Multiple sequence alignment - TraesCS4D01G229200

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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 TraesCS4D01G229200 chr4D 100.000 4697 0 0 1 4697 388932607 388927911 0.000000e+00 8674
1 TraesCS4D01G229200 chr4B 94.670 3527 136 17 419 3935 477230763 477227279 0.000000e+00 5424
2 TraesCS4D01G229200 chr4B 93.521 710 31 7 3995 4697 477227164 477226463 0.000000e+00 1042
3 TraesCS4D01G229200 chr4B 86.207 174 11 9 1 162 477231401 477231229 4.830000e-40 176
4 TraesCS4D01G229200 chr4A 92.984 1411 67 15 3067 4467 70312968 70311580 0.000000e+00 2028
5 TraesCS4D01G229200 chr4A 90.708 1539 90 23 1599 3113 70314464 70312955 0.000000e+00 2001
6 TraesCS4D01G229200 chr4A 94.031 1089 56 8 416 1500 70315598 70314515 0.000000e+00 1642
7 TraesCS4D01G229200 chr4A 91.827 208 11 1 4496 4697 70311515 70311308 7.690000e-73 285


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 TraesCS4D01G229200 chr4D 388927911 388932607 4696 True 8674 8674 100.0000 1 4697 1 chr4D.!!$R1 4696
1 TraesCS4D01G229200 chr4B 477226463 477231401 4938 True 2214 5424 91.4660 1 4697 3 chr4B.!!$R1 4696
2 TraesCS4D01G229200 chr4A 70311308 70315598 4290 True 1489 2028 92.3875 416 4697 4 chr4A.!!$R1 4281

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
193 206 0.106519 CCTCCCTCGGCATCCAAAAT 60.107 55.000 0.00 0.0 0.00 1.82 F
195 208 0.106719 TCCCTCGGCATCCAAAATCC 60.107 55.000 0.00 0.0 0.00 3.01 F
218 231 0.249238 ATCTTCAGATCCACGCGAGC 60.249 55.000 15.93 0.0 0.00 5.03 F
334 347 0.317854 AAAAGAAGAAGGCAACGCGC 60.318 50.000 5.73 0.0 46.39 6.86 F
908 1133 1.343821 CCGCGAATCGAAGTTTCCG 59.656 57.895 8.23 0.0 41.67 4.30 F
1307 1532 1.631072 CTAACCTCGATTGCGTGCG 59.369 57.895 0.00 0.0 38.98 5.34 F
2769 3026 1.586422 CTCGCAGGGATGTTATGGTG 58.414 55.000 0.00 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 1509 0.179111 CGCAATCGAGGTTAGCAGGA 60.179 55.000 0.00 0.00 38.10 3.86 R
1731 1964 1.618487 TGGCATGTGTCAAGATTGCA 58.382 45.000 0.00 0.00 0.00 4.08 R
2331 2588 4.722700 TCCGGGCCAGCTTTGCTC 62.723 66.667 4.39 0.00 36.40 4.26 R
2595 2852 3.733443 ACTGTCCCTGCAAAATCAAAC 57.267 42.857 0.00 0.00 0.00 2.93 R
2769 3026 0.390998 GGAGACCAGCAGCTGACTTC 60.391 60.000 24.90 16.49 32.44 3.01 R
2781 3038 0.401356 TGATGCTTTGCTGGAGACCA 59.599 50.000 0.00 0.00 0.00 4.02 R
4086 4442 0.034059 CCAGGGACATGATAGCCGAC 59.966 60.000 0.00 0.00 0.00 4.79 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.318955 CCGGTAAAACTCGACACGGT 60.319 55.000 0.00 0.00 35.47 4.83
30 31 2.428888 AAACTCGACACGGTAGAACC 57.571 50.000 0.00 0.00 34.05 3.62
54 55 1.742831 GCTGGAATTGCGAACATGGTA 59.257 47.619 0.00 0.00 0.00 3.25
55 56 2.223340 GCTGGAATTGCGAACATGGTAG 60.223 50.000 0.00 0.00 0.00 3.18
57 58 2.026729 TGGAATTGCGAACATGGTAGGA 60.027 45.455 0.00 0.00 0.00 2.94
58 59 2.614057 GGAATTGCGAACATGGTAGGAG 59.386 50.000 0.00 0.00 0.00 3.69
59 60 3.270877 GAATTGCGAACATGGTAGGAGT 58.729 45.455 0.00 0.00 0.00 3.85
60 61 4.439057 GAATTGCGAACATGGTAGGAGTA 58.561 43.478 0.00 0.00 0.00 2.59
78 87 5.574970 GAGTAGATCCAATCCTGGGATTT 57.425 43.478 11.72 0.00 45.05 2.17
100 113 1.072331 CCCCCACTATCATGCCACTAC 59.928 57.143 0.00 0.00 0.00 2.73
101 114 1.768275 CCCCACTATCATGCCACTACA 59.232 52.381 0.00 0.00 0.00 2.74
105 118 4.202398 CCCACTATCATGCCACTACAATCT 60.202 45.833 0.00 0.00 0.00 2.40
107 120 5.468072 CCACTATCATGCCACTACAATCTTC 59.532 44.000 0.00 0.00 0.00 2.87
169 182 3.360886 AAAAACCAAACCGCAGCAG 57.639 47.368 0.00 0.00 0.00 4.24
170 183 0.809636 AAAAACCAAACCGCAGCAGC 60.810 50.000 0.00 0.00 37.42 5.25
174 187 3.741476 CAAACCGCAGCAGCCCTC 61.741 66.667 0.00 0.00 37.52 4.30
181 194 3.478274 CAGCAGCCCTCCTCCCTC 61.478 72.222 0.00 0.00 0.00 4.30
187 200 3.237741 CCCTCCTCCCTCGGCATC 61.238 72.222 0.00 0.00 0.00 3.91
188 201 3.237741 CCTCCTCCCTCGGCATCC 61.238 72.222 0.00 0.00 0.00 3.51
189 202 2.444706 CTCCTCCCTCGGCATCCA 60.445 66.667 0.00 0.00 0.00 3.41
190 203 2.040442 TCCTCCCTCGGCATCCAA 59.960 61.111 0.00 0.00 0.00 3.53
191 204 1.615124 TCCTCCCTCGGCATCCAAA 60.615 57.895 0.00 0.00 0.00 3.28
192 205 1.204786 TCCTCCCTCGGCATCCAAAA 61.205 55.000 0.00 0.00 0.00 2.44
193 206 0.106519 CCTCCCTCGGCATCCAAAAT 60.107 55.000 0.00 0.00 0.00 1.82
194 207 1.312815 CTCCCTCGGCATCCAAAATC 58.687 55.000 0.00 0.00 0.00 2.17
195 208 0.106719 TCCCTCGGCATCCAAAATCC 60.107 55.000 0.00 0.00 0.00 3.01
196 209 0.395586 CCCTCGGCATCCAAAATCCA 60.396 55.000 0.00 0.00 0.00 3.41
197 210 1.473258 CCTCGGCATCCAAAATCCAA 58.527 50.000 0.00 0.00 0.00 3.53
198 211 1.824230 CCTCGGCATCCAAAATCCAAA 59.176 47.619 0.00 0.00 0.00 3.28
199 212 2.233431 CCTCGGCATCCAAAATCCAAAA 59.767 45.455 0.00 0.00 0.00 2.44
200 213 3.118665 CCTCGGCATCCAAAATCCAAAAT 60.119 43.478 0.00 0.00 0.00 1.82
201 214 4.114794 CTCGGCATCCAAAATCCAAAATC 58.885 43.478 0.00 0.00 0.00 2.17
202 215 3.768757 TCGGCATCCAAAATCCAAAATCT 59.231 39.130 0.00 0.00 0.00 2.40
203 216 4.222588 TCGGCATCCAAAATCCAAAATCTT 59.777 37.500 0.00 0.00 0.00 2.40
204 217 4.567959 CGGCATCCAAAATCCAAAATCTTC 59.432 41.667 0.00 0.00 0.00 2.87
205 218 5.490159 GGCATCCAAAATCCAAAATCTTCA 58.510 37.500 0.00 0.00 0.00 3.02
206 219 5.583457 GGCATCCAAAATCCAAAATCTTCAG 59.417 40.000 0.00 0.00 0.00 3.02
207 220 6.400568 GCATCCAAAATCCAAAATCTTCAGA 58.599 36.000 0.00 0.00 0.00 3.27
208 221 7.046033 GCATCCAAAATCCAAAATCTTCAGAT 58.954 34.615 0.00 0.00 36.07 2.90
209 222 7.224167 GCATCCAAAATCCAAAATCTTCAGATC 59.776 37.037 0.00 0.00 32.75 2.75
210 223 7.174107 TCCAAAATCCAAAATCTTCAGATCC 57.826 36.000 0.00 0.00 32.75 3.36
211 224 6.725369 TCCAAAATCCAAAATCTTCAGATCCA 59.275 34.615 0.00 0.00 32.75 3.41
212 225 6.815142 CCAAAATCCAAAATCTTCAGATCCAC 59.185 38.462 0.00 0.00 32.75 4.02
213 226 5.824904 AATCCAAAATCTTCAGATCCACG 57.175 39.130 0.00 0.00 32.75 4.94
214 227 3.009723 TCCAAAATCTTCAGATCCACGC 58.990 45.455 0.00 0.00 32.75 5.34
215 228 2.223112 CCAAAATCTTCAGATCCACGCG 60.223 50.000 3.53 3.53 32.75 6.01
216 229 2.672874 CAAAATCTTCAGATCCACGCGA 59.327 45.455 15.93 0.00 32.75 5.87
217 230 2.215907 AATCTTCAGATCCACGCGAG 57.784 50.000 15.93 4.16 32.75 5.03
218 231 0.249238 ATCTTCAGATCCACGCGAGC 60.249 55.000 15.93 0.00 0.00 5.03
219 232 2.202610 TTCAGATCCACGCGAGCG 60.203 61.111 15.93 16.38 46.03 5.03
220 233 3.699955 TTCAGATCCACGCGAGCGG 62.700 63.158 21.69 10.69 44.69 5.52
222 235 4.194720 AGATCCACGCGAGCGGAC 62.195 66.667 21.69 10.18 46.55 4.79
223 236 4.194720 GATCCACGCGAGCGGACT 62.195 66.667 21.69 5.93 46.55 3.85
224 237 4.194720 ATCCACGCGAGCGGACTC 62.195 66.667 21.69 0.00 46.55 3.36
251 264 4.394078 GCGCGTTCGGGGGTTTTC 62.394 66.667 8.43 0.00 35.95 2.29
252 265 4.079748 CGCGTTCGGGGGTTTTCG 62.080 66.667 0.00 0.00 0.00 3.46
253 266 4.394078 GCGTTCGGGGGTTTTCGC 62.394 66.667 0.00 0.00 37.17 4.70
254 267 2.667199 CGTTCGGGGGTTTTCGCT 60.667 61.111 0.00 0.00 0.00 4.93
255 268 2.951458 GTTCGGGGGTTTTCGCTG 59.049 61.111 0.00 0.00 36.17 5.18
256 269 2.281900 TTCGGGGGTTTTCGCTGG 60.282 61.111 0.00 0.00 35.61 4.85
259 272 4.986708 GGGGGTTTTCGCTGGCCA 62.987 66.667 4.71 4.71 0.00 5.36
260 273 2.679996 GGGGTTTTCGCTGGCCAT 60.680 61.111 5.51 0.00 0.00 4.40
261 274 2.710902 GGGGTTTTCGCTGGCCATC 61.711 63.158 5.51 0.00 0.00 3.51
262 275 2.485122 GGTTTTCGCTGGCCATCG 59.515 61.111 22.70 22.70 0.00 3.84
263 276 2.202479 GTTTTCGCTGGCCATCGC 60.202 61.111 23.79 15.45 0.00 4.58
264 277 2.671276 TTTTCGCTGGCCATCGCA 60.671 55.556 23.79 11.07 36.38 5.10
265 278 2.689785 TTTTCGCTGGCCATCGCAG 61.690 57.895 23.79 12.30 36.38 5.18
266 279 3.604129 TTTCGCTGGCCATCGCAGA 62.604 57.895 23.79 14.26 45.75 4.26
267 280 3.604129 TTCGCTGGCCATCGCAGAA 62.604 57.895 23.79 18.61 43.58 3.02
268 281 3.869272 CGCTGGCCATCGCAGAAC 61.869 66.667 17.04 0.00 43.58 3.01
269 282 3.869272 GCTGGCCATCGCAGAACG 61.869 66.667 5.51 0.00 43.58 3.95
292 305 4.712425 GACGGGGACACGGTCACG 62.712 72.222 10.32 14.11 45.68 4.35
295 308 4.065281 GGGGACACGGTCACGGAG 62.065 72.222 6.41 0.00 46.48 4.63
296 309 4.736896 GGGACACGGTCACGGAGC 62.737 72.222 6.41 0.00 46.48 4.70
297 310 4.736896 GGACACGGTCACGGAGCC 62.737 72.222 6.41 0.00 46.48 4.70
313 326 2.740826 CCGCGCGGGAAGAAGAAA 60.741 61.111 40.50 0.00 38.47 2.52
314 327 2.322081 CCGCGCGGGAAGAAGAAAA 61.322 57.895 40.50 0.00 38.47 2.29
315 328 1.572447 CGCGCGGGAAGAAGAAAAA 59.428 52.632 24.84 0.00 0.00 1.94
333 346 2.119671 AAAAAGAAGAAGGCAACGCG 57.880 45.000 3.53 3.53 46.39 6.01
334 347 0.317854 AAAAGAAGAAGGCAACGCGC 60.318 50.000 5.73 0.00 46.39 6.86
357 370 4.767255 CTCCCACCGCACAGCCTC 62.767 72.222 0.00 0.00 0.00 4.70
383 396 4.093952 CTGGCAGCCACGCGAAAG 62.094 66.667 15.93 0.92 0.00 2.62
851 1074 1.542915 CACACAAGAGCCAAATCCCTG 59.457 52.381 0.00 0.00 0.00 4.45
861 1084 3.682292 AAATCCCTGCCGCCGAGAC 62.682 63.158 0.00 0.00 0.00 3.36
902 1126 1.355971 TTTCTTCCCGCGAATCGAAG 58.644 50.000 8.23 12.83 41.67 3.79
908 1133 1.343821 CCGCGAATCGAAGTTTCCG 59.656 57.895 8.23 0.00 41.67 4.30
934 1159 4.295119 CGGTCGATTAGGGCGGGG 62.295 72.222 0.00 0.00 0.00 5.73
1255 1480 5.357257 GGTTAGATCGATTGCCTGTTTCTA 58.643 41.667 0.00 0.00 0.00 2.10
1307 1532 1.631072 CTAACCTCGATTGCGTGCG 59.369 57.895 0.00 0.00 38.98 5.34
1393 1618 4.839121 TGTTACAGGCCTACAGTATTTGG 58.161 43.478 3.98 0.00 0.00 3.28
1396 1621 3.182152 ACAGGCCTACAGTATTTGGAGT 58.818 45.455 3.98 0.00 35.83 3.85
1443 1668 4.098960 GCCCATGATGTCTTGATTTGTCAT 59.901 41.667 0.00 0.00 0.00 3.06
1469 1694 6.017933 CGCATTGCTAGTTTTGAGACTAAAG 58.982 40.000 7.12 0.00 32.10 1.85
1510 1735 3.594603 TCCGGAGATCTCACTTGAAAC 57.405 47.619 23.85 3.37 0.00 2.78
1521 1746 3.443037 TCACTTGAAACGGCAAACATTG 58.557 40.909 0.00 0.00 0.00 2.82
1547 1772 7.686127 GCAAATTCCTCCAGATTTAGCAATGAT 60.686 37.037 0.00 0.00 0.00 2.45
1620 1846 4.288626 TCTTGGATTTGGTTACTAGCACCT 59.711 41.667 11.97 0.00 35.07 4.00
1621 1847 4.650972 TGGATTTGGTTACTAGCACCTT 57.349 40.909 11.97 0.00 35.07 3.50
1625 1851 7.179269 TGGATTTGGTTACTAGCACCTTTTAT 58.821 34.615 11.97 2.27 35.07 1.40
1631 1857 5.585047 GGTTACTAGCACCTTTTATCCACAG 59.415 44.000 4.68 0.00 0.00 3.66
1700 1927 4.082949 GCGTTACTTGCCTTATCCTGTTTT 60.083 41.667 0.00 0.00 0.00 2.43
1712 1939 8.523658 GCCTTATCCTGTTTTCTATCTTGTTTT 58.476 33.333 0.00 0.00 0.00 2.43
1713 1940 9.846248 CCTTATCCTGTTTTCTATCTTGTTTTG 57.154 33.333 0.00 0.00 0.00 2.44
1714 1941 9.846248 CTTATCCTGTTTTCTATCTTGTTTTGG 57.154 33.333 0.00 0.00 0.00 3.28
1717 1944 8.754991 TCCTGTTTTCTATCTTGTTTTGGTTA 57.245 30.769 0.00 0.00 0.00 2.85
1718 1945 9.362151 TCCTGTTTTCTATCTTGTTTTGGTTAT 57.638 29.630 0.00 0.00 0.00 1.89
1719 1946 9.626045 CCTGTTTTCTATCTTGTTTTGGTTATC 57.374 33.333 0.00 0.00 0.00 1.75
1836 2069 7.231317 TCTGTTCTGGAATTTGCTGTCTTAAAT 59.769 33.333 0.00 0.00 0.00 1.40
1838 2071 7.652909 TGTTCTGGAATTTGCTGTCTTAAATTG 59.347 33.333 0.00 0.00 36.81 2.32
1839 2072 7.523293 TCTGGAATTTGCTGTCTTAAATTGA 57.477 32.000 0.00 0.00 36.81 2.57
1840 2073 7.370383 TCTGGAATTTGCTGTCTTAAATTGAC 58.630 34.615 0.00 0.00 36.81 3.18
1841 2074 7.231317 TCTGGAATTTGCTGTCTTAAATTGACT 59.769 33.333 0.00 0.00 36.81 3.41
1843 2076 7.652909 TGGAATTTGCTGTCTTAAATTGACTTG 59.347 33.333 0.00 0.00 36.81 3.16
1995 2248 8.304596 TGACTAACTGTGTAAAGAAGATACAGG 58.695 37.037 0.00 0.00 42.18 4.00
2105 2359 5.199024 TGCATTATTTCTGTGTGTGCTTT 57.801 34.783 0.00 0.00 32.67 3.51
2260 2517 7.237255 AGAGAAAAGGAGGAATGACAAGAAAT 58.763 34.615 0.00 0.00 0.00 2.17
2331 2588 6.900568 AAGAAGAGAAAGCATGAAGATACG 57.099 37.500 0.00 0.00 0.00 3.06
2336 2593 4.507710 AGAAAGCATGAAGATACGAGCAA 58.492 39.130 0.00 0.00 0.00 3.91
2595 2852 3.826236 CAAGAGTTGCTGACCATGAAG 57.174 47.619 0.00 0.00 0.00 3.02
2597 2854 3.498774 AGAGTTGCTGACCATGAAGTT 57.501 42.857 0.00 0.00 0.00 2.66
2732 2989 5.505181 ACACCTTCATCCTTGTTGAGTAT 57.495 39.130 0.00 0.00 0.00 2.12
2769 3026 1.586422 CTCGCAGGGATGTTATGGTG 58.414 55.000 0.00 0.00 0.00 4.17
2781 3038 2.038952 TGTTATGGTGAAGTCAGCTGCT 59.961 45.455 9.47 6.85 44.12 4.24
2807 3064 0.815734 CAGCAAAGCATCAAGAGGGG 59.184 55.000 0.00 0.00 0.00 4.79
2920 3177 2.750350 CCCCAACCTCAGCGAAGT 59.250 61.111 0.00 0.00 0.00 3.01
3075 3332 0.606673 GAGTTGTTCCTCCACCTGCC 60.607 60.000 0.00 0.00 0.00 4.85
3128 3418 4.016444 GCCAAGGTTATTGACATTCCTCA 58.984 43.478 0.00 0.00 27.97 3.86
3130 3420 5.127682 GCCAAGGTTATTGACATTCCTCATT 59.872 40.000 0.00 0.00 27.97 2.57
3175 3465 1.133181 TCTGGTGCCATCCAAGGTGA 61.133 55.000 0.00 0.00 37.01 4.02
3180 3470 1.224592 GCCATCCAAGGTGATCCGT 59.775 57.895 0.00 0.00 39.05 4.69
3337 3630 1.285023 CAGCAGTCAAGCACCTTGC 59.715 57.895 0.22 0.00 45.46 4.01
3450 3743 3.621958 GCAAGGCTGAGAAGGAAGAGAAT 60.622 47.826 0.00 0.00 0.00 2.40
3517 3810 2.045047 TCCTTGGAGATTGAGGAGACCT 59.955 50.000 0.00 0.00 34.74 3.85
3570 3863 1.615392 GGTGCAAAGAAACCTGATGCT 59.385 47.619 0.00 0.00 37.86 3.79
3571 3864 2.036346 GGTGCAAAGAAACCTGATGCTT 59.964 45.455 0.00 0.00 37.86 3.91
3572 3865 3.255642 GGTGCAAAGAAACCTGATGCTTA 59.744 43.478 0.00 0.00 37.86 3.09
3598 3891 0.601558 CAGCTGCAAGGCAAGTGATT 59.398 50.000 0.00 0.00 38.41 2.57
3661 3954 3.181483 GGCTATTCATTTGCCTGACCTTG 60.181 47.826 0.00 0.00 43.05 3.61
3664 3957 4.730949 ATTCATTTGCCTGACCTTGATG 57.269 40.909 0.00 0.00 0.00 3.07
3666 3959 3.084039 TCATTTGCCTGACCTTGATGTC 58.916 45.455 0.00 0.00 35.77 3.06
3911 4205 3.328382 TTGATCTACGGACAACCTTGG 57.672 47.619 0.00 0.00 0.00 3.61
3983 4299 8.978874 TCAGATAGCACACCATGTAAATAAAT 57.021 30.769 0.00 0.00 0.00 1.40
3984 4300 9.056005 TCAGATAGCACACCATGTAAATAAATC 57.944 33.333 0.00 0.00 0.00 2.17
3989 4305 6.767902 AGCACACCATGTAAATAAATCGAGAT 59.232 34.615 0.00 0.00 0.00 2.75
4000 4356 2.898729 AATCGAGATGAATCGTGGCT 57.101 45.000 0.00 0.00 43.20 4.75
4082 4438 1.619654 TTTTCTCTGTGGGTGGCATG 58.380 50.000 0.00 0.00 0.00 4.06
4086 4442 0.675837 CTCTGTGGGTGGCATGTCTG 60.676 60.000 0.00 0.00 0.00 3.51
4111 4467 0.327480 TATCATGTCCCTGGGTGCCT 60.327 55.000 13.56 0.00 0.00 4.75
4187 4543 5.163519 ACAAAAGACAACCAAACTCATCCAG 60.164 40.000 0.00 0.00 0.00 3.86
4252 4608 3.869272 GGATCGGCTGCAGCGTTG 61.869 66.667 31.19 22.78 43.26 4.10
4385 4741 0.957395 GGTAGGTCTCGTCGTCCACA 60.957 60.000 0.00 0.00 0.00 4.17
4436 4792 4.516195 GCGTCCTCTTCTCCCCGC 62.516 72.222 0.00 0.00 0.00 6.13
4471 4827 1.066257 GCCACCACACACAAGCAAG 59.934 57.895 0.00 0.00 0.00 4.01
4642 5040 1.300620 CCACCTCGTCGTGCTTCAA 60.301 57.895 0.00 0.00 32.10 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.677902 CGCAATTCCAGCTCAGGTTCTA 60.678 50.000 0.00 0.00 0.00 2.10
30 31 1.159285 TGTTCGCAATTCCAGCTCAG 58.841 50.000 0.00 0.00 0.00 3.35
95 108 2.345641 CGCCTGAACGAAGATTGTAGTG 59.654 50.000 0.00 0.00 34.06 2.74
96 109 2.607187 CGCCTGAACGAAGATTGTAGT 58.393 47.619 0.00 0.00 34.06 2.73
100 113 1.059369 CGCGCCTGAACGAAGATTG 59.941 57.895 0.00 0.00 34.06 2.67
101 114 1.078759 CTCGCGCCTGAACGAAGATT 61.079 55.000 0.00 0.00 37.94 2.40
105 118 0.171679 TAATCTCGCGCCTGAACGAA 59.828 50.000 0.00 0.00 37.94 3.85
107 120 0.996462 TTTAATCTCGCGCCTGAACG 59.004 50.000 0.00 0.00 0.00 3.95
136 149 1.827789 TTTTTGTGAGGCGGCAGCT 60.828 52.632 13.08 0.00 44.37 4.24
157 170 3.741476 GAGGGCTGCTGCGGTTTG 61.741 66.667 10.62 0.00 40.82 2.93
164 177 3.478274 GAGGGAGGAGGGCTGCTG 61.478 72.222 0.00 0.00 0.00 4.41
170 183 3.237741 GATGCCGAGGGAGGAGGG 61.238 72.222 0.00 0.00 0.00 4.30
172 185 1.626356 TTTGGATGCCGAGGGAGGAG 61.626 60.000 0.00 0.00 0.00 3.69
173 186 1.204786 TTTTGGATGCCGAGGGAGGA 61.205 55.000 0.00 0.00 0.00 3.71
174 187 0.106519 ATTTTGGATGCCGAGGGAGG 60.107 55.000 0.00 0.00 0.00 4.30
175 188 1.312815 GATTTTGGATGCCGAGGGAG 58.687 55.000 0.00 0.00 0.00 4.30
176 189 0.106719 GGATTTTGGATGCCGAGGGA 60.107 55.000 0.00 0.00 0.00 4.20
177 190 0.395586 TGGATTTTGGATGCCGAGGG 60.396 55.000 0.00 0.00 0.00 4.30
178 191 1.473258 TTGGATTTTGGATGCCGAGG 58.527 50.000 0.00 0.00 0.00 4.63
179 192 3.591196 TTTTGGATTTTGGATGCCGAG 57.409 42.857 0.00 0.00 0.00 4.63
180 193 3.768757 AGATTTTGGATTTTGGATGCCGA 59.231 39.130 0.00 0.00 0.00 5.54
181 194 4.127566 AGATTTTGGATTTTGGATGCCG 57.872 40.909 0.00 0.00 0.00 5.69
182 195 5.490159 TGAAGATTTTGGATTTTGGATGCC 58.510 37.500 0.00 0.00 0.00 4.40
183 196 6.400568 TCTGAAGATTTTGGATTTTGGATGC 58.599 36.000 0.00 0.00 0.00 3.91
184 197 7.709613 GGATCTGAAGATTTTGGATTTTGGATG 59.290 37.037 0.00 0.00 34.37 3.51
185 198 7.400915 TGGATCTGAAGATTTTGGATTTTGGAT 59.599 33.333 0.00 0.00 34.37 3.41
186 199 6.725369 TGGATCTGAAGATTTTGGATTTTGGA 59.275 34.615 0.00 0.00 34.37 3.53
187 200 6.815142 GTGGATCTGAAGATTTTGGATTTTGG 59.185 38.462 0.00 0.00 34.37 3.28
188 201 6.529125 CGTGGATCTGAAGATTTTGGATTTTG 59.471 38.462 0.00 0.00 34.37 2.44
189 202 6.624423 CGTGGATCTGAAGATTTTGGATTTT 58.376 36.000 0.00 0.00 34.37 1.82
190 203 5.393461 GCGTGGATCTGAAGATTTTGGATTT 60.393 40.000 0.00 0.00 34.37 2.17
191 204 4.096984 GCGTGGATCTGAAGATTTTGGATT 59.903 41.667 0.00 0.00 34.37 3.01
192 205 3.629398 GCGTGGATCTGAAGATTTTGGAT 59.371 43.478 0.00 0.00 34.37 3.41
193 206 3.009723 GCGTGGATCTGAAGATTTTGGA 58.990 45.455 0.00 0.00 34.37 3.53
194 207 2.223112 CGCGTGGATCTGAAGATTTTGG 60.223 50.000 0.00 0.00 34.37 3.28
195 208 2.672874 TCGCGTGGATCTGAAGATTTTG 59.327 45.455 5.77 0.00 34.37 2.44
196 209 2.932614 CTCGCGTGGATCTGAAGATTTT 59.067 45.455 5.77 0.00 34.37 1.82
197 210 2.544685 CTCGCGTGGATCTGAAGATTT 58.455 47.619 5.77 0.00 34.37 2.17
198 211 1.804372 GCTCGCGTGGATCTGAAGATT 60.804 52.381 5.77 0.00 34.37 2.40
199 212 0.249238 GCTCGCGTGGATCTGAAGAT 60.249 55.000 5.77 0.00 37.51 2.40
200 213 1.139734 GCTCGCGTGGATCTGAAGA 59.860 57.895 5.77 0.00 0.00 2.87
201 214 2.226896 CGCTCGCGTGGATCTGAAG 61.227 63.158 5.77 0.00 34.35 3.02
202 215 2.202610 CGCTCGCGTGGATCTGAA 60.203 61.111 5.77 0.00 34.35 3.02
203 216 4.193334 CCGCTCGCGTGGATCTGA 62.193 66.667 5.77 0.00 43.70 3.27
204 217 4.193334 TCCGCTCGCGTGGATCTG 62.193 66.667 5.77 0.00 44.63 2.90
234 247 4.394078 GAAAACCCCCGAACGCGC 62.394 66.667 5.73 0.00 35.83 6.86
235 248 4.079748 CGAAAACCCCCGAACGCG 62.080 66.667 3.53 3.53 37.24 6.01
236 249 4.394078 GCGAAAACCCCCGAACGC 62.394 66.667 0.00 0.00 39.33 4.84
237 250 2.667199 AGCGAAAACCCCCGAACG 60.667 61.111 0.00 0.00 0.00 3.95
238 251 2.622962 CCAGCGAAAACCCCCGAAC 61.623 63.158 0.00 0.00 0.00 3.95
239 252 2.281900 CCAGCGAAAACCCCCGAA 60.282 61.111 0.00 0.00 0.00 4.30
242 255 4.986708 TGGCCAGCGAAAACCCCC 62.987 66.667 0.00 0.00 0.00 5.40
243 256 2.679996 ATGGCCAGCGAAAACCCC 60.680 61.111 13.05 0.00 0.00 4.95
244 257 2.885113 GATGGCCAGCGAAAACCC 59.115 61.111 13.05 0.00 0.00 4.11
245 258 2.485122 CGATGGCCAGCGAAAACC 59.515 61.111 38.89 4.41 43.75 3.27
246 259 2.202479 GCGATGGCCAGCGAAAAC 60.202 61.111 44.64 24.43 43.75 2.43
247 260 2.671276 TGCGATGGCCAGCGAAAA 60.671 55.556 44.64 26.60 43.75 2.29
248 261 3.126879 CTGCGATGGCCAGCGAAA 61.127 61.111 44.64 29.84 43.75 3.46
249 262 3.604129 TTCTGCGATGGCCAGCGAA 62.604 57.895 44.64 35.66 43.75 4.70
250 263 4.081185 TTCTGCGATGGCCAGCGA 62.081 61.111 44.64 27.70 43.75 4.93
251 264 3.869272 GTTCTGCGATGGCCAGCG 61.869 66.667 37.66 37.66 43.89 5.18
252 265 3.869272 CGTTCTGCGATGGCCAGC 61.869 66.667 12.07 12.07 44.77 4.85
253 266 2.125552 TCGTTCTGCGATGGCCAG 60.126 61.111 13.05 0.00 45.68 4.85
261 274 3.467119 CGTCCCGTTCGTTCTGCG 61.467 66.667 0.00 0.00 43.01 5.18
262 275 3.110178 CCGTCCCGTTCGTTCTGC 61.110 66.667 0.00 0.00 0.00 4.26
263 276 2.431942 CCCGTCCCGTTCGTTCTG 60.432 66.667 0.00 0.00 0.00 3.02
264 277 3.688159 CCCCGTCCCGTTCGTTCT 61.688 66.667 0.00 0.00 0.00 3.01
265 278 3.683937 TCCCCGTCCCGTTCGTTC 61.684 66.667 0.00 0.00 0.00 3.95
266 279 3.994853 GTCCCCGTCCCGTTCGTT 61.995 66.667 0.00 0.00 0.00 3.85
268 281 4.729856 GTGTCCCCGTCCCGTTCG 62.730 72.222 0.00 0.00 0.00 3.95
269 282 4.729856 CGTGTCCCCGTCCCGTTC 62.730 72.222 0.00 0.00 0.00 3.95
274 287 4.368543 GTGACCGTGTCCCCGTCC 62.369 72.222 2.23 0.00 0.00 4.79
275 288 4.712425 CGTGACCGTGTCCCCGTC 62.712 72.222 2.23 0.00 0.00 4.79
278 291 4.065281 CTCCGTGACCGTGTCCCC 62.065 72.222 2.23 0.00 0.00 4.81
279 292 4.736896 GCTCCGTGACCGTGTCCC 62.737 72.222 2.23 0.00 0.00 4.46
280 293 4.736896 GGCTCCGTGACCGTGTCC 62.737 72.222 2.23 0.00 0.00 4.02
296 309 1.847890 TTTTTCTTCTTCCCGCGCGG 61.848 55.000 41.00 41.00 0.00 6.46
297 310 1.572447 TTTTTCTTCTTCCCGCGCG 59.428 52.632 25.67 25.67 0.00 6.86
314 327 1.864029 GCGCGTTGCCTTCTTCTTTTT 60.864 47.619 8.43 0.00 37.76 1.94
315 328 0.317854 GCGCGTTGCCTTCTTCTTTT 60.318 50.000 8.43 0.00 37.76 2.27
316 329 1.282875 GCGCGTTGCCTTCTTCTTT 59.717 52.632 8.43 0.00 37.76 2.52
317 330 2.946762 GCGCGTTGCCTTCTTCTT 59.053 55.556 8.43 0.00 37.76 2.52
340 353 4.767255 GAGGCTGTGCGGTGGGAG 62.767 72.222 0.00 0.00 0.00 4.30
366 379 4.093952 CTTTCGCGTGGCTGCCAG 62.094 66.667 24.10 16.83 32.34 4.85
401 414 4.547367 AAGGCGGTGATAGCGGGC 62.547 66.667 2.54 0.00 39.82 6.13
402 415 1.461091 TAGAAGGCGGTGATAGCGGG 61.461 60.000 2.54 0.00 39.82 6.13
403 416 0.039074 CTAGAAGGCGGTGATAGCGG 60.039 60.000 2.54 0.00 39.82 5.52
404 417 0.039074 CCTAGAAGGCGGTGATAGCG 60.039 60.000 0.00 0.00 42.73 4.26
405 418 1.000052 GACCTAGAAGGCGGTGATAGC 60.000 57.143 0.00 0.00 39.63 2.97
406 419 1.267261 CGACCTAGAAGGCGGTGATAG 59.733 57.143 0.00 0.00 39.63 2.08
407 420 1.315690 CGACCTAGAAGGCGGTGATA 58.684 55.000 0.00 0.00 39.63 2.15
408 421 1.392710 CCGACCTAGAAGGCGGTGAT 61.393 60.000 16.01 0.00 44.44 3.06
409 422 2.050350 CCGACCTAGAAGGCGGTGA 61.050 63.158 16.01 0.00 44.44 4.02
410 423 2.494918 CCGACCTAGAAGGCGGTG 59.505 66.667 16.01 0.00 44.44 4.94
413 426 1.141234 GGAACCGACCTAGAAGGCG 59.859 63.158 0.00 0.00 39.63 5.52
414 427 1.141234 CGGAACCGACCTAGAAGGC 59.859 63.158 7.53 0.00 39.63 4.35
642 865 1.673808 AATCGGGCCTCTACACGGAC 61.674 60.000 0.84 0.00 0.00 4.79
902 1126 2.006288 GACCGCGAATCGACGGAAAC 62.006 60.000 32.45 22.10 44.39 2.78
951 1176 2.165301 CGCGAACCCTCGGAATCAC 61.165 63.158 0.00 0.00 45.55 3.06
1209 1434 1.153449 CATCGGCGGCAAGGTTAGA 60.153 57.895 10.53 0.00 0.00 2.10
1284 1509 0.179111 CGCAATCGAGGTTAGCAGGA 60.179 55.000 0.00 0.00 38.10 3.86
1307 1532 8.770438 TTGCATTCAGGTTATTTCCAATTTAC 57.230 30.769 0.00 0.00 0.00 2.01
1443 1668 4.065088 AGTCTCAAAACTAGCAATGCGAA 58.935 39.130 0.00 0.00 0.00 4.70
1521 1746 4.989279 TGCTAAATCTGGAGGAATTTGC 57.011 40.909 0.00 0.00 36.57 3.68
1524 1749 9.425248 TTTATCATTGCTAAATCTGGAGGAATT 57.575 29.630 0.00 0.00 32.07 2.17
1547 1772 5.898972 AGCAAGCCAGGAAATTATGGATTTA 59.101 36.000 8.13 0.00 42.33 1.40
1620 1846 6.371548 GTGAGCACACTAATCTGTGGATAAAA 59.628 38.462 7.06 0.00 41.71 1.52
1621 1847 5.874810 GTGAGCACACTAATCTGTGGATAAA 59.125 40.000 7.06 0.00 41.71 1.40
1625 1851 3.319137 GTGAGCACACTAATCTGTGGA 57.681 47.619 7.06 0.00 41.71 4.02
1712 1939 8.486210 AGATTGCAAGACTACATAAGATAACCA 58.514 33.333 4.94 0.00 0.00 3.67
1713 1940 8.894768 AGATTGCAAGACTACATAAGATAACC 57.105 34.615 4.94 0.00 0.00 2.85
1717 1944 8.043113 TGTCAAGATTGCAAGACTACATAAGAT 58.957 33.333 15.17 0.00 32.41 2.40
1718 1945 7.331934 GTGTCAAGATTGCAAGACTACATAAGA 59.668 37.037 15.17 4.07 32.41 2.10
1719 1946 7.118245 TGTGTCAAGATTGCAAGACTACATAAG 59.882 37.037 15.17 2.37 32.41 1.73
1721 1948 6.463360 TGTGTCAAGATTGCAAGACTACATA 58.537 36.000 15.17 9.87 32.41 2.29
1731 1964 1.618487 TGGCATGTGTCAAGATTGCA 58.382 45.000 0.00 0.00 0.00 4.08
2331 2588 4.722700 TCCGGGCCAGCTTTGCTC 62.723 66.667 4.39 0.00 36.40 4.26
2595 2852 3.733443 ACTGTCCCTGCAAAATCAAAC 57.267 42.857 0.00 0.00 0.00 2.93
2597 2854 4.098914 AGTACTGTCCCTGCAAAATCAA 57.901 40.909 0.00 0.00 0.00 2.57
2769 3026 0.390998 GGAGACCAGCAGCTGACTTC 60.391 60.000 24.90 16.49 32.44 3.01
2781 3038 0.401356 TGATGCTTTGCTGGAGACCA 59.599 50.000 0.00 0.00 0.00 4.02
2807 3064 4.829064 TGTTTTGGCACAGATTGAGTAC 57.171 40.909 0.00 0.00 42.39 2.73
2920 3177 4.080807 TGGGGTATCTATCTTTTGCGTGAA 60.081 41.667 0.00 0.00 0.00 3.18
3075 3332 1.739562 GACTCTCTGTGCCGCCTTG 60.740 63.158 0.00 0.00 0.00 3.61
3128 3418 2.158971 ACCTTTTGCAACGCCTTTGAAT 60.159 40.909 0.00 0.00 37.39 2.57
3130 3420 0.820871 ACCTTTTGCAACGCCTTTGA 59.179 45.000 0.00 0.00 37.39 2.69
3175 3465 1.145945 TGGAGGAGCATCTCTACGGAT 59.854 52.381 6.34 0.00 34.39 4.18
3180 3470 2.243478 ACTCTGTGGAGGAGCATCTCTA 59.757 50.000 6.34 0.00 43.46 2.43
3270 3560 2.094286 CACCTTTGGTTTGTGCAGAACA 60.094 45.455 13.21 0.00 32.24 3.18
3337 3630 1.807142 GGAACAAGGCTCTTCTTTCGG 59.193 52.381 0.00 0.00 0.00 4.30
3382 3675 3.507411 ACTGCTTAACCTCTGGTACTGA 58.493 45.455 0.00 0.00 33.12 3.41
3450 3743 5.511363 AGATCTCGGAACTTCCTCTCTTTA 58.489 41.667 6.25 0.00 33.30 1.85
3517 3810 2.721167 CCTGGTCGCCGAGATTCCA 61.721 63.158 0.00 0.00 0.00 3.53
3546 3839 1.454847 AGGTTTCTTTGCACCGCCA 60.455 52.632 0.00 0.00 38.21 5.69
3570 3863 0.953727 CCTTGCAGCTGCTGTTGTAA 59.046 50.000 36.61 21.37 42.66 2.41
3571 3864 1.518056 GCCTTGCAGCTGCTGTTGTA 61.518 55.000 36.61 15.23 42.66 2.41
3572 3865 2.853290 GCCTTGCAGCTGCTGTTGT 61.853 57.895 36.61 0.00 42.66 3.32
3598 3891 2.676121 CTCCATGGGCGCCAAACA 60.676 61.111 30.85 18.18 36.95 2.83
3661 3954 6.484643 ACAACATATGGCAACTGATAGACATC 59.515 38.462 7.80 0.00 37.61 3.06
3664 3957 6.238484 GGAACAACATATGGCAACTGATAGAC 60.238 42.308 7.80 0.00 37.61 2.59
3666 3959 5.009010 GGGAACAACATATGGCAACTGATAG 59.991 44.000 7.80 0.00 37.61 2.08
3873 4167 5.993441 AGATCAATTGCTTGGAAACCAAAAG 59.007 36.000 0.00 0.00 43.44 2.27
3965 4281 6.358118 TCTCGATTTATTTACATGGTGTGC 57.642 37.500 0.00 0.00 0.00 4.57
3966 4282 8.141835 TCATCTCGATTTATTTACATGGTGTG 57.858 34.615 0.00 0.00 0.00 3.82
3967 4283 8.731275 TTCATCTCGATTTATTTACATGGTGT 57.269 30.769 0.00 0.00 0.00 4.16
3968 4284 9.817365 GATTCATCTCGATTTATTTACATGGTG 57.183 33.333 0.00 0.00 0.00 4.17
3969 4285 8.712363 CGATTCATCTCGATTTATTTACATGGT 58.288 33.333 0.00 0.00 41.12 3.55
3983 4299 2.672874 CAAAAGCCACGATTCATCTCGA 59.327 45.455 0.00 0.00 41.12 4.04
3984 4300 2.416547 ACAAAAGCCACGATTCATCTCG 59.583 45.455 0.00 0.00 44.14 4.04
3989 4305 1.606668 GGACACAAAAGCCACGATTCA 59.393 47.619 0.00 0.00 0.00 2.57
4000 4356 4.517075 TGATGCTGTAATTCGGACACAAAA 59.483 37.500 0.00 0.00 0.00 2.44
4082 4438 1.269831 GGGACATGATAGCCGACAGAC 60.270 57.143 0.00 0.00 0.00 3.51
4086 4442 0.034059 CCAGGGACATGATAGCCGAC 59.966 60.000 0.00 0.00 0.00 4.79
4111 4467 1.068895 CAAAGCAGGTGCCACATTTCA 59.931 47.619 0.00 0.00 43.38 2.69
4161 4517 5.748630 GGATGAGTTTGGTTGTCTTTTGTTC 59.251 40.000 0.00 0.00 0.00 3.18
4202 4558 7.763356 TCGATTGACCTTTTGTTCTTTTTACA 58.237 30.769 0.00 0.00 0.00 2.41
4213 4569 2.813754 TCCAGCTTCGATTGACCTTTTG 59.186 45.455 0.00 0.00 0.00 2.44
4214 4570 3.077359 CTCCAGCTTCGATTGACCTTTT 58.923 45.455 0.00 0.00 0.00 2.27
4411 4767 4.117661 AAGAGGACGCGACGAGCC 62.118 66.667 15.93 5.83 44.76 4.70
4436 4792 3.388308 GTGGCAGATACTGAGCATACTG 58.612 50.000 2.81 0.00 32.44 2.74
4471 4827 5.288472 CCTGCAGTTTTTGAAGTGTTAACAC 59.712 40.000 27.72 27.72 46.77 3.32
4483 4839 5.174943 GGAAAAATACGTCCTGCAGTTTTTG 59.825 40.000 21.13 4.58 31.28 2.44
4522 4914 3.009584 TCTCTCTCTCAGTAGCAGGTTCA 59.990 47.826 0.00 0.00 0.00 3.18
4525 4917 2.679639 CGTCTCTCTCTCAGTAGCAGGT 60.680 54.545 0.00 0.00 0.00 4.00
4642 5040 4.316823 TGGACCCGAGCCTGGACT 62.317 66.667 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.