Multiple sequence alignment - TraesCS7A01G024000

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 TraesCS7A01G024000 chr7A 100.000 2618 0 0 1 2618 9493645 9491028 0.000000e+00 4835
1 TraesCS7A01G024000 chr6B 99.546 2203 10 0 416 2618 132949312 132947110 0.000000e+00 4013
2 TraesCS7A01G024000 chr6B 98.951 2193 23 0 426 2618 463401708 463403900 0.000000e+00 3923
3 TraesCS7A01G024000 chr6B 89.351 1634 113 24 991 2618 536157639 536156061 0.000000e+00 1997
4 TraesCS7A01G024000 chr6B 86.935 199 15 10 454 652 536157856 536157669 2.040000e-51 213
5 TraesCS7A01G024000 chr5A 99.455 2202 12 0 417 2618 680744192 680746393 0.000000e+00 4000
6 TraesCS7A01G024000 chr4B 97.893 2231 14 2 417 2618 245452941 245455167 0.000000e+00 3829
7 TraesCS7A01G024000 chr1A 99.637 1930 7 0 428 2357 517178423 517180352 0.000000e+00 3526
8 TraesCS7A01G024000 chr3B 87.916 2135 152 46 447 2575 145882970 145880936 0.000000e+00 2416
9 TraesCS7A01G024000 chr2B 89.394 1650 112 25 976 2618 706803192 706801599 0.000000e+00 2019
10 TraesCS7A01G024000 chr2B 91.830 306 21 4 625 929 706803998 706803696 8.660000e-115 424
11 TraesCS7A01G024000 chr2B 87.864 206 14 10 447 652 706804137 706803943 5.630000e-57 231
12 TraesCS7A01G024000 chr1D 87.241 917 79 22 1707 2618 404279089 404279972 0.000000e+00 1011
13 TraesCS7A01G024000 chr1D 80.585 1334 158 61 425 1715 404274512 404275787 0.000000e+00 935
14 TraesCS7A01G024000 chr2A 87.093 860 86 10 927 1770 545739371 545738521 0.000000e+00 950
15 TraesCS7A01G024000 chr7B 79.734 977 124 38 417 1366 610360841 610361770 7.900000e-180 640
16 TraesCS7A01G024000 chr4A 83.681 288 24 12 1 278 729236122 729235848 1.560000e-62 250
17 TraesCS7A01G024000 chr4A 95.556 135 6 0 1 135 728586517 728586383 1.580000e-52 217
18 TraesCS7A01G024000 chr5D 88.696 115 8 2 5 114 487291708 487291822 4.540000e-28 135
19 TraesCS7A01G024000 chr5B 89.091 110 7 2 10 114 599656352 599656461 5.880000e-27 132
20 TraesCS7A01G024000 chr3A 81.529 157 19 8 413 563 31833573 31833725 1.270000e-23 121


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 TraesCS7A01G024000 chr7A 9491028 9493645 2617 True 4835.000000 4835 100.000 1 2618 1 chr7A.!!$R1 2617
1 TraesCS7A01G024000 chr6B 132947110 132949312 2202 True 4013.000000 4013 99.546 416 2618 1 chr6B.!!$R1 2202
2 TraesCS7A01G024000 chr6B 463401708 463403900 2192 False 3923.000000 3923 98.951 426 2618 1 chr6B.!!$F1 2192
3 TraesCS7A01G024000 chr6B 536156061 536157856 1795 True 1105.000000 1997 88.143 454 2618 2 chr6B.!!$R2 2164
4 TraesCS7A01G024000 chr5A 680744192 680746393 2201 False 4000.000000 4000 99.455 417 2618 1 chr5A.!!$F1 2201
5 TraesCS7A01G024000 chr4B 245452941 245455167 2226 False 3829.000000 3829 97.893 417 2618 1 chr4B.!!$F1 2201
6 TraesCS7A01G024000 chr1A 517178423 517180352 1929 False 3526.000000 3526 99.637 428 2357 1 chr1A.!!$F1 1929
7 TraesCS7A01G024000 chr3B 145880936 145882970 2034 True 2416.000000 2416 87.916 447 2575 1 chr3B.!!$R1 2128
8 TraesCS7A01G024000 chr2B 706801599 706804137 2538 True 891.333333 2019 89.696 447 2618 3 chr2B.!!$R1 2171
9 TraesCS7A01G024000 chr1D 404274512 404279972 5460 False 973.000000 1011 83.913 425 2618 2 chr1D.!!$F1 2193
10 TraesCS7A01G024000 chr2A 545738521 545739371 850 True 950.000000 950 87.093 927 1770 1 chr2A.!!$R1 843
11 TraesCS7A01G024000 chr7B 610360841 610361770 929 False 640.000000 640 79.734 417 1366 1 chr7B.!!$F1 949

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
359 360 0.036022 GCAGCTCCTCCAGTGTTTCT 59.964 55.0 0.0 0.00 0.00 2.52 F
404 405 0.110823 GTGAACGCACCGTGTCATTC 60.111 55.0 0.0 3.02 39.99 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1367 1931 2.906458 CAGCCTCGCCTCCAATCT 59.094 61.111 0.0 0.0 0.00 2.40 R
2049 5992 5.647225 GGCATCCAGATTTGAGGAATATCTC 59.353 44.000 0.0 0.0 37.48 2.75 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
35 36 4.166011 CGGCTTGCCGCTGCTAAC 62.166 66.667 21.17 0.00 38.36 2.34
36 37 2.747855 GGCTTGCCGCTGCTAACT 60.748 61.111 0.70 0.00 39.13 2.24
37 38 2.482374 GCTTGCCGCTGCTAACTG 59.518 61.111 0.70 0.00 38.71 3.16
38 39 2.482374 CTTGCCGCTGCTAACTGC 59.518 61.111 0.70 0.00 43.25 4.40
44 45 2.863153 GCTGCTAACTGCGTGTGG 59.137 61.111 0.00 0.00 46.63 4.17
45 46 1.961277 GCTGCTAACTGCGTGTGGT 60.961 57.895 0.00 0.00 46.63 4.16
46 47 1.507141 GCTGCTAACTGCGTGTGGTT 61.507 55.000 0.00 0.00 46.63 3.67
47 48 0.235665 CTGCTAACTGCGTGTGGTTG 59.764 55.000 0.00 0.00 46.63 3.77
48 49 1.082104 GCTAACTGCGTGTGGTTGC 60.082 57.895 0.00 0.00 0.00 4.17
49 50 1.204062 CTAACTGCGTGTGGTTGCG 59.796 57.895 0.00 0.00 0.00 4.85
50 51 1.495584 CTAACTGCGTGTGGTTGCGT 61.496 55.000 0.00 0.00 0.00 5.24
51 52 1.767127 TAACTGCGTGTGGTTGCGTG 61.767 55.000 0.00 0.00 0.00 5.34
52 53 4.312231 CTGCGTGTGGTTGCGTGG 62.312 66.667 0.00 0.00 0.00 4.94
84 85 4.446413 GTCGTGGGTCGGCCGAAT 62.446 66.667 32.93 0.00 38.31 3.34
85 86 4.137872 TCGTGGGTCGGCCGAATC 62.138 66.667 32.93 24.42 40.32 2.52
96 97 4.824166 CCGAATCGCCGTCGTCGT 62.824 66.667 0.00 0.00 36.77 4.34
97 98 3.594827 CGAATCGCCGTCGTCGTG 61.595 66.667 0.71 0.00 36.96 4.35
98 99 3.898640 GAATCGCCGTCGTCGTGC 61.899 66.667 0.71 3.64 36.96 5.34
99 100 4.415332 AATCGCCGTCGTCGTGCT 62.415 61.111 11.85 0.00 36.96 4.40
105 106 3.756677 CGTCGTCGTGCTGCTGTG 61.757 66.667 0.00 0.00 0.00 3.66
106 107 2.658593 GTCGTCGTGCTGCTGTGT 60.659 61.111 0.00 0.00 0.00 3.72
107 108 2.658268 TCGTCGTGCTGCTGTGTG 60.658 61.111 0.00 0.00 0.00 3.82
108 109 4.360027 CGTCGTGCTGCTGTGTGC 62.360 66.667 0.00 0.00 43.25 4.57
109 110 4.017877 GTCGTGCTGCTGTGTGCC 62.018 66.667 0.00 0.00 42.00 5.01
115 116 3.046087 CTGCTGTGTGCCGGTGAG 61.046 66.667 1.90 0.00 42.00 3.51
127 128 2.887568 GGTGAGCGGCAGACGATG 60.888 66.667 0.00 0.00 43.91 3.84
128 129 2.125912 GTGAGCGGCAGACGATGT 60.126 61.111 0.00 0.00 43.91 3.06
129 130 2.125952 TGAGCGGCAGACGATGTG 60.126 61.111 0.00 0.00 43.91 3.21
130 131 2.125912 GAGCGGCAGACGATGTGT 60.126 61.111 0.00 0.00 43.91 3.72
131 132 2.447887 GAGCGGCAGACGATGTGTG 61.448 63.158 0.00 0.00 43.91 3.82
135 136 4.152625 GCAGACGATGTGTGCCGC 62.153 66.667 7.76 0.00 45.22 6.53
136 137 2.433145 CAGACGATGTGTGCCGCT 60.433 61.111 0.00 0.00 0.00 5.52
137 138 2.029288 CAGACGATGTGTGCCGCTT 61.029 57.895 0.00 0.00 0.00 4.68
138 139 2.029288 AGACGATGTGTGCCGCTTG 61.029 57.895 0.00 0.00 0.00 4.01
139 140 3.651480 GACGATGTGTGCCGCTTGC 62.651 63.158 0.00 0.00 41.77 4.01
140 141 4.465512 CGATGTGTGCCGCTTGCC 62.466 66.667 0.00 0.00 40.16 4.52
141 142 4.465512 GATGTGTGCCGCTTGCCG 62.466 66.667 0.00 0.00 40.16 5.69
180 181 4.678269 GCTGCTGTGCGCTGTGTG 62.678 66.667 9.73 0.00 39.51 3.82
181 182 3.274586 CTGCTGTGCGCTGTGTGT 61.275 61.111 9.73 0.00 40.11 3.72
182 183 3.232645 CTGCTGTGCGCTGTGTGTC 62.233 63.158 9.73 0.00 40.11 3.67
183 184 4.360027 GCTGTGCGCTGTGTGTCG 62.360 66.667 9.73 0.00 35.14 4.35
184 185 2.658268 CTGTGCGCTGTGTGTCGA 60.658 61.111 9.73 0.00 0.00 4.20
185 186 2.023771 CTGTGCGCTGTGTGTCGAT 61.024 57.895 9.73 0.00 0.00 3.59
186 187 1.949015 CTGTGCGCTGTGTGTCGATC 61.949 60.000 9.73 0.00 0.00 3.69
187 188 2.432456 TGCGCTGTGTGTCGATCC 60.432 61.111 9.73 0.00 0.00 3.36
188 189 3.545481 GCGCTGTGTGTCGATCCG 61.545 66.667 0.00 0.00 0.00 4.18
189 190 2.126463 CGCTGTGTGTCGATCCGT 60.126 61.111 0.00 0.00 0.00 4.69
190 191 2.152699 CGCTGTGTGTCGATCCGTC 61.153 63.158 0.00 0.00 0.00 4.79
200 201 4.944372 GATCCGTCGGGCGCGATT 62.944 66.667 29.06 14.06 39.71 3.34
201 202 4.524318 ATCCGTCGGGCGCGATTT 62.524 61.111 29.06 11.24 39.71 2.17
210 211 4.842091 GCGCGATTTGGCTGCCAG 62.842 66.667 22.17 11.36 33.81 4.85
211 212 3.434319 CGCGATTTGGCTGCCAGT 61.434 61.111 22.17 14.66 33.81 4.00
212 213 2.964978 GCGATTTGGCTGCCAGTT 59.035 55.556 22.17 13.17 33.81 3.16
213 214 1.290009 GCGATTTGGCTGCCAGTTT 59.710 52.632 22.17 10.51 33.81 2.66
214 215 0.319813 GCGATTTGGCTGCCAGTTTT 60.320 50.000 22.17 7.91 33.81 2.43
215 216 1.873486 GCGATTTGGCTGCCAGTTTTT 60.873 47.619 22.17 6.07 33.81 1.94
239 240 4.473520 CTGGGTGCCGGGCTACTG 62.474 72.222 21.46 10.14 0.00 2.74
241 242 4.778143 GGGTGCCGGGCTACTGTG 62.778 72.222 21.46 0.00 0.00 3.66
242 243 4.016706 GGTGCCGGGCTACTGTGT 62.017 66.667 21.46 0.00 0.00 3.72
243 244 2.742372 GTGCCGGGCTACTGTGTG 60.742 66.667 21.46 0.00 0.00 3.82
244 245 3.238497 TGCCGGGCTACTGTGTGT 61.238 61.111 21.46 0.00 0.00 3.72
245 246 2.032071 GCCGGGCTACTGTGTGTT 59.968 61.111 12.87 0.00 0.00 3.32
246 247 2.325082 GCCGGGCTACTGTGTGTTG 61.325 63.158 12.87 0.00 0.00 3.33
247 248 1.671054 CCGGGCTACTGTGTGTTGG 60.671 63.158 0.00 0.00 0.00 3.77
248 249 1.671054 CGGGCTACTGTGTGTTGGG 60.671 63.158 0.00 0.00 0.00 4.12
249 250 1.454539 GGGCTACTGTGTGTTGGGT 59.545 57.895 0.00 0.00 0.00 4.51
250 251 0.889186 GGGCTACTGTGTGTTGGGTG 60.889 60.000 0.00 0.00 0.00 4.61
251 252 0.179029 GGCTACTGTGTGTTGGGTGT 60.179 55.000 0.00 0.00 0.00 4.16
252 253 0.944386 GCTACTGTGTGTTGGGTGTG 59.056 55.000 0.00 0.00 0.00 3.82
253 254 0.944386 CTACTGTGTGTTGGGTGTGC 59.056 55.000 0.00 0.00 0.00 4.57
254 255 0.544223 TACTGTGTGTTGGGTGTGCT 59.456 50.000 0.00 0.00 0.00 4.40
255 256 1.031571 ACTGTGTGTTGGGTGTGCTG 61.032 55.000 0.00 0.00 0.00 4.41
256 257 1.727511 CTGTGTGTTGGGTGTGCTGG 61.728 60.000 0.00 0.00 0.00 4.85
257 258 1.752694 GTGTGTTGGGTGTGCTGGT 60.753 57.895 0.00 0.00 0.00 4.00
258 259 1.453015 TGTGTTGGGTGTGCTGGTC 60.453 57.895 0.00 0.00 0.00 4.02
259 260 1.453015 GTGTTGGGTGTGCTGGTCA 60.453 57.895 0.00 0.00 0.00 4.02
260 261 1.152984 TGTTGGGTGTGCTGGTCAG 60.153 57.895 0.00 0.00 0.00 3.51
261 262 1.148273 GTTGGGTGTGCTGGTCAGA 59.852 57.895 1.65 0.00 0.00 3.27
262 263 0.250901 GTTGGGTGTGCTGGTCAGAT 60.251 55.000 1.65 0.00 0.00 2.90
263 264 0.250858 TTGGGTGTGCTGGTCAGATG 60.251 55.000 1.65 0.00 0.00 2.90
264 265 2.042831 GGGTGTGCTGGTCAGATGC 61.043 63.158 1.65 0.00 0.00 3.91
265 266 1.002868 GGTGTGCTGGTCAGATGCT 60.003 57.895 1.65 0.00 0.00 3.79
266 267 1.303799 GGTGTGCTGGTCAGATGCTG 61.304 60.000 1.65 0.00 0.00 4.41
267 268 0.604780 GTGTGCTGGTCAGATGCTGT 60.605 55.000 1.65 0.00 32.61 4.40
268 269 0.604511 TGTGCTGGTCAGATGCTGTG 60.605 55.000 1.65 0.00 32.61 3.66
269 270 1.002990 TGCTGGTCAGATGCTGTGG 60.003 57.895 1.65 0.00 32.61 4.17
270 271 1.748122 GCTGGTCAGATGCTGTGGG 60.748 63.158 1.65 0.00 32.61 4.61
271 272 1.748122 CTGGTCAGATGCTGTGGGC 60.748 63.158 0.00 0.00 42.22 5.36
272 273 2.194388 CTGGTCAGATGCTGTGGGCT 62.194 60.000 0.00 0.00 42.39 5.19
273 274 1.748122 GGTCAGATGCTGTGGGCTG 60.748 63.158 0.00 0.00 42.39 4.85
274 275 1.748122 GTCAGATGCTGTGGGCTGG 60.748 63.158 0.00 0.00 42.39 4.85
275 276 2.439701 CAGATGCTGTGGGCTGGG 60.440 66.667 0.00 0.00 42.39 4.45
276 277 4.437587 AGATGCTGTGGGCTGGGC 62.438 66.667 0.00 0.00 42.39 5.36
288 289 2.454336 GGCTGGGCCTAGGTAAATTT 57.546 50.000 18.96 0.00 46.69 1.82
289 290 2.031870 GGCTGGGCCTAGGTAAATTTG 58.968 52.381 18.96 0.00 46.69 2.32
290 291 2.031870 GCTGGGCCTAGGTAAATTTGG 58.968 52.381 18.96 0.00 0.00 3.28
291 292 2.623239 GCTGGGCCTAGGTAAATTTGGT 60.623 50.000 18.96 0.00 0.00 3.67
292 293 3.023832 CTGGGCCTAGGTAAATTTGGTG 58.976 50.000 8.57 0.00 0.00 4.17
293 294 1.754803 GGGCCTAGGTAAATTTGGTGC 59.245 52.381 11.31 0.00 0.00 5.01
294 295 2.623239 GGGCCTAGGTAAATTTGGTGCT 60.623 50.000 11.31 0.00 0.00 4.40
295 296 2.688446 GGCCTAGGTAAATTTGGTGCTC 59.312 50.000 11.31 0.00 0.00 4.26
296 297 2.688446 GCCTAGGTAAATTTGGTGCTCC 59.312 50.000 11.31 0.00 0.00 4.70
297 298 3.876156 GCCTAGGTAAATTTGGTGCTCCA 60.876 47.826 11.31 2.64 42.66 3.86
298 299 3.947834 CCTAGGTAAATTTGGTGCTCCAG 59.052 47.826 7.68 0.00 45.22 3.86
299 300 2.171003 AGGTAAATTTGGTGCTCCAGC 58.829 47.619 7.68 0.00 45.22 4.85
300 301 1.135402 GGTAAATTTGGTGCTCCAGCG 60.135 52.381 7.68 0.00 45.22 5.18
325 326 4.840005 GCTGGCTGGGCTACGGTC 62.840 72.222 0.00 0.00 0.00 4.79
326 327 3.390521 CTGGCTGGGCTACGGTCA 61.391 66.667 0.00 0.00 37.85 4.02
327 328 3.390521 TGGCTGGGCTACGGTCAG 61.391 66.667 0.00 0.00 34.48 3.51
328 329 4.162690 GGCTGGGCTACGGTCAGG 62.163 72.222 0.00 0.00 0.00 3.86
329 330 3.391382 GCTGGGCTACGGTCAGGT 61.391 66.667 0.00 0.00 0.00 4.00
330 331 2.893398 CTGGGCTACGGTCAGGTC 59.107 66.667 0.00 0.00 0.00 3.85
331 332 3.064987 CTGGGCTACGGTCAGGTCG 62.065 68.421 0.00 0.00 0.00 4.79
332 333 3.834799 GGGCTACGGTCAGGTCGG 61.835 72.222 0.00 0.00 0.00 4.79
333 334 4.509737 GGCTACGGTCAGGTCGGC 62.510 72.222 0.00 0.00 0.00 5.54
334 335 4.509737 GCTACGGTCAGGTCGGCC 62.510 72.222 0.00 0.00 0.00 6.13
335 336 3.834799 CTACGGTCAGGTCGGCCC 61.835 72.222 0.08 0.00 34.57 5.80
339 340 4.083862 GGTCAGGTCGGCCCTCAC 62.084 72.222 0.08 0.00 43.86 3.51
340 341 4.436998 GTCAGGTCGGCCCTCACG 62.437 72.222 0.08 0.00 43.86 4.35
349 350 4.828925 GCCCTCACGCAGCTCCTC 62.829 72.222 0.00 0.00 0.00 3.71
350 351 4.154347 CCCTCACGCAGCTCCTCC 62.154 72.222 0.00 0.00 0.00 4.30
351 352 3.385384 CCTCACGCAGCTCCTCCA 61.385 66.667 0.00 0.00 0.00 3.86
352 353 2.183811 CTCACGCAGCTCCTCCAG 59.816 66.667 0.00 0.00 0.00 3.86
353 354 2.601666 TCACGCAGCTCCTCCAGT 60.602 61.111 0.00 0.00 0.00 4.00
354 355 2.433838 CACGCAGCTCCTCCAGTG 60.434 66.667 0.00 0.00 0.00 3.66
355 356 2.919856 ACGCAGCTCCTCCAGTGT 60.920 61.111 0.00 0.00 0.00 3.55
356 357 2.345244 CGCAGCTCCTCCAGTGTT 59.655 61.111 0.00 0.00 0.00 3.32
357 358 1.302033 CGCAGCTCCTCCAGTGTTT 60.302 57.895 0.00 0.00 0.00 2.83
358 359 1.294659 CGCAGCTCCTCCAGTGTTTC 61.295 60.000 0.00 0.00 0.00 2.78
359 360 0.036022 GCAGCTCCTCCAGTGTTTCT 59.964 55.000 0.00 0.00 0.00 2.52
360 361 1.943507 GCAGCTCCTCCAGTGTTTCTC 60.944 57.143 0.00 0.00 0.00 2.87
361 362 1.345741 CAGCTCCTCCAGTGTTTCTCA 59.654 52.381 0.00 0.00 0.00 3.27
362 363 2.050144 AGCTCCTCCAGTGTTTCTCAA 58.950 47.619 0.00 0.00 0.00 3.02
363 364 2.439507 AGCTCCTCCAGTGTTTCTCAAA 59.560 45.455 0.00 0.00 0.00 2.69
364 365 3.117888 AGCTCCTCCAGTGTTTCTCAAAA 60.118 43.478 0.00 0.00 0.00 2.44
365 366 3.632145 GCTCCTCCAGTGTTTCTCAAAAA 59.368 43.478 0.00 0.00 0.00 1.94
384 385 4.783667 AAAAACGTAGCTCCGCCA 57.216 50.000 0.00 0.00 0.00 5.69
385 386 2.540145 AAAAACGTAGCTCCGCCAG 58.460 52.632 0.00 0.00 0.00 4.85
386 387 0.250166 AAAAACGTAGCTCCGCCAGT 60.250 50.000 0.00 0.00 0.00 4.00
387 388 0.949105 AAAACGTAGCTCCGCCAGTG 60.949 55.000 0.00 0.00 0.00 3.66
388 389 1.812686 AAACGTAGCTCCGCCAGTGA 61.813 55.000 0.00 0.00 0.00 3.41
389 390 1.812686 AACGTAGCTCCGCCAGTGAA 61.813 55.000 0.00 0.00 0.00 3.18
390 391 1.805945 CGTAGCTCCGCCAGTGAAC 60.806 63.158 0.00 0.00 0.00 3.18
391 392 1.805945 GTAGCTCCGCCAGTGAACG 60.806 63.158 0.00 0.00 0.00 3.95
392 393 3.642778 TAGCTCCGCCAGTGAACGC 62.643 63.158 0.00 0.00 0.00 4.84
394 395 3.414700 CTCCGCCAGTGAACGCAC 61.415 66.667 0.00 0.00 45.49 5.34
395 396 4.980805 TCCGCCAGTGAACGCACC 62.981 66.667 0.00 0.00 46.32 5.01
398 399 4.012895 GCCAGTGAACGCACCGTG 62.013 66.667 0.00 0.00 46.32 4.94
399 400 2.587753 CCAGTGAACGCACCGTGT 60.588 61.111 0.00 0.00 46.32 4.49
400 401 2.594962 CCAGTGAACGCACCGTGTC 61.595 63.158 0.00 0.00 46.32 3.67
401 402 1.880796 CAGTGAACGCACCGTGTCA 60.881 57.895 0.00 0.00 46.32 3.58
402 403 1.069090 AGTGAACGCACCGTGTCAT 59.931 52.632 0.00 0.00 46.32 3.06
403 404 0.531974 AGTGAACGCACCGTGTCATT 60.532 50.000 0.00 0.00 46.32 2.57
404 405 0.110823 GTGAACGCACCGTGTCATTC 60.111 55.000 0.00 3.02 39.99 2.67
405 406 0.249699 TGAACGCACCGTGTCATTCT 60.250 50.000 0.00 0.00 39.99 2.40
406 407 0.163788 GAACGCACCGTGTCATTCTG 59.836 55.000 0.00 0.00 39.99 3.02
407 408 0.531974 AACGCACCGTGTCATTCTGT 60.532 50.000 0.00 0.00 39.99 3.41
408 409 0.944311 ACGCACCGTGTCATTCTGTC 60.944 55.000 0.00 0.00 39.18 3.51
409 410 0.667487 CGCACCGTGTCATTCTGTCT 60.667 55.000 0.00 0.00 0.00 3.41
410 411 1.071605 GCACCGTGTCATTCTGTCTC 58.928 55.000 0.00 0.00 0.00 3.36
411 412 1.337260 GCACCGTGTCATTCTGTCTCT 60.337 52.381 0.00 0.00 0.00 3.10
412 413 2.868044 GCACCGTGTCATTCTGTCTCTT 60.868 50.000 0.00 0.00 0.00 2.85
413 414 2.989840 CACCGTGTCATTCTGTCTCTTC 59.010 50.000 0.00 0.00 0.00 2.87
414 415 2.028930 ACCGTGTCATTCTGTCTCTTCC 60.029 50.000 0.00 0.00 0.00 3.46
1017 1575 1.226717 GATGACCGTGTCGCTCCTC 60.227 63.158 0.59 0.00 34.95 3.71
2049 5992 2.693762 CGGTGCTTGCTGTCCATGG 61.694 63.158 4.97 4.97 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.482374 GCAGTTAGCAGCGGCAAG 59.518 61.111 12.44 0.00 44.61 4.01
27 28 1.507141 AACCACACGCAGTTAGCAGC 61.507 55.000 0.00 0.00 41.61 5.25
28 29 0.235665 CAACCACACGCAGTTAGCAG 59.764 55.000 0.00 0.00 41.61 4.24
29 30 1.781025 GCAACCACACGCAGTTAGCA 61.781 55.000 0.00 0.00 41.61 3.49
30 31 1.082104 GCAACCACACGCAGTTAGC 60.082 57.895 0.00 0.00 41.61 3.09
31 32 1.204062 CGCAACCACACGCAGTTAG 59.796 57.895 0.00 0.00 41.61 2.34
32 33 1.521906 ACGCAACCACACGCAGTTA 60.522 52.632 0.00 0.00 41.61 2.24
33 34 2.822255 ACGCAACCACACGCAGTT 60.822 55.556 0.00 0.00 41.61 3.16
35 36 4.312231 CCACGCAACCACACGCAG 62.312 66.667 0.00 0.00 0.00 5.18
67 68 4.446413 ATTCGGCCGACCCACGAC 62.446 66.667 31.19 0.00 45.77 4.34
68 69 4.137872 GATTCGGCCGACCCACGA 62.138 66.667 31.19 13.31 45.77 4.35
79 80 4.824166 ACGACGACGGCGATTCGG 62.824 66.667 32.70 9.47 44.46 4.30
80 81 3.594827 CACGACGACGGCGATTCG 61.595 66.667 32.70 21.25 44.46 3.34
81 82 3.898640 GCACGACGACGGCGATTC 61.899 66.667 32.70 13.99 44.46 2.52
82 83 4.415332 AGCACGACGACGGCGATT 62.415 61.111 32.70 11.64 44.46 3.34
88 89 3.756677 CACAGCAGCACGACGACG 61.757 66.667 5.58 5.58 45.75 5.12
89 90 2.658593 ACACAGCAGCACGACGAC 60.659 61.111 0.00 0.00 0.00 4.34
90 91 2.658268 CACACAGCAGCACGACGA 60.658 61.111 0.00 0.00 0.00 4.20
91 92 4.360027 GCACACAGCAGCACGACG 62.360 66.667 0.00 0.00 44.79 5.12
109 110 4.498520 ATCGTCTGCCGCTCACCG 62.499 66.667 0.00 0.00 36.19 4.94
110 111 2.887568 CATCGTCTGCCGCTCACC 60.888 66.667 0.00 0.00 36.19 4.02
111 112 2.125912 ACATCGTCTGCCGCTCAC 60.126 61.111 0.00 0.00 36.19 3.51
112 113 2.125952 CACATCGTCTGCCGCTCA 60.126 61.111 0.00 0.00 36.19 4.26
113 114 2.125912 ACACATCGTCTGCCGCTC 60.126 61.111 0.00 0.00 36.19 5.03
114 115 2.433145 CACACATCGTCTGCCGCT 60.433 61.111 0.00 0.00 36.19 5.52
115 116 4.152625 GCACACATCGTCTGCCGC 62.153 66.667 0.00 0.00 36.19 6.53
116 117 3.490759 GGCACACATCGTCTGCCG 61.491 66.667 0.00 0.00 37.80 5.69
117 118 3.490759 CGGCACACATCGTCTGCC 61.491 66.667 3.56 3.56 42.71 4.85
118 119 4.152625 GCGGCACACATCGTCTGC 62.153 66.667 0.00 0.00 0.00 4.26
119 120 2.029288 AAGCGGCACACATCGTCTG 61.029 57.895 1.45 0.00 0.00 3.51
120 121 2.029288 CAAGCGGCACACATCGTCT 61.029 57.895 1.45 0.00 0.00 4.18
121 122 2.476051 CAAGCGGCACACATCGTC 59.524 61.111 1.45 0.00 0.00 4.20
122 123 3.726517 GCAAGCGGCACACATCGT 61.727 61.111 1.45 0.00 43.97 3.73
167 168 1.949015 GATCGACACACAGCGCACAG 61.949 60.000 11.47 0.64 0.00 3.66
168 169 2.021584 GATCGACACACAGCGCACA 61.022 57.895 11.47 0.00 0.00 4.57
169 170 2.730672 GGATCGACACACAGCGCAC 61.731 63.158 11.47 0.00 0.00 5.34
170 171 2.432456 GGATCGACACACAGCGCA 60.432 61.111 11.47 0.00 0.00 6.09
171 172 3.545481 CGGATCGACACACAGCGC 61.545 66.667 0.00 0.00 0.00 5.92
172 173 2.126463 ACGGATCGACACACAGCG 60.126 61.111 0.00 0.00 0.00 5.18
173 174 3.768632 GACGGATCGACACACAGC 58.231 61.111 0.00 0.00 0.00 4.40
193 194 4.842091 CTGGCAGCCAAATCGCGC 62.842 66.667 17.03 0.00 30.80 6.86
194 195 2.476534 AAACTGGCAGCCAAATCGCG 62.477 55.000 17.03 4.95 30.80 5.87
195 196 0.319813 AAAACTGGCAGCCAAATCGC 60.320 50.000 17.03 0.00 30.80 4.58
196 197 2.153366 AAAAACTGGCAGCCAAATCG 57.847 45.000 17.03 6.19 30.80 3.34
216 217 2.203567 CCCGGCACCCAGGAAAAA 60.204 61.111 0.00 0.00 0.00 1.94
217 218 4.986708 GCCCGGCACCCAGGAAAA 62.987 66.667 3.91 0.00 0.00 2.29
222 223 4.473520 CAGTAGCCCGGCACCCAG 62.474 72.222 13.15 0.00 0.00 4.45
224 225 4.778143 CACAGTAGCCCGGCACCC 62.778 72.222 13.15 0.00 0.00 4.61
225 226 4.016706 ACACAGTAGCCCGGCACC 62.017 66.667 13.15 0.69 0.00 5.01
226 227 2.742372 CACACAGTAGCCCGGCAC 60.742 66.667 13.15 7.98 0.00 5.01
227 228 2.813726 AACACACAGTAGCCCGGCA 61.814 57.895 13.15 0.00 0.00 5.69
228 229 2.032071 AACACACAGTAGCCCGGC 59.968 61.111 0.00 0.00 0.00 6.13
229 230 1.671054 CCAACACACAGTAGCCCGG 60.671 63.158 0.00 0.00 0.00 5.73
230 231 1.671054 CCCAACACACAGTAGCCCG 60.671 63.158 0.00 0.00 0.00 6.13
231 232 0.889186 CACCCAACACACAGTAGCCC 60.889 60.000 0.00 0.00 0.00 5.19
232 233 0.179029 ACACCCAACACACAGTAGCC 60.179 55.000 0.00 0.00 0.00 3.93
233 234 0.944386 CACACCCAACACACAGTAGC 59.056 55.000 0.00 0.00 0.00 3.58
234 235 0.944386 GCACACCCAACACACAGTAG 59.056 55.000 0.00 0.00 0.00 2.57
235 236 0.544223 AGCACACCCAACACACAGTA 59.456 50.000 0.00 0.00 0.00 2.74
236 237 1.031571 CAGCACACCCAACACACAGT 61.032 55.000 0.00 0.00 0.00 3.55
237 238 1.727511 CCAGCACACCCAACACACAG 61.728 60.000 0.00 0.00 0.00 3.66
238 239 1.752310 CCAGCACACCCAACACACA 60.752 57.895 0.00 0.00 0.00 3.72
239 240 1.724582 GACCAGCACACCCAACACAC 61.725 60.000 0.00 0.00 0.00 3.82
240 241 1.453015 GACCAGCACACCCAACACA 60.453 57.895 0.00 0.00 0.00 3.72
241 242 1.447317 CTGACCAGCACACCCAACAC 61.447 60.000 0.00 0.00 0.00 3.32
242 243 1.152984 CTGACCAGCACACCCAACA 60.153 57.895 0.00 0.00 0.00 3.33
243 244 0.250901 ATCTGACCAGCACACCCAAC 60.251 55.000 0.00 0.00 0.00 3.77
244 245 0.250858 CATCTGACCAGCACACCCAA 60.251 55.000 0.00 0.00 0.00 4.12
245 246 1.376086 CATCTGACCAGCACACCCA 59.624 57.895 0.00 0.00 0.00 4.51
246 247 2.042831 GCATCTGACCAGCACACCC 61.043 63.158 0.00 0.00 0.00 4.61
247 248 1.002868 AGCATCTGACCAGCACACC 60.003 57.895 0.00 0.00 0.00 4.16
248 249 0.604780 ACAGCATCTGACCAGCACAC 60.605 55.000 0.29 0.00 35.18 3.82
249 250 0.604511 CACAGCATCTGACCAGCACA 60.605 55.000 0.29 0.00 35.18 4.57
250 251 1.303799 CCACAGCATCTGACCAGCAC 61.304 60.000 0.29 0.00 35.18 4.40
251 252 1.002990 CCACAGCATCTGACCAGCA 60.003 57.895 0.29 0.00 35.18 4.41
252 253 1.748122 CCCACAGCATCTGACCAGC 60.748 63.158 0.29 0.00 35.18 4.85
253 254 1.748122 GCCCACAGCATCTGACCAG 60.748 63.158 0.29 0.00 42.97 4.00
254 255 2.352422 GCCCACAGCATCTGACCA 59.648 61.111 0.29 0.00 42.97 4.02
270 271 2.031870 CCAAATTTACCTAGGCCCAGC 58.968 52.381 9.30 0.00 0.00 4.85
271 272 3.023832 CACCAAATTTACCTAGGCCCAG 58.976 50.000 9.30 0.00 0.00 4.45
272 273 2.886391 GCACCAAATTTACCTAGGCCCA 60.886 50.000 9.30 0.00 0.00 5.36
273 274 1.754803 GCACCAAATTTACCTAGGCCC 59.245 52.381 9.30 0.00 0.00 5.80
274 275 2.688446 GAGCACCAAATTTACCTAGGCC 59.312 50.000 9.30 0.00 0.00 5.19
275 276 2.688446 GGAGCACCAAATTTACCTAGGC 59.312 50.000 9.30 0.00 35.97 3.93
276 277 3.947834 CTGGAGCACCAAATTTACCTAGG 59.052 47.826 7.41 7.41 46.32 3.02
277 278 3.378427 GCTGGAGCACCAAATTTACCTAG 59.622 47.826 3.90 0.00 46.32 3.02
278 279 3.352648 GCTGGAGCACCAAATTTACCTA 58.647 45.455 3.90 0.00 46.32 3.08
279 280 2.171003 GCTGGAGCACCAAATTTACCT 58.829 47.619 3.90 0.00 46.32 3.08
280 281 1.135402 CGCTGGAGCACCAAATTTACC 60.135 52.381 3.90 0.00 46.32 2.85
281 282 1.732405 GCGCTGGAGCACCAAATTTAC 60.732 52.381 3.90 0.00 46.32 2.01
282 283 0.525761 GCGCTGGAGCACCAAATTTA 59.474 50.000 3.90 0.00 46.32 1.40
283 284 1.181098 AGCGCTGGAGCACCAAATTT 61.181 50.000 10.39 0.00 46.32 1.82
284 285 1.604593 AGCGCTGGAGCACCAAATT 60.605 52.632 10.39 0.00 46.32 1.82
285 286 2.034687 AGCGCTGGAGCACCAAAT 59.965 55.556 10.39 0.00 46.32 2.32
286 287 2.979676 CAGCGCTGGAGCACCAAA 60.980 61.111 29.88 0.00 46.32 3.28
308 309 4.840005 GACCGTAGCCCAGCCAGC 62.840 72.222 0.00 0.00 0.00 4.85
309 310 3.376935 CTGACCGTAGCCCAGCCAG 62.377 68.421 0.00 0.00 0.00 4.85
310 311 3.390521 CTGACCGTAGCCCAGCCA 61.391 66.667 0.00 0.00 0.00 4.75
311 312 4.162690 CCTGACCGTAGCCCAGCC 62.163 72.222 0.00 0.00 0.00 4.85
312 313 3.372554 GACCTGACCGTAGCCCAGC 62.373 68.421 0.00 0.00 0.00 4.85
313 314 2.893398 GACCTGACCGTAGCCCAG 59.107 66.667 0.00 0.00 0.00 4.45
314 315 3.066190 CGACCTGACCGTAGCCCA 61.066 66.667 0.00 0.00 0.00 5.36
315 316 3.834799 CCGACCTGACCGTAGCCC 61.835 72.222 0.00 0.00 0.00 5.19
316 317 4.509737 GCCGACCTGACCGTAGCC 62.510 72.222 0.00 0.00 0.00 3.93
317 318 4.509737 GGCCGACCTGACCGTAGC 62.510 72.222 0.00 0.00 0.00 3.58
318 319 3.834799 GGGCCGACCTGACCGTAG 61.835 72.222 0.00 0.00 35.85 3.51
332 333 4.828925 GAGGAGCTGCGTGAGGGC 62.829 72.222 0.00 0.00 0.00 5.19
333 334 4.154347 GGAGGAGCTGCGTGAGGG 62.154 72.222 0.00 0.00 0.00 4.30
334 335 3.368190 CTGGAGGAGCTGCGTGAGG 62.368 68.421 0.00 0.00 0.00 3.86
335 336 2.183811 CTGGAGGAGCTGCGTGAG 59.816 66.667 0.00 0.00 0.00 3.51
336 337 2.601666 ACTGGAGGAGCTGCGTGA 60.602 61.111 0.00 0.00 0.00 4.35
337 338 2.433838 CACTGGAGGAGCTGCGTG 60.434 66.667 0.00 0.00 0.00 5.34
338 339 2.044806 AAACACTGGAGGAGCTGCGT 62.045 55.000 0.00 0.00 0.00 5.24
339 340 1.294659 GAAACACTGGAGGAGCTGCG 61.295 60.000 0.00 0.00 0.00 5.18
340 341 0.036022 AGAAACACTGGAGGAGCTGC 59.964 55.000 0.00 0.00 0.00 5.25
341 342 1.345741 TGAGAAACACTGGAGGAGCTG 59.654 52.381 0.00 0.00 0.00 4.24
342 343 1.722034 TGAGAAACACTGGAGGAGCT 58.278 50.000 0.00 0.00 0.00 4.09
343 344 2.550830 TTGAGAAACACTGGAGGAGC 57.449 50.000 0.00 0.00 0.00 4.70
377 378 3.414700 GTGCGTTCACTGGCGGAG 61.415 66.667 0.00 0.00 40.03 4.63
378 379 4.980805 GGTGCGTTCACTGGCGGA 62.981 66.667 0.00 0.00 42.72 5.54
384 385 0.531974 AATGACACGGTGCGTTCACT 60.532 50.000 8.30 0.00 42.72 3.41
385 386 0.110823 GAATGACACGGTGCGTTCAC 60.111 55.000 21.68 6.57 38.32 3.18
386 387 0.249699 AGAATGACACGGTGCGTTCA 60.250 50.000 25.19 16.61 38.32 3.18
387 388 0.163788 CAGAATGACACGGTGCGTTC 59.836 55.000 20.24 20.24 36.38 3.95
388 389 0.531974 ACAGAATGACACGGTGCGTT 60.532 50.000 8.30 8.68 36.38 4.84
389 390 0.944311 GACAGAATGACACGGTGCGT 60.944 55.000 8.30 0.00 38.84 5.24
390 391 0.667487 AGACAGAATGACACGGTGCG 60.667 55.000 8.30 0.00 39.69 5.34
391 392 1.071605 GAGACAGAATGACACGGTGC 58.928 55.000 8.30 1.81 39.69 5.01
392 393 2.732412 AGAGACAGAATGACACGGTG 57.268 50.000 6.58 6.58 39.69 4.94
393 394 2.028930 GGAAGAGACAGAATGACACGGT 60.029 50.000 0.00 0.00 39.69 4.83
394 395 2.029020 TGGAAGAGACAGAATGACACGG 60.029 50.000 0.00 0.00 39.69 4.94
395 396 3.303881 TGGAAGAGACAGAATGACACG 57.696 47.619 0.00 0.00 39.69 4.49
396 397 5.486526 AGATTGGAAGAGACAGAATGACAC 58.513 41.667 0.00 0.00 39.69 3.67
397 398 5.752036 AGATTGGAAGAGACAGAATGACA 57.248 39.130 0.00 0.00 39.69 3.58
398 399 6.093357 GGAAAGATTGGAAGAGACAGAATGAC 59.907 42.308 0.00 0.00 39.69 3.06
399 400 6.176183 GGAAAGATTGGAAGAGACAGAATGA 58.824 40.000 0.00 0.00 39.69 2.57
400 401 5.356470 GGGAAAGATTGGAAGAGACAGAATG 59.644 44.000 0.00 0.00 46.00 2.67
401 402 5.252630 AGGGAAAGATTGGAAGAGACAGAAT 59.747 40.000 0.00 0.00 0.00 2.40
402 403 4.599241 AGGGAAAGATTGGAAGAGACAGAA 59.401 41.667 0.00 0.00 0.00 3.02
403 404 4.171234 AGGGAAAGATTGGAAGAGACAGA 58.829 43.478 0.00 0.00 0.00 3.41
404 405 4.566426 AGGGAAAGATTGGAAGAGACAG 57.434 45.455 0.00 0.00 0.00 3.51
405 406 5.094387 AGTAGGGAAAGATTGGAAGAGACA 58.906 41.667 0.00 0.00 0.00 3.41
406 407 5.685520 AGTAGGGAAAGATTGGAAGAGAC 57.314 43.478 0.00 0.00 0.00 3.36
407 408 7.996758 ATTAGTAGGGAAAGATTGGAAGAGA 57.003 36.000 0.00 0.00 0.00 3.10
410 411 8.841300 GCTTTATTAGTAGGGAAAGATTGGAAG 58.159 37.037 0.00 0.00 31.83 3.46
411 412 8.333235 TGCTTTATTAGTAGGGAAAGATTGGAA 58.667 33.333 0.00 0.00 31.83 3.53
412 413 7.773690 GTGCTTTATTAGTAGGGAAAGATTGGA 59.226 37.037 0.00 0.00 31.83 3.53
413 414 7.254795 CGTGCTTTATTAGTAGGGAAAGATTGG 60.255 40.741 0.00 0.00 31.83 3.16
414 415 7.254795 CCGTGCTTTATTAGTAGGGAAAGATTG 60.255 40.741 0.00 0.00 44.42 2.67
1367 1931 2.906458 CAGCCTCGCCTCCAATCT 59.094 61.111 0.00 0.00 0.00 2.40
2049 5992 5.647225 GGCATCCAGATTTGAGGAATATCTC 59.353 44.000 0.00 0.00 37.48 2.75


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

AutoCloner maintained by Alex Coulton.