615 0.00 0.00 0.00 1.52
259 1013 7.650504 GCGTTTCCCTCTTTAGTTTTGTTTTAT 59.349 33.333 0.00 0.00 0.00 1.40
260 1014 8.964150 CGTTTCCCTCTTTAGTTTTGTTTTATG 58.036 33.333 0.00 0.00 0.00 1.90
261 1015 8.761497 GTTTCCCTCTTTAGTTTTGTTTTATGC 58.239 33.333 0.00 0.00 0.00 3.14
262 1016 7.833285 TCCCTCTTTAGTTTTGTTTTATGCT 57.167 32.000 0.00 0.00 0.00 3.79
263 1017 7.657336 TCCCTCTTTAGTTTTGTTTTATGCTG 58.343 34.615 0.00 0.00 0.00 4.41
264 1018 6.366061 CCCTCTTTAGTTTTGTTTTATGCTGC 59.634 38.462 0.00 0.00 0.00 5.25
265 1019 6.366061 CCTCTTTAGTTTTGTTTTATGCTGCC 59.634 38.462 0.00 0.00 0.00 4.85
266 1020 5.918011 TCTTTAGTTTTGTTTTATGCTGCCG 59.082 36.000 0.00 0.00 0.00 5.69
267 1021 3.726291 AGTTTTGTTTTATGCTGCCGT 57.274 38.095 0.00 0.00 0.00 5.68
268 1022 4.053469 AGTTTTGTTTTATGCTGCCGTT 57.947 36.364 0.00 0.00 0.00 4.44
269 1023 3.801594 AGTTTTGTTTTATGCTGCCGTTG 59.198 39.130 0.00 0.00 0.00 4.10
270 1024 2.430546 TTGTTTTATGCTGCCGTTGG 57.569 45.000 0.00 0.00 0.00 3.77
271 1025 0.600557 TGTTTTATGCTGCCGTTGGG 59.399 50.000 0.00 0.00 0.00 4.12
272 1026 0.601057 GTTTTATGCTGCCGTTGGGT 59.399 50.000 0.00 0.00 34.97 4.51
273 1027 1.000394 GTTTTATGCTGCCGTTGGGTT 60.000 47.619 0.00 0.00 34.97 4.11
274 1028 0.885196 TTTATGCTGCCGTTGGGTTC 59.115 50.000 0.00 0.00 34.97 3.62
275 1029 0.250945 TTATGCTGCCGTTGGGTTCA 60.251 50.000 0.00 0.00 34.97 3.18
276 1030 0.034574 TATGCTGCCGTTGGGTTCAT 60.035 50.000 0.00 0.00 34.97 2.57
277 1031 0.899717 ATGCTGCCGTTGGGTTCATT 60.900 50.000 0.00 0.00 34.97 2.57
278 1032 1.212751 GCTGCCGTTGGGTTCATTC 59.787 57.895 0.00 0.00 34.97 2.67
279 1033 1.501741 CTGCCGTTGGGTTCATTCG 59.498 57.895 0.00 0.00 34.97 3.34
280 1034 2.178273 GCCGTTGGGTTCATTCGC 59.822 61.111 0.00 0.00 34.97 4.70
281 1035 2.332654 GCCGTTGGGTTCATTCGCT 61.333 57.895 0.00 0.00 34.97 4.93
282 1036 1.501741 CCGTTGGGTTCATTCGCTG 59.498 57.895 0.00 0.00 0.00 5.18
283 1037 1.501741 CGTTGGGTTCATTCGCTGG 59.498 57.895 0.00 0.00 0.00 4.85
284 1038 1.883021 GTTGGGTTCATTCGCTGGG 59.117 57.895 0.00 0.00 0.00 4.45
285 1039 0.893727 GTTGGGTTCATTCGCTGGGT 60.894 55.000 0.00 0.00 0.00 4.51
286 1040 0.693622 TTGGGTTCATTCGCTGGGTA 59.306 50.000 0.00 0.00 0.00 3.69
287 1041 0.251916 TGGGTTCATTCGCTGGGTAG 59.748 55.000 0.00 0.00 0.00 3.18
288 1042 0.252197 GGGTTCATTCGCTGGGTAGT 59.748 55.000 0.00 0.00 0.00 2.73
289 1043 1.483415 GGGTTCATTCGCTGGGTAGTA 59.517 52.381 0.00 0.00 0.00 1.82
290 1044 2.483188 GGGTTCATTCGCTGGGTAGTAG 60.483 54.545 0.00 0.00 0.00 2.57
329 1091 4.532126 TCTGCCTGGTTTAGAGAAATCTGA 59.468 41.667 0.00 0.00 28.58 3.27
332 1094 5.882557 TGCCTGGTTTAGAGAAATCTGATTC 59.117 40.000 2.92 0.00 28.58 2.52
389 1151 2.409870 CCAGCCGTTCCTTCCATGC 61.410 63.158 0.00 0.00 0.00 4.06
390 1152 1.675310 CAGCCGTTCCTTCCATGCA 60.675 57.895 0.00 0.00 0.00 3.96
535 1298 7.800380 CACCTAATTTCATGACTTCGATATTGC 59.200 37.037 0.00 0.00 0.00 3.56
584 1347 8.200120 TCAGGAATCTGTTGATAGTACTCATTG 58.800 37.037 0.00 0.00 41.59 2.82
619 1385 4.044308 ACACATCATAGGTGGGGATACAA 58.956 43.478 0.00 0.00 40.54 2.41
942 1718 2.442236 AGATTGCCCGGTGATTGATT 57.558 45.000 0.00 0.00 0.00 2.57
1024 1804 2.475111 GCGTCGTTCACAAATCTCTCAA 59.525 45.455 0.00 0.00 0.00 3.02
1059 1839 2.035632 CTCGCCATCCTCTTTCCTACT 58.964 52.381 0.00 0.00 0.00 2.57
1141 1924 5.303165 CCTCTGCTTATCATGCTTACATCA 58.697 41.667 0.00 0.00 32.87 3.07
1575 2358 1.269206 CGGTGCAACAACAAGCTCATT 60.269 47.619 0.98 0.00 39.98 2.57
1663 2450 4.697756 CGGCAGCCGGGAACTTCA 62.698 66.667 27.32 0.00 44.15 3.02
1840 2634 1.512310 GACGTGCTCTCGTTCTCCG 60.512 63.158 0.00 0.00 44.21 4.63
2269 3075 1.465387 GTGTGGTGTTGTTCAACGACA 59.535 47.619 6.50 6.50 40.03 4.35
2372 3191 2.565394 CTTACGCCGCATCGTCGAC 61.565 63.158 5.18 5.18 43.15 4.20
2466 3285 2.920912 TCTTCGCGGGGTCCAAGT 60.921 61.111 6.13 0.00 0.00 3.16
3044 3877 2.280524 CAAGGTGGACGTGCCGAA 60.281 61.111 4.04 0.00 40.66 4.30
3251 4156 0.390472 TGAATGATGTACGTGCCGCA 60.390 50.000 0.00 0.00 0.00 5.69
3564 4471 2.701951 TCCGTCCCTGTAAACTTCTGTT 59.298 45.455 0.00 0.00 38.16 3.16
3704 4620 8.006298 TGTGAAAATTGTTGGTGTTAATCTCT 57.994 30.769 0.00 0.00 0.00 3.10
3716 4632 6.043938 TGGTGTTAATCTCTTCAGTAGGGTTT 59.956 38.462 0.00 0.00 0.00 3.27
3727 4643 4.523083 TCAGTAGGGTTTTATGGATGTGC 58.477 43.478 0.00 0.00 0.00 4.57
3736 4652 6.451393 GGTTTTATGGATGTGCAAGTTTGTA 58.549 36.000 0.00 0.00 0.00 2.41
3753 4669 3.981071 TGTAGGTTTCCTGGAGACATG 57.019 47.619 17.97 0.00 41.51 3.21
3754 4670 2.027192 TGTAGGTTTCCTGGAGACATGC 60.027 50.000 17.97 14.94 41.51 4.06
3755 4671 0.036010 AGGTTTCCTGGAGACATGCG 60.036 55.000 17.97 0.00 41.51 4.73
3766 4690 3.244078 TGGAGACATGCGTGAGTTTAAGT 60.244 43.478 14.17 0.00 33.40 2.24
3770 4694 5.403246 AGACATGCGTGAGTTTAAGTCTAG 58.597 41.667 14.17 0.00 33.72 2.43
3802 4753 7.558161 TTGCCTTCACATATGAATACTTCAG 57.442 36.000 10.38 0.00 43.92 3.02
3834 4785 9.319143 GCGTATATATGCTAGATCCAAAATTCT 57.681 33.333 17.98 0.00 35.39 2.40
3842 4793 6.541278 TGCTAGATCCAAAATTCTGATCACTG 59.459 38.462 11.92 0.00 37.86 3.66
3854 4805 8.985315 AATTCTGATCACTGGATATGCTAAAA 57.015 30.769 0.00 0.00 32.67 1.52
3911 4862 6.764308 AATGCTAGTGCTATCAAACATTGT 57.236 33.333 0.00 0.00 40.48 2.71
3936 4887 1.619654 CCACTTTCCATCAAGCACCA 58.380 50.000 0.00 0.00 0.00 4.17
3946 4897 0.895100 TCAAGCACCAACATCCAGGC 60.895 55.000 0.00 0.00 0.00 4.85
3947 4898 1.607467 AAGCACCAACATCCAGGCC 60.607 57.895 0.00 0.00 0.00 5.19
3977 4968 9.329913 GTAGTACAATGCATTCTTGTTTTACAG 57.670 33.333 9.53 0.00 37.89 2.74
3978 4969 6.863126 AGTACAATGCATTCTTGTTTTACAGC 59.137 34.615 9.53 0.00 37.89 4.40
4009 5000 8.023706 GGACTAACTGAATCTCATTCCAAAAAC 58.976 37.037 0.00 0.00 38.50 2.43
4010 5001 8.697507 ACTAACTGAATCTCATTCCAAAAACT 57.302 30.769 0.00 0.00 38.50 2.66
4011 5002 8.571336 ACTAACTGAATCTCATTCCAAAAACTG 58.429 33.333 0.00 0.00 38.50 3.16
4025 5018 3.277142 AAAACTGTTTCCCTGAGACGT 57.723 42.857 6.20 0.00 0.00 4.34
4037 5030 2.478709 CCTGAGACGTTCAATCTCTCCG 60.479 54.545 0.00 0.00 42.68 4.63
4043 5036 4.217983 AGACGTTCAATCTCTCCGTTAGTT 59.782 41.667 0.00 0.00 0.00 2.24
4067 5060 7.990541 TTGTGAGATCTTGAACATTGTTTTG 57.009 32.000 3.08 0.00 0.00 2.44
4068 5061 6.506147 TGTGAGATCTTGAACATTGTTTTGG 58.494 36.000 3.08 0.00 0.00 3.28
4111 5105 1.394917 GCACTGCATTCTGTTACCGAG 59.605 52.381 0.00 0.00 0.00 4.63
4118 5112 3.535561 CATTCTGTTACCGAGCTTCCAT 58.464 45.455 0.00 0.00 0.00 3.41
4137 5131 0.615331 TTGGCTCCTGTCTCATGGAC 59.385 55.000 7.22 7.22 44.70 4.02
4154 5148 3.030291 TGGACATGTTTTCTTTGGCTGT 58.970 40.909 0.00 0.00 0.00 4.40
4156 5150 3.803778 GGACATGTTTTCTTTGGCTGTTG 59.196 43.478 0.00 0.00 0.00 3.33
4164 5158 0.390124 CTTTGGCTGTTGTGGCACAT 59.610 50.000 22.73 0.00 44.52 3.21
4179 5173 5.822519 TGTGGCACATACCTAATTCTTGATC 59.177 40.000 17.96 0.00 44.52 2.92
4204 5205 9.330063 TCTTTGATGCGAAGTCAGAAATATTAT 57.670 29.630 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 8.292448 CACTAATCTAACAGCACAAAAGTCATT 58.708 33.333 0.00 0.00 0.00 2.57
17 18 6.296026 TCCACTAATCTAACAGCACAAAAGT 58.704 36.000 0.00 0.00 0.00 2.66
19 20 6.714810 ACATCCACTAATCTAACAGCACAAAA 59.285 34.615 0.00 0.00 0.00 2.44
37 38 1.478105 GGGCCAGATGAAAACATCCAC 59.522 52.381 4.39 0.00 32.22 4.02
42 43 2.380064 AACAGGGCCAGATGAAAACA 57.620 45.000 6.18 0.00 0.00 2.83
54 55 4.627035 GCATTTGAACTGATTAAACAGGGC 59.373 41.667 16.16 8.46 41.59 5.19
65 66 3.930336 AGAGACGATGCATTTGAACTGA 58.070 40.909 0.00 0.00 0.00 3.41
66 67 5.220548 CCTTAGAGACGATGCATTTGAACTG 60.221 44.000 0.00 0.00 0.00 3.16
68 69 4.870426 TCCTTAGAGACGATGCATTTGAAC 59.130 41.667 0.00 0.00 0.00 3.18
106 107 4.622701 ATCGCAGCAACTCCTTTATTTC 57.377 40.909 0.00 0.00 0.00 2.17
121 122 6.563753 GCTCTGCTTCTATTTTCTTATCGCAG 60.564 42.308 0.00 0.00 42.54 5.18
127 128 5.045578 ACTGGGCTCTGCTTCTATTTTCTTA 60.046 40.000 0.00 0.00 0.00 2.10
137 138 2.991250 TCAATAACTGGGCTCTGCTTC 58.009 47.619 0.00 0.00 0.00 3.86
140 141 4.904241 AGATATCAATAACTGGGCTCTGC 58.096 43.478 5.32 0.00 0.00 4.26
161 247 4.505191 CACAAGACCAAAATGCTTCACAAG 59.495 41.667 0.00 0.00 0.00 3.16
163 249 3.698539 TCACAAGACCAAAATGCTTCACA 59.301 39.130 0.00 0.00 0.00 3.58
164 250 4.305989 TCACAAGACCAAAATGCTTCAC 57.694 40.909 0.00 0.00 0.00 3.18
167 253 3.132646 TGCTTCACAAGACCAAAATGCTT 59.867 39.130 0.00 0.00 0.00 3.91
168 254 2.694628 TGCTTCACAAGACCAAAATGCT 59.305 40.909 0.00 0.00 0.00 3.79
169 255 3.096489 TGCTTCACAAGACCAAAATGC 57.904 42.857 0.00 0.00 0.00 3.56
184 938 7.820648 TCTGTTTCTTTATCTCCAAATGCTTC 58.179 34.615 0.00 0.00 0.00 3.86
185 939 7.765695 TCTGTTTCTTTATCTCCAAATGCTT 57.234 32.000 0.00 0.00 0.00 3.91
192 946 7.106239 GGTCTTGATCTGTTTCTTTATCTCCA 58.894 38.462 0.00 0.00 0.00 3.86
193 947 6.256757 CGGTCTTGATCTGTTTCTTTATCTCC 59.743 42.308 0.00 0.00 0.00 3.71
194 948 7.036220 TCGGTCTTGATCTGTTTCTTTATCTC 58.964 38.462 0.00 0.00 0.00 2.75
195 949 6.936279 TCGGTCTTGATCTGTTTCTTTATCT 58.064 36.000 0.00 0.00 0.00 1.98
196 950 7.625553 CATCGGTCTTGATCTGTTTCTTTATC 58.374 38.462 0.00 0.00 0.00 1.75
197 951 6.037610 GCATCGGTCTTGATCTGTTTCTTTAT 59.962 38.462 0.00 0.00 0.00 1.40
198 952 5.351465 GCATCGGTCTTGATCTGTTTCTTTA 59.649 40.000 0.00 0.00 0.00 1.85
199 953 4.154918 GCATCGGTCTTGATCTGTTTCTTT 59.845 41.667 0.00 0.00 0.00 2.52
200 954 3.686726 GCATCGGTCTTGATCTGTTTCTT 59.313 43.478 0.00 0.00 0.00 2.52
201 955 3.265791 GCATCGGTCTTGATCTGTTTCT 58.734 45.455 0.00 0.00 0.00 2.52
202 956 2.029728 CGCATCGGTCTTGATCTGTTTC 59.970 50.000 0.00 0.00 0.00 2.78
203 957 2.002586 CGCATCGGTCTTGATCTGTTT 58.997 47.619 0.00 0.00 0.00 2.83
204 958 1.645034 CGCATCGGTCTTGATCTGTT 58.355 50.000 0.00 0.00 0.00 3.16
205 959 0.179100 CCGCATCGGTCTTGATCTGT 60.179 55.000 0.00 0.00 42.73 3.41
206 960 0.877649 CCCGCATCGGTCTTGATCTG 60.878 60.000 4.47 0.00 46.80 2.90
207 961 1.330655 ACCCGCATCGGTCTTGATCT 61.331 55.000 4.47 0.00 46.80 2.75
208 962 1.144057 ACCCGCATCGGTCTTGATC 59.856 57.895 4.47 0.00 46.80 2.92
209 963 3.309582 ACCCGCATCGGTCTTGAT 58.690 55.556 4.47 0.00 46.80 2.57
215 969 4.082523 CCACTGACCCGCATCGGT 62.083 66.667 4.47 0.00 46.80 4.69
222 976 3.047877 GAAACGCCCACTGACCCG 61.048 66.667 0.00 0.00 0.00 5.28
223 977 2.671963 GGAAACGCCCACTGACCC 60.672 66.667 0.00 0.00 0.00 4.46
232 986 3.317149 ACAAAACTAAAGAGGGAAACGCC 59.683 43.478 0.00 0.00 0.00 5.68
233 987 4.563337 ACAAAACTAAAGAGGGAAACGC 57.437 40.909 0.00 0.00 0.00 4.84
234 988 8.964150 CATAAAACAAAACTAAAGAGGGAAACG 58.036 33.333 0.00 0.00 0.00 3.60
235 989 8.761497 GCATAAAACAAAACTAAAGAGGGAAAC 58.239 33.333 0.00 0.00 0.00 2.78
236 990 8.700973 AGCATAAAACAAAACTAAAGAGGGAAA 58.299 29.630 0.00 0.00 0.00 3.13
237 991 8.141268 CAGCATAAAACAAAACTAAAGAGGGAA 58.859 33.333 0.00 0.00 0.00 3.97
238 992 7.657336 CAGCATAAAACAAAACTAAAGAGGGA 58.343 34.615 0.00 0.00 0.00 4.20
239 993 6.366061 GCAGCATAAAACAAAACTAAAGAGGG 59.634 38.462 0.00 0.00 0.00 4.30
240 994 6.366061 GGCAGCATAAAACAAAACTAAAGAGG 59.634 38.462 0.00 0.00 0.00 3.69
241 995 6.088085 CGGCAGCATAAAACAAAACTAAAGAG 59.912 38.462 0.00 0.00 0.00 2.85
242 996 5.918011 CGGCAGCATAAAACAAAACTAAAGA 59.082 36.000 0.00 0.00 0.00 2.52
243 997 5.689961 ACGGCAGCATAAAACAAAACTAAAG 59.310 36.000 0.00 0.00 0.00 1.85
244 998 5.593010 ACGGCAGCATAAAACAAAACTAAA 58.407 33.333 0.00 0.00 0.00 1.85
245 999 5.189659 ACGGCAGCATAAAACAAAACTAA 57.810 34.783 0.00 0.00 0.00 2.24
246 1000 4.839668 ACGGCAGCATAAAACAAAACTA 57.160 36.364 0.00 0.00 0.00 2.24
247 1001 3.726291 ACGGCAGCATAAAACAAAACT 57.274 38.095 0.00 0.00 0.00 2.66
248 1002 3.059935 CCAACGGCAGCATAAAACAAAAC 60.060 43.478 0.00 0.00 0.00 2.43
249 1003 3.126831 CCAACGGCAGCATAAAACAAAA 58.873 40.909 0.00 0.00 0.00 2.44
250 1004 2.546795 CCCAACGGCAGCATAAAACAAA 60.547 45.455 0.00 0.00 0.00 2.83
251 1005 1.000283 CCCAACGGCAGCATAAAACAA 60.000 47.619 0.00 0.00 0.00 2.83
252 1006 0.600557 CCCAACGGCAGCATAAAACA 59.399 50.000 0.00 0.00 0.00 2.83
253 1007 0.601057 ACCCAACGGCAGCATAAAAC 59.399 50.000 0.00 0.00 0.00 2.43
254 1008 1.271102 GAACCCAACGGCAGCATAAAA 59.729 47.619 0.00 0.00 0.00 1.52
255 1009 0.885196 GAACCCAACGGCAGCATAAA 59.115 50.000 0.00 0.00 0.00 1.40
256 1010 0.250945 TGAACCCAACGGCAGCATAA 60.251 50.000 0.00 0.00 0.00 1.90
257 1011 0.034574 ATGAACCCAACGGCAGCATA 60.035 50.000 0.00 0.00 0.00 3.14
258 1012 0.899717 AATGAACCCAACGGCAGCAT 60.900 50.000 0.00 0.00 0.00 3.79
259 1013 1.523154 GAATGAACCCAACGGCAGCA 61.523 55.000 0.00 0.00 0.00 4.41
260 1014 1.212751 GAATGAACCCAACGGCAGC 59.787 57.895 0.00 0.00 0.00 5.25
261 1015 1.501741 CGAATGAACCCAACGGCAG 59.498 57.895 0.00 0.00 0.00 4.85
262 1016 2.622011 GCGAATGAACCCAACGGCA 61.622 57.895 0.00 0.00 0.00 5.69
263 1017 2.178273 GCGAATGAACCCAACGGC 59.822 61.111 0.00 0.00 0.00 5.68
264 1018 1.501741 CAGCGAATGAACCCAACGG 59.498 57.895 0.00 0.00 0.00 4.44
265 1019 1.501741 CCAGCGAATGAACCCAACG 59.498 57.895 0.00 0.00 0.00 4.10
266 1020 0.893727 ACCCAGCGAATGAACCCAAC 60.894 55.000 0.00 0.00 0.00 3.77
267 1021 0.693622 TACCCAGCGAATGAACCCAA 59.306 50.000 0.00 0.00 0.00 4.12
268 1022 0.251916 CTACCCAGCGAATGAACCCA 59.748 55.000 0.00 0.00 0.00 4.51
269 1023 0.252197 ACTACCCAGCGAATGAACCC 59.748 55.000 0.00 0.00 0.00 4.11
270 1024 2.167900 ACTACTACCCAGCGAATGAACC 59.832 50.000 0.00 0.00 0.00 3.62
271 1025 3.521947 ACTACTACCCAGCGAATGAAC 57.478 47.619 0.00 0.00 0.00 3.18
272 1026 3.635373 CCTACTACTACCCAGCGAATGAA 59.365 47.826 0.00 0.00 0.00 2.57
273 1027 3.220110 CCTACTACTACCCAGCGAATGA 58.780 50.000 0.00 0.00 0.00 2.57
274 1028 2.957006 ACCTACTACTACCCAGCGAATG 59.043 50.000 0.00 0.00 0.00 2.67
275 1029 3.309600 ACCTACTACTACCCAGCGAAT 57.690 47.619 0.00 0.00 0.00 3.34
276 1030 2.814805 ACCTACTACTACCCAGCGAA 57.185 50.000 0.00 0.00 0.00 4.70
277 1031 4.141413 TGAATACCTACTACTACCCAGCGA 60.141 45.833 0.00 0.00 0.00 4.93
278 1032 4.139786 TGAATACCTACTACTACCCAGCG 58.860 47.826 0.00 0.00 0.00 5.18
279 1033 5.009811 CACTGAATACCTACTACTACCCAGC 59.990 48.000 0.00 0.00 0.00 4.85
280 1034 6.127793 ACACTGAATACCTACTACTACCCAG 58.872 44.000 0.00 0.00 0.00 4.45
281 1035 6.083487 ACACTGAATACCTACTACTACCCA 57.917 41.667 0.00 0.00 0.00 4.51
282 1036 7.341512 AGAAACACTGAATACCTACTACTACCC 59.658 40.741 0.00 0.00 0.00 3.69
283 1037 8.291191 AGAAACACTGAATACCTACTACTACC 57.709 38.462 0.00 0.00 0.00 3.18
329 1091 0.250234 TCTGCTGGTGCTTAGCGAAT 59.750 50.000 0.00 0.00 44.01 3.34
332 1094 0.376152 CAATCTGCTGGTGCTTAGCG 59.624 55.000 0.00 0.00 44.01 4.26
389 1151 5.458041 AAGAAAATGACAGAATGGGTGTG 57.542 39.130 0.00 0.00 43.62 3.82
390 1152 4.524328 GGAAGAAAATGACAGAATGGGTGT 59.476 41.667 0.00 0.00 43.62 4.16
468 1231 5.607119 TCTTTTACGCTCAAAACCTGATC 57.393 39.130 0.00 0.00 32.14 2.92
469 1232 6.385649 TTTCTTTTACGCTCAAAACCTGAT 57.614 33.333 0.00 0.00 32.14 2.90
470 1233 5.821516 TTTCTTTTACGCTCAAAACCTGA 57.178 34.783 0.00 0.00 0.00 3.86
471 1234 6.695278 TCATTTTCTTTTACGCTCAAAACCTG 59.305 34.615 0.00 0.00 0.00 4.00
584 1347 9.363763 CACCTATGATGTGTTATCATCTCATAC 57.636 37.037 5.72 0.00 43.03 2.39
619 1385 8.785329 TTTTCAAAATTAACAGCTTCTGGTTT 57.215 26.923 0.00 0.00 35.51 3.27
772 1541 0.256752 TGTGGGATGGCAGGAATGAG 59.743 55.000 0.00 0.00 0.00 2.90
1024 1804 1.134670 GGCGAGCAAGAGAAGTGGTAT 60.135 52.381 0.00 0.00 0.00 2.73
1575 2358 1.003003 TCGATGAATGACTTGGCACCA 59.997 47.619 0.00 0.00 0.00 4.17
1663 2450 2.279252 GTATGACGCGCCGGTGAT 60.279 61.111 21.76 5.36 0.00 3.06
2209 3015 0.034896 ATTCTGCGGACGTTGGACTT 59.965 50.000 0.00 0.00 0.00 3.01
2248 3054 1.465387 GTCGTTGAACAACACCACACA 59.535 47.619 16.13 0.00 41.20 3.72
2372 3191 4.079850 AGGCCACAGAGCTGCTCG 62.080 66.667 22.77 19.05 35.36 5.03
2466 3285 3.593442 AGGATGTTGAGGTTGGTGAAA 57.407 42.857 0.00 0.00 0.00 2.69
2931 3755 1.831343 CGGTTATCGTCGGGTAGTTG 58.169 55.000 0.00 0.00 0.00 3.16
3044 3877 4.363990 CACGCACCGTCAGAGGCT 62.364 66.667 0.00 0.00 38.32 4.58
3292 4197 6.125327 TGTTGACGCAAAAGAAATACTGAA 57.875 33.333 0.00 0.00 0.00 3.02
3638 4554 3.382278 AGAGGGAGATCTGCATCAAAGA 58.618 45.455 27.21 0.00 34.15 2.52
3704 4620 4.947388 GCACATCCATAAAACCCTACTGAA 59.053 41.667 0.00 0.00 0.00 3.02
3716 4632 5.321102 ACCTACAAACTTGCACATCCATAA 58.679 37.500 0.00 0.00 0.00 1.90
3727 4643 4.515567 GTCTCCAGGAAACCTACAAACTTG 59.484 45.833 0.00 0.00 29.64 3.16
3736 4652 0.036010 CGCATGTCTCCAGGAAACCT 60.036 55.000 0.00 0.00 0.00 3.50
3753 4669 5.233689 ACACAAACTAGACTTAAACTCACGC 59.766 40.000 0.00 0.00 0.00 5.34
3754 4670 6.823678 ACACAAACTAGACTTAAACTCACG 57.176 37.500 0.00 0.00 0.00 4.35
3755 4671 7.428472 GCAAACACAAACTAGACTTAAACTCAC 59.572 37.037 0.00 0.00 0.00 3.51
3766 4690 4.265893 TGTGAAGGCAAACACAAACTAGA 58.734 39.130 0.00 0.00 42.72 2.43
3770 4694 6.646240 ATTCATATGTGAAGGCAAACACAAAC 59.354 34.615 10.79 0.00 46.75 2.93
3802 4753 8.100508 TGGATCTAGCATATATACGCTCATAC 57.899 38.462 6.58 2.62 39.70 2.39
3825 4776 6.264744 AGCATATCCAGTGATCAGAATTTTGG 59.735 38.462 0.00 0.00 32.18 3.28
3874 4825 5.343325 GCACTAGCATTACTCAAAAACTTGC 59.657 40.000 0.00 0.00 41.58 4.01
3876 4827 6.884280 AGCACTAGCATTACTCAAAAACTT 57.116 33.333 0.00 0.00 45.49 2.66
3879 4830 8.560355 TTGATAGCACTAGCATTACTCAAAAA 57.440 30.769 0.00 0.00 45.49 1.94
3881 4832 7.606073 TGTTTGATAGCACTAGCATTACTCAAA 59.394 33.333 0.00 0.00 45.49 2.69
3886 4837 7.697691 ACAATGTTTGATAGCACTAGCATTAC 58.302 34.615 0.00 0.15 45.49 1.89
3936 4887 1.861982 ACTACTACGGCCTGGATGTT 58.138 50.000 0.00 0.00 0.00 2.71
3946 4897 5.810587 ACAAGAATGCATTGTACTACTACGG 59.189 40.000 18.59 3.03 39.06 4.02
3947 4898 6.887376 ACAAGAATGCATTGTACTACTACG 57.113 37.500 18.59 4.32 39.06 3.51
3977 4968 3.119101 TGAGATTCAGTTAGTCCTTCCGC 60.119 47.826 0.00 0.00 0.00 5.54
3978 4969 4.720649 TGAGATTCAGTTAGTCCTTCCG 57.279 45.455 0.00 0.00 0.00 4.30
4009 5000 2.526304 TGAACGTCTCAGGGAAACAG 57.474 50.000 0.00 0.00 0.00 3.16
4010 5001 2.992124 TTGAACGTCTCAGGGAAACA 57.008 45.000 0.00 0.00 34.81 2.83
4011 5002 3.665190 AGATTGAACGTCTCAGGGAAAC 58.335 45.455 0.00 0.00 34.81 2.78
4025 5018 5.849510 TCACAAACTAACGGAGAGATTGAA 58.150 37.500 9.41 0.00 0.00 2.69
4037 5030 8.345565 ACAATGTTCAAGATCTCACAAACTAAC 58.654 33.333 0.00 0.00 0.00 2.34
4043 5036 6.979817 CCAAAACAATGTTCAAGATCTCACAA 59.020 34.615 0.00 0.00 0.00 3.33
4079 5073 1.601166 TGCAGTGCATGATATCCTGC 58.399 50.000 21.95 21.95 46.64 4.85
4095 5089 2.346803 GAAGCTCGGTAACAGAATGCA 58.653 47.619 0.00 0.00 42.53 3.96
4111 5105 0.034670 AGACAGGAGCCAATGGAAGC 60.035 55.000 2.05 0.00 0.00 3.86
4118 5112 0.615331 GTCCATGAGACAGGAGCCAA 59.385 55.000 0.00 0.00 45.55 4.52
4137 5131 3.556775 CCACAACAGCCAAAGAAAACATG 59.443 43.478 0.00 0.00 0.00 3.21
4154 5148 5.565509 TCAAGAATTAGGTATGTGCCACAA 58.434 37.500 0.00 0.00 0.00 3.33
4156 5150 6.058183 AGATCAAGAATTAGGTATGTGCCAC 58.942 40.000 0.00 0.00 0.00 5.01
4164 5158 7.272244 TCGCATCAAAGATCAAGAATTAGGTA 58.728 34.615 0.00 0.00 0.00 3.08
4179 5173 9.378597 CATAATATTTCTGACTTCGCATCAAAG 57.621 33.333 0.00 0.00 0.00 2.77
4186 5180 5.992217 ACTCCCATAATATTTCTGACTTCGC 59.008 40.000 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.