Multiple sequence alignment - TraesCS2B01G307700

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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 TraesCS2B01G307700 chr2B 100.000 2976 0 0 1 2976 440357641 440354666 0.000000e+00 5496.0
1 TraesCS2B01G307700 chr2B 80.645 155 22 8 1194 1344 110370935 110371085 2.420000e-21 113.0
2 TraesCS2B01G307700 chr2D 91.569 1708 90 13 326 2010 371243341 371241665 0.000000e+00 2307.0
3 TraesCS2B01G307700 chr2D 87.642 793 52 15 2014 2779 371241605 371240832 0.000000e+00 880.0
4 TraesCS2B01G307700 chr2D 85.380 171 20 3 331 497 8384513 8384344 3.940000e-39 172.0
5 TraesCS2B01G307700 chr2D 83.333 174 22 5 326 495 579606700 579606870 1.430000e-33 154.0
6 TraesCS2B01G307700 chr2A 94.703 1095 37 8 916 2010 502064576 502063503 0.000000e+00 1681.0
7 TraesCS2B01G307700 chr2A 88.407 992 72 17 2016 2976 502063452 502062473 0.000000e+00 1155.0
8 TraesCS2B01G307700 chr2A 93.140 379 17 2 560 929 502066835 502066457 5.610000e-152 547.0
9 TraesCS2B01G307700 chr2A 88.199 161 15 3 317 476 502067621 502067464 3.920000e-44 189.0
10 TraesCS2B01G307700 chr2A 75.789 285 56 11 1194 1474 71587239 71587514 6.690000e-27 132.0
11 TraesCS2B01G307700 chr3B 90.196 255 16 5 1 248 253893422 253893170 1.030000e-84 324.0
12 TraesCS2B01G307700 chr3B 89.062 256 18 6 1 247 660482411 660482157 2.880000e-80 309.0
13 TraesCS2B01G307700 chr7A 88.760 258 18 8 1 248 265203923 265204179 3.730000e-79 305.0
14 TraesCS2B01G307700 chr7A 88.372 258 16 9 1 248 584381578 584381831 6.240000e-77 298.0
15 TraesCS2B01G307700 chr7A 87.500 264 21 10 1 253 663489937 663489675 8.070000e-76 294.0
16 TraesCS2B01G307700 chr7A 84.615 182 24 4 333 510 105644078 105643897 8.480000e-41 178.0
17 TraesCS2B01G307700 chr6D 88.258 264 20 6 1 254 426200719 426200981 3.730000e-79 305.0
18 TraesCS2B01G307700 chr6B 88.716 257 19 4 1 248 256976178 256975923 3.730000e-79 305.0
19 TraesCS2B01G307700 chr4D 88.672 256 18 7 1 247 91232513 91232260 4.820000e-78 302.0
20 TraesCS2B01G307700 chr3A 88.627 255 20 4 3 248 654557435 654557689 4.820000e-78 302.0
21 TraesCS2B01G307700 chr4B 83.060 183 27 4 326 505 522506186 522506367 2.370000e-36 163.0
22 TraesCS2B01G307700 chr5B 85.000 160 19 5 324 479 112531026 112531184 1.100000e-34 158.0
23 TraesCS2B01G307700 chr3D 83.133 166 25 3 331 495 598082214 598082051 6.650000e-32 148.0
24 TraesCS2B01G307700 chr5A 82.222 180 21 8 336 510 108577077 108576904 8.600000e-31 145.0
25 TraesCS2B01G307700 chr7B 89.231 65 6 1 2303 2366 385062650 385062586 2.460000e-11 80.5


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 TraesCS2B01G307700 chr2B 440354666 440357641 2975 True 5496.0 5496 100.00000 1 2976 1 chr2B.!!$R1 2975
1 TraesCS2B01G307700 chr2D 371240832 371243341 2509 True 1593.5 2307 89.60550 326 2779 2 chr2D.!!$R2 2453
2 TraesCS2B01G307700 chr2A 502062473 502067621 5148 True 893.0 1681 91.11225 317 2976 4 chr2A.!!$R1 2659

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
701 1270 0.248702 TCCGGCGAACAAAAAGCAAC 60.249 50.0 9.3 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 4645 0.245266 TGACCGACGCTTAGCATGAA 59.755 50.0 4.7 0.0 0.0 2.57 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
21 22 4.406001 CCTCCGTTTCTTTTTAGTCTGC 57.594 45.455 0.00 0.00 0.00 4.26
22 23 3.813166 CCTCCGTTTCTTTTTAGTCTGCA 59.187 43.478 0.00 0.00 0.00 4.41
23 24 4.455877 CCTCCGTTTCTTTTTAGTCTGCAT 59.544 41.667 0.00 0.00 0.00 3.96
24 25 5.642063 CCTCCGTTTCTTTTTAGTCTGCATA 59.358 40.000 0.00 0.00 0.00 3.14
25 26 6.316390 CCTCCGTTTCTTTTTAGTCTGCATAT 59.684 38.462 0.00 0.00 0.00 1.78
26 27 7.494625 CCTCCGTTTCTTTTTAGTCTGCATATA 59.505 37.037 0.00 0.00 0.00 0.86
27 28 8.780846 TCCGTTTCTTTTTAGTCTGCATATAA 57.219 30.769 0.00 0.00 0.00 0.98
28 29 8.879759 TCCGTTTCTTTTTAGTCTGCATATAAG 58.120 33.333 0.00 0.00 0.00 1.73
29 30 8.879759 CCGTTTCTTTTTAGTCTGCATATAAGA 58.120 33.333 0.00 0.00 0.00 2.10
184 185 9.944663 TGTAGATGTTGTTTTACAAAGTTGATC 57.055 29.630 0.00 0.00 40.15 2.92
185 186 9.944663 GTAGATGTTGTTTTACAAAGTTGATCA 57.055 29.630 0.00 0.00 40.15 2.92
187 188 9.868277 AGATGTTGTTTTACAAAGTTGATCAAA 57.132 25.926 10.35 0.00 40.15 2.69
188 189 9.900264 GATGTTGTTTTACAAAGTTGATCAAAC 57.100 29.630 10.35 4.88 40.15 2.93
207 208 5.844301 AAACTTTGCACAGTTTGACTTTG 57.156 34.783 25.96 0.00 43.88 2.77
208 209 4.782019 ACTTTGCACAGTTTGACTTTGA 57.218 36.364 0.00 0.00 27.60 2.69
209 210 4.485163 ACTTTGCACAGTTTGACTTTGAC 58.515 39.130 0.00 0.00 27.60 3.18
210 211 3.502191 TTGCACAGTTTGACTTTGACC 57.498 42.857 0.00 0.00 27.60 4.02
211 212 2.441410 TGCACAGTTTGACTTTGACCA 58.559 42.857 0.00 0.00 27.60 4.02
212 213 2.822561 TGCACAGTTTGACTTTGACCAA 59.177 40.909 0.00 0.00 27.60 3.67
213 214 3.256879 TGCACAGTTTGACTTTGACCAAA 59.743 39.130 0.00 0.00 27.60 3.28
214 215 4.081752 TGCACAGTTTGACTTTGACCAAAT 60.082 37.500 0.00 0.00 35.14 2.32
215 216 4.504097 GCACAGTTTGACTTTGACCAAATC 59.496 41.667 0.00 0.00 35.14 2.17
216 217 5.679638 GCACAGTTTGACTTTGACCAAATCT 60.680 40.000 0.00 0.00 35.14 2.40
217 218 6.332630 CACAGTTTGACTTTGACCAAATCTT 58.667 36.000 0.00 0.00 35.14 2.40
218 219 6.254157 CACAGTTTGACTTTGACCAAATCTTG 59.746 38.462 0.00 0.00 35.14 3.02
219 220 6.071391 ACAGTTTGACTTTGACCAAATCTTGT 60.071 34.615 0.00 0.00 35.14 3.16
220 221 7.122055 ACAGTTTGACTTTGACCAAATCTTGTA 59.878 33.333 0.00 0.00 35.14 2.41
221 222 8.137437 CAGTTTGACTTTGACCAAATCTTGTAT 58.863 33.333 0.00 0.00 35.14 2.29
222 223 8.137437 AGTTTGACTTTGACCAAATCTTGTATG 58.863 33.333 0.00 0.00 35.14 2.39
223 224 6.012658 TGACTTTGACCAAATCTTGTATGC 57.987 37.500 0.00 0.00 0.00 3.14
224 225 5.534278 TGACTTTGACCAAATCTTGTATGCA 59.466 36.000 0.00 0.00 0.00 3.96
225 226 6.040278 TGACTTTGACCAAATCTTGTATGCAA 59.960 34.615 0.00 0.00 0.00 4.08
226 227 6.815089 ACTTTGACCAAATCTTGTATGCAAA 58.185 32.000 0.00 0.00 33.73 3.68
227 228 7.444299 ACTTTGACCAAATCTTGTATGCAAAT 58.556 30.769 0.00 0.00 33.73 2.32
228 229 7.933033 ACTTTGACCAAATCTTGTATGCAAATT 59.067 29.630 0.00 0.00 33.73 1.82
229 230 9.421806 CTTTGACCAAATCTTGTATGCAAATTA 57.578 29.630 0.00 0.00 33.73 1.40
230 231 9.770097 TTTGACCAAATCTTGTATGCAAATTAA 57.230 25.926 0.00 0.00 33.73 1.40
231 232 9.770097 TTGACCAAATCTTGTATGCAAATTAAA 57.230 25.926 0.00 0.00 33.73 1.52
232 233 9.770097 TGACCAAATCTTGTATGCAAATTAAAA 57.230 25.926 0.00 0.00 33.73 1.52
257 258 8.953223 AAAACGGAGGGAGTATATTACTATCT 57.047 34.615 0.00 0.00 39.59 1.98
258 259 8.953223 AAACGGAGGGAGTATATTACTATCTT 57.047 34.615 0.00 0.00 39.59 2.40
259 260 8.578448 AACGGAGGGAGTATATTACTATCTTC 57.422 38.462 0.00 0.00 39.59 2.87
260 261 7.696981 ACGGAGGGAGTATATTACTATCTTCA 58.303 38.462 0.00 0.00 39.59 3.02
261 262 7.611079 ACGGAGGGAGTATATTACTATCTTCAC 59.389 40.741 0.00 0.00 39.59 3.18
262 263 7.610692 CGGAGGGAGTATATTACTATCTTCACA 59.389 40.741 0.00 0.00 39.59 3.58
263 264 8.962679 GGAGGGAGTATATTACTATCTTCACAG 58.037 40.741 0.00 0.00 39.59 3.66
264 265 9.523168 GAGGGAGTATATTACTATCTTCACAGT 57.477 37.037 0.00 0.00 39.59 3.55
265 266 9.303116 AGGGAGTATATTACTATCTTCACAGTG 57.697 37.037 0.00 0.00 39.59 3.66
266 267 9.298250 GGGAGTATATTACTATCTTCACAGTGA 57.702 37.037 0.00 0.00 39.59 3.41
269 270 9.869667 AGTATATTACTATCTTCACAGTGAGGT 57.130 33.333 12.17 6.52 37.23 3.85
274 275 8.503458 TTACTATCTTCACAGTGAGGTACTAC 57.497 38.462 12.17 0.00 41.55 2.73
275 276 5.887035 ACTATCTTCACAGTGAGGTACTACC 59.113 44.000 12.17 0.00 41.55 3.18
286 287 1.844687 GGTACTACCTCCGTCCAAGT 58.155 55.000 0.00 0.00 34.73 3.16
287 288 2.174360 GGTACTACCTCCGTCCAAGTT 58.826 52.381 0.00 0.00 34.73 2.66
288 289 2.564504 GGTACTACCTCCGTCCAAGTTT 59.435 50.000 0.00 0.00 34.73 2.66
289 290 3.763897 GGTACTACCTCCGTCCAAGTTTA 59.236 47.826 0.00 0.00 34.73 2.01
290 291 4.220602 GGTACTACCTCCGTCCAAGTTTAA 59.779 45.833 0.00 0.00 34.73 1.52
291 292 4.961438 ACTACCTCCGTCCAAGTTTAAA 57.039 40.909 0.00 0.00 0.00 1.52
292 293 5.294734 ACTACCTCCGTCCAAGTTTAAAA 57.705 39.130 0.00 0.00 0.00 1.52
293 294 5.303165 ACTACCTCCGTCCAAGTTTAAAAG 58.697 41.667 0.00 0.00 0.00 2.27
294 295 4.426736 ACCTCCGTCCAAGTTTAAAAGA 57.573 40.909 0.00 0.00 0.00 2.52
295 296 4.132336 ACCTCCGTCCAAGTTTAAAAGAC 58.868 43.478 0.00 0.00 0.00 3.01
296 297 3.501062 CCTCCGTCCAAGTTTAAAAGACC 59.499 47.826 0.00 0.00 0.00 3.85
297 298 3.479489 TCCGTCCAAGTTTAAAAGACCC 58.521 45.455 0.00 0.00 0.00 4.46
298 299 2.224784 CCGTCCAAGTTTAAAAGACCCG 59.775 50.000 0.00 0.00 0.00 5.28
299 300 2.874086 CGTCCAAGTTTAAAAGACCCGT 59.126 45.455 0.00 0.00 0.00 5.28
300 301 3.059393 CGTCCAAGTTTAAAAGACCCGTC 60.059 47.826 0.00 0.00 0.00 4.79
301 302 3.878699 GTCCAAGTTTAAAAGACCCGTCA 59.121 43.478 0.00 0.00 0.00 4.35
302 303 4.024302 GTCCAAGTTTAAAAGACCCGTCAG 60.024 45.833 0.00 0.00 0.00 3.51
303 304 3.304458 CCAAGTTTAAAAGACCCGTCAGC 60.304 47.826 0.00 0.00 0.00 4.26
304 305 3.487120 AGTTTAAAAGACCCGTCAGCT 57.513 42.857 0.00 0.00 0.00 4.24
305 306 4.612264 AGTTTAAAAGACCCGTCAGCTA 57.388 40.909 0.00 0.00 0.00 3.32
306 307 5.161943 AGTTTAAAAGACCCGTCAGCTAT 57.838 39.130 0.00 0.00 0.00 2.97
307 308 4.935808 AGTTTAAAAGACCCGTCAGCTATG 59.064 41.667 0.00 0.00 0.00 2.23
308 309 4.546829 TTAAAAGACCCGTCAGCTATGT 57.453 40.909 0.00 0.00 0.00 2.29
309 310 3.418684 AAAAGACCCGTCAGCTATGTT 57.581 42.857 0.00 0.00 0.00 2.71
310 311 4.546829 AAAAGACCCGTCAGCTATGTTA 57.453 40.909 0.00 0.00 0.00 2.41
311 312 3.521947 AAGACCCGTCAGCTATGTTAC 57.478 47.619 0.00 0.00 0.00 2.50
312 313 2.736347 AGACCCGTCAGCTATGTTACT 58.264 47.619 0.00 0.00 0.00 2.24
313 314 2.688958 AGACCCGTCAGCTATGTTACTC 59.311 50.000 0.00 0.00 0.00 2.59
314 315 2.426024 GACCCGTCAGCTATGTTACTCA 59.574 50.000 0.00 0.00 0.00 3.41
315 316 2.165845 ACCCGTCAGCTATGTTACTCAC 59.834 50.000 0.00 0.00 0.00 3.51
322 323 4.956075 TCAGCTATGTTACTCACATGGAGA 59.044 41.667 15.51 4.41 45.22 3.71
323 324 5.600069 TCAGCTATGTTACTCACATGGAGAT 59.400 40.000 15.51 4.19 45.22 2.75
341 342 6.283694 TGGAGATAGTATCATGCAACACTTC 58.716 40.000 12.66 0.00 0.00 3.01
353 355 8.504812 TCATGCAACACTTCATTATTAGCTTA 57.495 30.769 0.00 0.00 0.00 3.09
354 356 8.397906 TCATGCAACACTTCATTATTAGCTTAC 58.602 33.333 0.00 0.00 0.00 2.34
387 389 8.707938 TCTTGTCTTGATATGTGTGATGTTAG 57.292 34.615 0.00 0.00 0.00 2.34
403 405 8.610035 TGTGATGTTAGTCATAGTACGAGTAAG 58.390 37.037 0.00 0.00 36.83 2.34
407 409 9.829507 ATGTTAGTCATAGTACGAGTAAGTAGT 57.170 33.333 0.00 0.00 34.67 2.73
499 778 5.730550 TGTCACTGCCGAAATTACTTCTAT 58.269 37.500 0.00 0.00 31.20 1.98
542 821 2.623889 AGCTATCTACAACTGTAGCCCG 59.376 50.000 11.34 4.14 45.69 6.13
622 1187 2.607635 CCAGAAAAGTACGCACGCATAT 59.392 45.455 0.00 0.00 0.00 1.78
656 1225 1.412710 CATATACATATCCGGCCGGCT 59.587 52.381 39.89 32.88 34.68 5.52
697 1266 1.602377 AGTCTTCCGGCGAACAAAAAG 59.398 47.619 9.30 2.25 0.00 2.27
701 1270 0.248702 TCCGGCGAACAAAAAGCAAC 60.249 50.000 9.30 0.00 0.00 4.17
732 1304 1.053424 GCCCGGTGGATATTACAGGA 58.947 55.000 0.00 0.00 35.73 3.86
776 1348 2.180204 GGGACAATGGTCGGCGATG 61.180 63.158 14.79 10.07 45.28 3.84
883 1460 3.877508 GAGATGCCCGTTTAGTGCTAAAT 59.122 43.478 7.54 0.00 37.37 1.40
957 3428 1.594293 ACGAGGGCTTTGTGTCACG 60.594 57.895 0.00 0.00 0.00 4.35
1015 3486 2.361992 CCATGGCAAGCAGCTCCA 60.362 61.111 5.32 5.32 44.79 3.86
1029 3500 0.955428 GCTCCAATGTCGTTCCTGCA 60.955 55.000 0.00 0.00 0.00 4.41
1066 3537 1.697982 AGACGTTGCCTACCTTTTCCT 59.302 47.619 0.00 0.00 0.00 3.36
1067 3538 1.804748 GACGTTGCCTACCTTTTCCTG 59.195 52.381 0.00 0.00 0.00 3.86
1068 3539 1.142262 ACGTTGCCTACCTTTTCCTGT 59.858 47.619 0.00 0.00 0.00 4.00
1069 3540 2.227194 CGTTGCCTACCTTTTCCTGTT 58.773 47.619 0.00 0.00 0.00 3.16
1070 3541 2.621526 CGTTGCCTACCTTTTCCTGTTT 59.378 45.455 0.00 0.00 0.00 2.83
1071 3542 3.067601 CGTTGCCTACCTTTTCCTGTTTT 59.932 43.478 0.00 0.00 0.00 2.43
1072 3543 4.440940 CGTTGCCTACCTTTTCCTGTTTTT 60.441 41.667 0.00 0.00 0.00 1.94
1110 3581 8.449251 ACTTTTTCCTGTTTTTATACCGTGTA 57.551 30.769 0.00 0.00 0.00 2.90
1116 3587 8.297470 TCCTGTTTTTATACCGTGTAGATACT 57.703 34.615 0.00 0.00 0.00 2.12
1117 3588 8.752187 TCCTGTTTTTATACCGTGTAGATACTT 58.248 33.333 0.00 0.00 0.00 2.24
1118 3589 8.814235 CCTGTTTTTATACCGTGTAGATACTTG 58.186 37.037 0.00 0.00 0.00 3.16
1119 3590 8.188531 TGTTTTTATACCGTGTAGATACTTGC 57.811 34.615 0.00 0.00 0.00 4.01
1162 3641 3.727970 GCACTTATGCCTTACGTGAAAGC 60.728 47.826 0.00 0.00 46.97 3.51
1165 3644 1.803334 ATGCCTTACGTGAAAGCGAA 58.197 45.000 0.00 0.00 35.59 4.70
1188 3667 4.757657 AGGTTAATTTGTCATGTGCGTACA 59.242 37.500 9.28 9.28 41.89 2.90
1862 4341 2.668632 GGGTCAAGGACATCGCCA 59.331 61.111 0.00 0.00 33.68 5.69
1888 4367 2.448705 GCTCTTTCTCGCCAGCGAC 61.449 63.158 11.27 0.00 44.01 5.19
1991 4470 4.008330 GGAGTAATGGAGACCGATCGATA 58.992 47.826 18.66 0.00 0.00 2.92
1996 4476 8.294954 AGTAATGGAGACCGATCGATATAAAT 57.705 34.615 18.66 0.46 0.00 1.40
2010 4490 7.864108 TCGATATAAATTATGCATCCAAGGG 57.136 36.000 0.19 0.00 0.00 3.95
2011 4491 7.629157 TCGATATAAATTATGCATCCAAGGGA 58.371 34.615 0.19 0.00 35.55 4.20
2012 4492 7.770433 TCGATATAAATTATGCATCCAAGGGAG 59.230 37.037 0.19 0.00 34.05 4.30
2034 4570 7.381678 GGGAGTAGTACTATTTATGTCGCTTTG 59.618 40.741 5.75 0.00 0.00 2.77
2049 4585 3.118334 TCGCTTTGTCGGGGGAAAATATA 60.118 43.478 0.00 0.00 0.00 0.86
2050 4586 3.002965 CGCTTTGTCGGGGGAAAATATAC 59.997 47.826 0.00 0.00 0.00 1.47
2052 4588 4.788679 CTTTGTCGGGGGAAAATATACCT 58.211 43.478 0.00 0.00 0.00 3.08
2053 4589 4.426736 TTGTCGGGGGAAAATATACCTC 57.573 45.455 0.00 0.00 0.00 3.85
2065 4604 4.431416 AATATACCTCCCGTGATTTGCA 57.569 40.909 0.00 0.00 0.00 4.08
2099 4638 7.000472 ACCTATGATTGAAATGGAATCACGAT 59.000 34.615 0.00 0.00 41.46 3.73
2100 4639 7.173907 ACCTATGATTGAAATGGAATCACGATC 59.826 37.037 0.00 0.00 41.46 3.69
2101 4640 6.947644 ATGATTGAAATGGAATCACGATCA 57.052 33.333 0.00 0.00 41.46 2.92
2102 4641 6.947644 TGATTGAAATGGAATCACGATCAT 57.052 33.333 0.00 0.00 35.38 2.45
2103 4642 6.731164 TGATTGAAATGGAATCACGATCATG 58.269 36.000 0.00 0.00 35.38 3.07
2104 4643 4.556942 TGAAATGGAATCACGATCATGC 57.443 40.909 0.00 0.00 0.00 4.06
2105 4644 3.946558 TGAAATGGAATCACGATCATGCA 59.053 39.130 0.00 0.00 0.00 3.96
2106 4645 4.581409 TGAAATGGAATCACGATCATGCAT 59.419 37.500 0.00 0.00 0.00 3.96
2132 4671 0.242825 TAAGCGTCGGTCAGGTGAAG 59.757 55.000 0.00 0.00 0.00 3.02
2171 4710 1.003355 CCACAGCAGTTGGATCCGT 60.003 57.895 7.39 0.00 0.00 4.69
2375 4933 6.371825 GGGTTGGTCTCATTTTAAGTACTCTG 59.628 42.308 0.00 0.00 0.00 3.35
2376 4934 7.159372 GGTTGGTCTCATTTTAAGTACTCTGA 58.841 38.462 0.00 0.00 0.00 3.27
2377 4935 7.332182 GGTTGGTCTCATTTTAAGTACTCTGAG 59.668 40.741 2.45 2.45 33.16 3.35
2400 4958 9.466497 TGAGAAAAATAATGTTGCTCTAGGAAT 57.534 29.630 0.00 0.00 0.00 3.01
2546 5106 3.202906 GCACTCGAGGGTTTGCAATATA 58.797 45.455 17.64 0.00 34.97 0.86
2548 5108 3.809832 CACTCGAGGGTTTGCAATATAGG 59.190 47.826 18.41 0.00 0.00 2.57
2555 5115 5.518865 AGGGTTTGCAATATAGGTCATGTT 58.481 37.500 0.00 0.00 0.00 2.71
2592 5152 3.959943 ACCTTCAAAACATTTTCGACCG 58.040 40.909 0.00 0.00 0.00 4.79
2665 5225 1.964608 CTCCTCATGCCTCCTCGCAA 61.965 60.000 0.00 0.00 43.24 4.85
2672 5232 2.651361 CCTCCTCGCAAGTGACGT 59.349 61.111 0.00 0.00 39.48 4.34
2723 5283 2.763645 AACCGCACCCCAGAAACCT 61.764 57.895 0.00 0.00 0.00 3.50
2790 5358 1.563435 CGCCATTGCCTGCTATCTCG 61.563 60.000 0.00 0.00 0.00 4.04
2792 5360 0.604780 CCATTGCCTGCTATCTCGGG 60.605 60.000 0.00 0.00 35.57 5.14
2816 5384 5.450550 GCCCTCCCGATTTGAAGAAAATAAG 60.451 44.000 0.00 0.00 38.64 1.73
2830 5398 5.325239 AGAAAATAAGGAGAAAGGGTGTGG 58.675 41.667 0.00 0.00 0.00 4.17
2833 5401 1.760405 AAGGAGAAAGGGTGTGGGAT 58.240 50.000 0.00 0.00 0.00 3.85
2835 5403 0.698818 GGAGAAAGGGTGTGGGATGT 59.301 55.000 0.00 0.00 0.00 3.06
2836 5404 1.340114 GGAGAAAGGGTGTGGGATGTC 60.340 57.143 0.00 0.00 0.00 3.06
2843 5411 3.770040 TGTGGGATGTCGAGGCCG 61.770 66.667 0.00 0.00 37.07 6.13
2859 5427 2.202690 CGCCGCCGTAGATCACAA 60.203 61.111 0.00 0.00 0.00 3.33
2862 5430 1.216977 CCGCCGTAGATCACAACCA 59.783 57.895 0.00 0.00 0.00 3.67
2916 5484 2.780595 GGGACCCATGTCATTGTCG 58.219 57.895 5.33 0.00 43.65 4.35
2921 5489 1.061411 CCATGTCATTGTCGCAGCG 59.939 57.895 9.06 9.06 0.00 5.18
2927 5495 2.203070 ATTGTCGCAGCGGGATCC 60.203 61.111 16.42 1.92 0.00 3.36
2929 5497 2.535485 ATTGTCGCAGCGGGATCCAA 62.535 55.000 16.42 10.55 0.00 3.53
2931 5499 4.812476 TCGCAGCGGGATCCAACG 62.812 66.667 16.42 10.17 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.813166 TGCAGACTAAAAAGAAACGGAGG 59.187 43.478 0.00 0.00 0.00 4.30
1 2 5.613358 ATGCAGACTAAAAAGAAACGGAG 57.387 39.130 0.00 0.00 0.00 4.63
2 3 8.780846 TTATATGCAGACTAAAAAGAAACGGA 57.219 30.769 0.00 0.00 0.00 4.69
3 4 8.879759 TCTTATATGCAGACTAAAAAGAAACGG 58.120 33.333 0.00 0.00 0.00 4.44
158 159 9.944663 GATCAACTTTGTAAAACAACATCTACA 57.055 29.630 0.00 0.00 37.90 2.74
159 160 9.944663 TGATCAACTTTGTAAAACAACATCTAC 57.055 29.630 0.00 0.00 37.90 2.59
161 162 9.868277 TTTGATCAACTTTGTAAAACAACATCT 57.132 25.926 7.89 0.00 37.90 2.90
162 163 9.900264 GTTTGATCAACTTTGTAAAACAACATC 57.100 29.630 7.89 0.00 37.90 3.06
163 164 9.651913 AGTTTGATCAACTTTGTAAAACAACAT 57.348 25.926 7.89 0.00 43.89 2.71
186 187 4.923281 GTCAAAGTCAAACTGTGCAAAGTT 59.077 37.500 16.88 16.88 42.21 2.66
187 188 4.485163 GTCAAAGTCAAACTGTGCAAAGT 58.515 39.130 2.82 2.82 33.44 2.66
188 189 3.859386 GGTCAAAGTCAAACTGTGCAAAG 59.141 43.478 1.09 1.09 33.44 2.77
189 190 3.256879 TGGTCAAAGTCAAACTGTGCAAA 59.743 39.130 0.00 0.00 33.44 3.68
190 191 2.822561 TGGTCAAAGTCAAACTGTGCAA 59.177 40.909 0.00 0.00 33.44 4.08
191 192 2.441410 TGGTCAAAGTCAAACTGTGCA 58.559 42.857 0.00 0.00 33.44 4.57
192 193 3.502191 TTGGTCAAAGTCAAACTGTGC 57.498 42.857 0.00 0.00 33.44 4.57
193 194 5.894807 AGATTTGGTCAAAGTCAAACTGTG 58.105 37.500 2.55 0.00 34.73 3.66
194 195 6.071391 ACAAGATTTGGTCAAAGTCAAACTGT 60.071 34.615 2.55 0.00 35.97 3.55
195 196 6.332630 ACAAGATTTGGTCAAAGTCAAACTG 58.667 36.000 2.55 0.00 35.97 3.16
196 197 6.530019 ACAAGATTTGGTCAAAGTCAAACT 57.470 33.333 2.55 0.00 35.97 2.66
197 198 7.096065 GCATACAAGATTTGGTCAAAGTCAAAC 60.096 37.037 2.55 0.00 35.97 2.93
198 199 6.922957 GCATACAAGATTTGGTCAAAGTCAAA 59.077 34.615 2.55 0.00 37.29 2.69
199 200 6.040278 TGCATACAAGATTTGGTCAAAGTCAA 59.960 34.615 2.55 0.00 33.32 3.18
200 201 5.534278 TGCATACAAGATTTGGTCAAAGTCA 59.466 36.000 2.55 0.00 33.32 3.41
201 202 6.012658 TGCATACAAGATTTGGTCAAAGTC 57.987 37.500 2.55 1.51 33.32 3.01
202 203 6.403866 TTGCATACAAGATTTGGTCAAAGT 57.596 33.333 2.55 0.00 33.32 2.66
203 204 7.894376 ATTTGCATACAAGATTTGGTCAAAG 57.106 32.000 2.55 0.00 37.04 2.77
204 205 9.770097 TTAATTTGCATACAAGATTTGGTCAAA 57.230 25.926 0.00 0.00 37.04 2.69
205 206 9.770097 TTTAATTTGCATACAAGATTTGGTCAA 57.230 25.926 0.00 0.00 37.04 3.18
206 207 9.770097 TTTTAATTTGCATACAAGATTTGGTCA 57.230 25.926 0.00 0.00 37.04 4.02
231 232 9.377238 AGATAGTAATATACTCCCTCCGTTTTT 57.623 33.333 0.00 0.00 40.14 1.94
232 233 8.953223 AGATAGTAATATACTCCCTCCGTTTT 57.047 34.615 0.00 0.00 40.14 2.43
233 234 8.953223 AAGATAGTAATATACTCCCTCCGTTT 57.047 34.615 0.00 0.00 40.14 3.60
234 235 8.168725 TGAAGATAGTAATATACTCCCTCCGTT 58.831 37.037 0.00 0.00 40.14 4.44
235 236 7.611079 GTGAAGATAGTAATATACTCCCTCCGT 59.389 40.741 0.00 0.00 40.14 4.69
236 237 7.610692 TGTGAAGATAGTAATATACTCCCTCCG 59.389 40.741 0.00 0.00 40.14 4.63
237 238 8.880991 TGTGAAGATAGTAATATACTCCCTCC 57.119 38.462 0.00 0.00 40.14 4.30
238 239 9.523168 ACTGTGAAGATAGTAATATACTCCCTC 57.477 37.037 0.00 0.00 40.14 4.30
239 240 9.303116 CACTGTGAAGATAGTAATATACTCCCT 57.697 37.037 0.32 0.00 40.14 4.20
240 241 9.298250 TCACTGTGAAGATAGTAATATACTCCC 57.702 37.037 8.27 0.00 40.14 4.30
243 244 9.869667 ACCTCACTGTGAAGATAGTAATATACT 57.130 33.333 13.08 0.00 42.68 2.12
246 247 9.869667 AGTACCTCACTGTGAAGATAGTAATAT 57.130 33.333 13.08 0.00 35.62 1.28
248 249 9.122779 GTAGTACCTCACTGTGAAGATAGTAAT 57.877 37.037 13.08 10.26 38.24 1.89
249 250 7.555554 GGTAGTACCTCACTGTGAAGATAGTAA 59.444 40.741 12.41 0.00 38.24 2.24
250 251 7.052873 GGTAGTACCTCACTGTGAAGATAGTA 58.947 42.308 12.41 9.00 38.24 1.82
251 252 5.887035 GGTAGTACCTCACTGTGAAGATAGT 59.113 44.000 12.41 9.83 38.24 2.12
252 253 6.380095 GGTAGTACCTCACTGTGAAGATAG 57.620 45.833 12.41 0.50 38.24 2.08
267 268 1.844687 ACTTGGACGGAGGTAGTACC 58.155 55.000 11.73 11.73 38.99 3.34
268 269 3.949842 AAACTTGGACGGAGGTAGTAC 57.050 47.619 0.00 0.00 0.00 2.73
269 270 6.267471 TCTTTTAAACTTGGACGGAGGTAGTA 59.733 38.462 0.00 0.00 0.00 1.82
270 271 4.961438 TTTAAACTTGGACGGAGGTAGT 57.039 40.909 0.00 0.00 0.00 2.73
271 272 5.407691 GTCTTTTAAACTTGGACGGAGGTAG 59.592 44.000 0.00 0.00 0.00 3.18
272 273 5.299949 GTCTTTTAAACTTGGACGGAGGTA 58.700 41.667 0.00 0.00 0.00 3.08
273 274 4.132336 GTCTTTTAAACTTGGACGGAGGT 58.868 43.478 0.00 0.00 0.00 3.85
274 275 3.501062 GGTCTTTTAAACTTGGACGGAGG 59.499 47.826 0.00 0.00 0.00 4.30
275 276 3.501062 GGGTCTTTTAAACTTGGACGGAG 59.499 47.826 0.00 0.00 0.00 4.63
276 277 3.479489 GGGTCTTTTAAACTTGGACGGA 58.521 45.455 0.00 0.00 0.00 4.69
277 278 2.224784 CGGGTCTTTTAAACTTGGACGG 59.775 50.000 0.00 0.00 0.00 4.79
278 279 2.874086 ACGGGTCTTTTAAACTTGGACG 59.126 45.455 0.00 0.00 0.00 4.79
279 280 3.878699 TGACGGGTCTTTTAAACTTGGAC 59.121 43.478 0.00 0.00 0.00 4.02
280 281 4.131596 CTGACGGGTCTTTTAAACTTGGA 58.868 43.478 0.00 0.00 0.00 3.53
281 282 3.304458 GCTGACGGGTCTTTTAAACTTGG 60.304 47.826 0.00 0.00 0.00 3.61
282 283 3.564225 AGCTGACGGGTCTTTTAAACTTG 59.436 43.478 0.00 0.00 0.00 3.16
283 284 3.816994 AGCTGACGGGTCTTTTAAACTT 58.183 40.909 0.00 0.00 0.00 2.66
284 285 3.487120 AGCTGACGGGTCTTTTAAACT 57.513 42.857 0.00 0.00 0.00 2.66
285 286 4.694037 ACATAGCTGACGGGTCTTTTAAAC 59.306 41.667 0.00 0.00 0.00 2.01
286 287 4.901868 ACATAGCTGACGGGTCTTTTAAA 58.098 39.130 0.00 0.00 0.00 1.52
287 288 4.546829 ACATAGCTGACGGGTCTTTTAA 57.453 40.909 0.00 0.00 0.00 1.52
288 289 4.546829 AACATAGCTGACGGGTCTTTTA 57.453 40.909 0.00 0.00 0.00 1.52
289 290 3.418684 AACATAGCTGACGGGTCTTTT 57.581 42.857 0.00 0.00 0.00 2.27
290 291 3.514309 AGTAACATAGCTGACGGGTCTTT 59.486 43.478 0.00 0.00 0.00 2.52
291 292 3.097614 AGTAACATAGCTGACGGGTCTT 58.902 45.455 0.00 0.00 0.00 3.01
292 293 2.688958 GAGTAACATAGCTGACGGGTCT 59.311 50.000 0.00 0.00 0.00 3.85
293 294 2.426024 TGAGTAACATAGCTGACGGGTC 59.574 50.000 0.00 0.00 0.00 4.46
294 295 2.165845 GTGAGTAACATAGCTGACGGGT 59.834 50.000 0.00 0.00 0.00 5.28
295 296 2.165641 TGTGAGTAACATAGCTGACGGG 59.834 50.000 0.00 0.00 32.36 5.28
296 297 3.503827 TGTGAGTAACATAGCTGACGG 57.496 47.619 0.00 0.00 32.36 4.79
306 307 8.579863 CATGATACTATCTCCATGTGAGTAACA 58.420 37.037 9.98 6.62 44.79 2.41
307 308 7.543868 GCATGATACTATCTCCATGTGAGTAAC 59.456 40.741 0.00 2.31 42.12 2.50
308 309 7.233348 TGCATGATACTATCTCCATGTGAGTAA 59.767 37.037 0.00 1.66 42.12 2.24
309 310 6.721208 TGCATGATACTATCTCCATGTGAGTA 59.279 38.462 0.00 2.71 42.12 2.59
310 311 5.541484 TGCATGATACTATCTCCATGTGAGT 59.459 40.000 0.00 0.84 42.12 3.41
311 312 6.034161 TGCATGATACTATCTCCATGTGAG 57.966 41.667 0.00 5.18 42.90 3.51
312 313 6.183360 TGTTGCATGATACTATCTCCATGTGA 60.183 38.462 0.00 0.00 38.78 3.58
313 314 5.993441 TGTTGCATGATACTATCTCCATGTG 59.007 40.000 0.00 0.00 38.78 3.21
314 315 5.994054 GTGTTGCATGATACTATCTCCATGT 59.006 40.000 0.00 0.00 38.78 3.21
315 316 6.228995 AGTGTTGCATGATACTATCTCCATG 58.771 40.000 0.00 0.00 39.35 3.66
353 355 8.045507 ACACATATCAAGACAAGATGAATCTGT 58.954 33.333 0.00 0.00 37.19 3.41
354 356 8.336080 CACACATATCAAGACAAGATGAATCTG 58.664 37.037 0.00 0.00 37.19 2.90
670 1239 0.038526 TCGCCGGAAGACTGAGTTTC 60.039 55.000 5.05 0.00 0.00 2.78
697 1266 1.326548 CGGGCGTTTCTATACTGTTGC 59.673 52.381 0.00 0.00 0.00 4.17
701 1270 1.567504 CACCGGGCGTTTCTATACTG 58.432 55.000 6.32 0.00 0.00 2.74
764 1336 1.449601 GACAACCATCGCCGACCAT 60.450 57.895 0.00 0.00 0.00 3.55
883 1460 4.774586 CGCCACTGATTAAACGTGTTTAA 58.225 39.130 17.42 17.42 45.56 1.52
957 3428 6.067350 ACTTGTACTAGTATACTACCCTGCC 58.933 44.000 8.27 0.00 0.00 4.85
1015 3486 1.580845 GCAGCTGCAGGAACGACATT 61.581 55.000 33.36 0.00 41.59 2.71
1029 3500 1.067495 GTCTCGTACTTCCTTGCAGCT 60.067 52.381 0.00 0.00 0.00 4.24
1082 3553 9.902196 CACGGTATAAAAACAGGAAAAAGTAAT 57.098 29.630 0.00 0.00 0.00 1.89
1083 3554 8.901793 ACACGGTATAAAAACAGGAAAAAGTAA 58.098 29.630 0.00 0.00 0.00 2.24
1084 3555 8.449251 ACACGGTATAAAAACAGGAAAAAGTA 57.551 30.769 0.00 0.00 0.00 2.24
1085 3556 7.337480 ACACGGTATAAAAACAGGAAAAAGT 57.663 32.000 0.00 0.00 0.00 2.66
1086 3557 8.776470 TCTACACGGTATAAAAACAGGAAAAAG 58.224 33.333 0.00 0.00 0.00 2.27
1087 3558 8.674263 TCTACACGGTATAAAAACAGGAAAAA 57.326 30.769 0.00 0.00 0.00 1.94
1088 3559 8.851541 ATCTACACGGTATAAAAACAGGAAAA 57.148 30.769 0.00 0.00 0.00 2.29
1089 3560 9.369904 GTATCTACACGGTATAAAAACAGGAAA 57.630 33.333 0.00 0.00 0.00 3.13
1090 3561 8.752187 AGTATCTACACGGTATAAAAACAGGAA 58.248 33.333 0.00 0.00 0.00 3.36
1091 3562 8.297470 AGTATCTACACGGTATAAAAACAGGA 57.703 34.615 0.00 0.00 0.00 3.86
1092 3563 8.814235 CAAGTATCTACACGGTATAAAAACAGG 58.186 37.037 0.00 0.00 0.00 4.00
1093 3564 8.325997 GCAAGTATCTACACGGTATAAAAACAG 58.674 37.037 0.00 0.00 0.00 3.16
1094 3565 8.036575 AGCAAGTATCTACACGGTATAAAAACA 58.963 33.333 0.00 0.00 0.00 2.83
1101 3572 6.896021 ACATAGCAAGTATCTACACGGTAT 57.104 37.500 0.00 0.00 0.00 2.73
1110 3581 9.730705 AATTACATGCATACATAGCAAGTATCT 57.269 29.630 0.00 0.00 46.27 1.98
1116 3587 5.562501 CGCCAATTACATGCATACATAGCAA 60.563 40.000 0.00 0.00 46.27 3.91
1118 3589 4.406069 CGCCAATTACATGCATACATAGC 58.594 43.478 0.00 0.00 33.67 2.97
1119 3590 4.083377 TGCGCCAATTACATGCATACATAG 60.083 41.667 4.18 0.00 33.67 2.23
1160 3639 4.615912 GCACATGACAAATTAACCTTCGCT 60.616 41.667 0.00 0.00 0.00 4.93
1162 3641 3.845775 CGCACATGACAAATTAACCTTCG 59.154 43.478 0.00 0.00 0.00 3.79
1165 3644 4.757657 TGTACGCACATGACAAATTAACCT 59.242 37.500 0.00 0.00 0.00 3.50
1188 3667 3.866379 TTGCCGTCCAGCCTGCAAT 62.866 57.895 0.00 0.00 38.68 3.56
1372 3851 3.053849 GACGTCCTCCTCGCTGGTC 62.054 68.421 3.51 0.00 37.07 4.02
1377 3856 4.477975 CCACGACGTCCTCCTCGC 62.478 72.222 10.58 0.00 32.98 5.03
1378 3857 4.477975 GCCACGACGTCCTCCTCG 62.478 72.222 10.58 0.00 35.96 4.63
1483 3962 2.847234 TCCTTGGTGCTGTCCCGT 60.847 61.111 0.00 0.00 0.00 5.28
1862 4341 2.048127 GAGAAAGAGCACGGCGGT 60.048 61.111 13.24 0.00 0.00 5.68
1991 4470 7.759607 ACTACTCCCTTGGATGCATAATTTAT 58.240 34.615 0.00 0.00 0.00 1.40
1996 4476 5.216622 AGTACTACTCCCTTGGATGCATAA 58.783 41.667 0.00 0.00 0.00 1.90
2010 4490 8.853469 ACAAAGCGACATAAATAGTACTACTC 57.147 34.615 4.31 0.00 0.00 2.59
2011 4491 7.642978 CGACAAAGCGACATAAATAGTACTACT 59.357 37.037 4.31 0.00 0.00 2.57
2012 4492 7.096722 CCGACAAAGCGACATAAATAGTACTAC 60.097 40.741 4.31 0.00 0.00 2.73
2034 4570 2.039480 GGGAGGTATATTTTCCCCCGAC 59.961 54.545 7.57 0.00 43.98 4.79
2049 4585 0.609131 CCTTGCAAATCACGGGAGGT 60.609 55.000 0.00 0.00 30.91 3.85
2050 4586 2.183409 CCTTGCAAATCACGGGAGG 58.817 57.895 0.00 0.00 30.91 4.30
2065 4604 6.324770 CCATTTCAATCATAGGTAAAGCCCTT 59.675 38.462 0.00 0.00 38.26 3.95
2104 4643 1.258982 GACCGACGCTTAGCATGAATG 59.741 52.381 4.70 0.00 0.00 2.67
2105 4644 1.134818 TGACCGACGCTTAGCATGAAT 60.135 47.619 4.70 0.00 0.00 2.57
2106 4645 0.245266 TGACCGACGCTTAGCATGAA 59.755 50.000 4.70 0.00 0.00 2.57
2132 4671 2.574399 GGCCTATCCGATCCGCTC 59.426 66.667 0.00 0.00 0.00 5.03
2171 4710 4.733371 TCGATGGCTGTTGCGCGA 62.733 61.111 12.10 0.00 40.82 5.87
2264 4803 4.162690 GTACGGGCTGGGAGCTGG 62.163 72.222 0.00 0.00 41.99 4.85
2350 4908 6.371825 CAGAGTACTTAAAATGAGACCAACCC 59.628 42.308 0.00 0.00 0.00 4.11
2400 4958 3.501828 AGCGCATGTCTCATGTTACAAAA 59.498 39.130 11.47 0.00 0.00 2.44
2451 5009 2.642427 ACAAGCGCAACATGGATCATA 58.358 42.857 11.47 0.00 0.00 2.15
2546 5106 2.029288 CGCGAGTGCAACATGACCT 61.029 57.895 0.00 0.00 42.97 3.85
2548 5108 0.443869 AATCGCGAGTGCAACATGAC 59.556 50.000 16.66 0.00 42.97 3.06
2592 5152 2.223386 ACAACATACCACACGTTGCAAC 60.223 45.455 19.89 19.89 42.98 4.17
2672 5232 1.268352 GTGGCGTGCTATTGGTGAAAA 59.732 47.619 0.00 0.00 0.00 2.29
2723 5283 2.268920 GCGATCCCTTGCTCCACA 59.731 61.111 0.00 0.00 0.00 4.17
2776 5336 2.505982 GCCCGAGATAGCAGGCAA 59.494 61.111 2.23 0.00 45.07 4.52
2792 5360 1.834188 TTTCTTCAAATCGGGAGGGC 58.166 50.000 0.00 0.00 0.00 5.19
2816 5384 0.698818 ACATCCCACACCCTTTCTCC 59.301 55.000 0.00 0.00 0.00 3.71
2843 5411 2.171725 GGTTGTGATCTACGGCGGC 61.172 63.158 13.24 0.00 0.00 6.53
2859 5427 0.471591 ACCACATTGGGCACATTGGT 60.472 50.000 14.91 12.81 43.37 3.67
2862 5430 1.070445 CACAACCACATTGGGCACATT 59.930 47.619 0.00 0.00 43.37 2.71


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

AutoCloner maintained by Alex Coulton.