Multiple sequence alignment - TraesCS7D01G201200

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 TraesCS7D01G201200 chr7D 100.000 2843 0 0 1 2843 160432761 160435603 0.000000e+00 5251
1 TraesCS7D01G201200 chr7D 92.327 404 31 0 1 404 23556839 23557242 2.460000e-160 575
2 TraesCS7D01G201200 chr7D 91.089 404 36 0 1 404 51201175 51200772 5.350000e-152 547
3 TraesCS7D01G201200 chr7B 96.012 2407 77 12 450 2842 120852615 120855016 0.000000e+00 3895
4 TraesCS7D01G201200 chr7A 96.054 1191 38 1 1661 2842 161215941 161217131 0.000000e+00 1930
5 TraesCS7D01G201200 chr7A 95.425 459 17 2 931 1389 161208898 161209352 0.000000e+00 728
6 TraesCS7D01G201200 chr7A 90.661 514 34 7 424 924 161208319 161208831 0.000000e+00 671
7 TraesCS7D01G201200 chr1D 92.327 404 31 0 1 404 408413100 408412697 2.460000e-160 575
8 TraesCS7D01G201200 chr1D 91.089 404 35 1 1 404 300632930 300633332 1.930000e-151 545
9 TraesCS7D01G201200 chr1D 89.647 425 40 4 1 424 408826022 408826443 3.220000e-149 538
10 TraesCS7D01G201200 chr1D 74.848 493 115 8 2354 2842 415402762 415403249 6.170000e-52 215
11 TraesCS7D01G201200 chr4D 92.079 404 32 0 1 404 502490784 502491187 1.140000e-158 569
12 TraesCS7D01G201200 chr3D 92.079 404 32 0 1 404 506000171 506000574 1.140000e-158 569
13 TraesCS7D01G201200 chr5D 91.089 404 36 0 1 404 30944218 30943815 5.350000e-152 547
14 TraesCS7D01G201200 chr5D 91.089 404 36 0 1 404 374655931 374655528 5.350000e-152 547
15 TraesCS7D01G201200 chr5D 75.400 874 177 28 979 1843 559915690 559916534 3.430000e-104 388
16 TraesCS7D01G201200 chr5D 76.686 519 106 14 2323 2832 558718883 558719395 1.000000e-69 274
17 TraesCS7D01G201200 chr5B 76.591 487 101 9 2352 2832 695550481 695550960 3.630000e-64 255
18 TraesCS7D01G201200 chr1B 76.268 493 108 8 2354 2842 561700257 561700744 1.310000e-63 254


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 TraesCS7D01G201200 chr7D 160432761 160435603 2842 False 5251.0 5251 100.000 1 2843 1 chr7D.!!$F2 2842
1 TraesCS7D01G201200 chr7B 120852615 120855016 2401 False 3895.0 3895 96.012 450 2842 1 chr7B.!!$F1 2392
2 TraesCS7D01G201200 chr7A 161215941 161217131 1190 False 1930.0 1930 96.054 1661 2842 1 chr7A.!!$F1 1181
3 TraesCS7D01G201200 chr7A 161208319 161209352 1033 False 699.5 728 93.043 424 1389 2 chr7A.!!$F2 965
4 TraesCS7D01G201200 chr5D 559915690 559916534 844 False 388.0 388 75.400 979 1843 1 chr5D.!!$F2 864
5 TraesCS7D01G201200 chr5D 558718883 558719395 512 False 274.0 274 76.686 2323 2832 1 chr5D.!!$F1 509

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
362 363 0.030908 GGTGGCGAGGATCTAGTTCG 59.969 60.0 0.00 0.0 37.40 3.95 F
365 366 0.039888 GGCGAGGATCTAGTTCGAGC 60.040 60.0 11.59 0.0 36.49 5.03 F
376 377 0.108138 AGTTCGAGCGAAATCCCTGG 60.108 55.0 6.91 0.0 35.75 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1583 1664 0.102300 AGACAAAAACCTGCAACGCC 59.898 50.000 0.00 0.00 0.00 5.68 R
1594 1675 7.500559 CCCACCAAATCCAAAAATAGACAAAAA 59.499 33.333 0.00 0.00 0.00 1.94 R
2205 2296 7.939386 GCAATTTTATCGCTGCGTAAAATTATC 59.061 33.333 34.43 29.26 43.34 1.75 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
53 54 3.302344 CAAACCCGGGGTGCCAAG 61.302 66.667 27.92 2.78 35.34 3.61
54 55 4.614036 AAACCCGGGGTGCCAAGG 62.614 66.667 27.92 0.00 35.34 3.61
57 58 4.820744 CCCGGGGTGCCAAGGATG 62.821 72.222 14.71 0.00 0.00 3.51
87 88 4.785453 CCTCGGTTGCCCTGCCTC 62.785 72.222 0.00 0.00 0.00 4.70
88 89 3.710722 CTCGGTTGCCCTGCCTCT 61.711 66.667 0.00 0.00 0.00 3.69
89 90 3.965539 CTCGGTTGCCCTGCCTCTG 62.966 68.421 0.00 0.00 0.00 3.35
98 99 4.020617 CTGCCTCTGCGTGGGGAA 62.021 66.667 0.00 0.00 41.78 3.97
99 100 4.329545 TGCCTCTGCGTGGGGAAC 62.330 66.667 0.00 0.00 41.78 3.62
112 113 3.231298 GGAACCCCGGATCTGGAG 58.769 66.667 23.02 11.90 0.00 3.86
113 114 2.506472 GAACCCCGGATCTGGAGC 59.494 66.667 23.02 4.29 0.00 4.70
114 115 2.285368 AACCCCGGATCTGGAGCA 60.285 61.111 23.02 0.00 0.00 4.26
115 116 2.317149 GAACCCCGGATCTGGAGCAG 62.317 65.000 23.02 9.90 0.00 4.24
116 117 4.247380 CCCCGGATCTGGAGCAGC 62.247 72.222 23.02 0.00 0.00 5.25
117 118 4.598894 CCCGGATCTGGAGCAGCG 62.599 72.222 23.02 0.00 0.00 5.18
118 119 4.598894 CCGGATCTGGAGCAGCGG 62.599 72.222 16.28 1.07 31.04 5.52
130 131 3.515286 CAGCGGCTCCATTGGCAG 61.515 66.667 0.00 0.00 0.00 4.85
131 132 4.809496 AGCGGCTCCATTGGCAGG 62.809 66.667 0.00 0.00 0.00 4.85
134 135 4.764771 GGCTCCATTGGCAGGGCA 62.765 66.667 0.00 0.00 0.00 5.36
135 136 3.455469 GCTCCATTGGCAGGGCAC 61.455 66.667 0.00 0.00 0.00 5.01
136 137 3.136123 CTCCATTGGCAGGGCACG 61.136 66.667 0.00 0.00 0.00 5.34
137 138 4.738998 TCCATTGGCAGGGCACGG 62.739 66.667 0.00 0.00 0.00 4.94
175 176 4.530857 CGGTGGATCTGGCGTCCC 62.531 72.222 0.00 0.00 34.76 4.46
176 177 4.530857 GGTGGATCTGGCGTCCCG 62.531 72.222 0.00 0.00 34.76 5.14
177 178 4.530857 GTGGATCTGGCGTCCCGG 62.531 72.222 0.00 0.00 38.98 5.73
208 209 4.438346 GGGATCCGATGGTCGTTG 57.562 61.111 5.45 0.00 38.40 4.10
209 210 1.227556 GGGATCCGATGGTCGTTGG 60.228 63.158 5.45 0.00 38.40 3.77
210 211 1.887707 GGATCCGATGGTCGTTGGC 60.888 63.158 0.00 0.00 38.40 4.52
211 212 2.202878 ATCCGATGGTCGTTGGCG 60.203 61.111 0.00 0.00 38.40 5.69
212 213 3.733344 ATCCGATGGTCGTTGGCGG 62.733 63.158 0.00 0.00 43.11 6.13
250 251 4.796231 GGTCGGTGCGCGTGATCT 62.796 66.667 8.43 0.00 0.00 2.75
251 252 3.545481 GTCGGTGCGCGTGATCTG 61.545 66.667 8.43 1.20 0.00 2.90
252 253 4.794439 TCGGTGCGCGTGATCTGG 62.794 66.667 8.43 0.00 0.00 3.86
259 260 3.567797 GCGTGATCTGGCGCCTTC 61.568 66.667 29.70 21.11 46.93 3.46
260 261 2.892425 CGTGATCTGGCGCCTTCC 60.892 66.667 29.70 14.38 0.00 3.46
261 262 2.514824 GTGATCTGGCGCCTTCCC 60.515 66.667 29.70 14.76 0.00 3.97
262 263 2.688666 TGATCTGGCGCCTTCCCT 60.689 61.111 29.70 7.68 0.00 4.20
263 264 2.110006 GATCTGGCGCCTTCCCTC 59.890 66.667 29.70 13.15 0.00 4.30
264 265 3.468326 GATCTGGCGCCTTCCCTCC 62.468 68.421 29.70 6.48 0.00 4.30
265 266 4.722535 TCTGGCGCCTTCCCTCCT 62.723 66.667 29.70 0.00 0.00 3.69
266 267 4.168291 CTGGCGCCTTCCCTCCTC 62.168 72.222 29.70 0.00 0.00 3.71
270 271 4.806339 CGCCTTCCCTCCTCCCCT 62.806 72.222 0.00 0.00 0.00 4.79
271 272 2.703430 GCCTTCCCTCCTCCCCTA 59.297 66.667 0.00 0.00 0.00 3.53
272 273 1.240428 GCCTTCCCTCCTCCCCTAT 59.760 63.158 0.00 0.00 0.00 2.57
273 274 0.402126 GCCTTCCCTCCTCCCCTATT 60.402 60.000 0.00 0.00 0.00 1.73
274 275 1.735926 CCTTCCCTCCTCCCCTATTC 58.264 60.000 0.00 0.00 0.00 1.75
275 276 1.343069 CTTCCCTCCTCCCCTATTCG 58.657 60.000 0.00 0.00 0.00 3.34
276 277 0.105142 TTCCCTCCTCCCCTATTCGG 60.105 60.000 0.00 0.00 0.00 4.30
277 278 2.217745 CCCTCCTCCCCTATTCGGC 61.218 68.421 0.00 0.00 0.00 5.54
278 279 2.574955 CCTCCTCCCCTATTCGGCG 61.575 68.421 0.00 0.00 0.00 6.46
279 280 1.833049 CTCCTCCCCTATTCGGCGT 60.833 63.158 6.85 0.00 0.00 5.68
280 281 2.088674 CTCCTCCCCTATTCGGCGTG 62.089 65.000 6.85 0.00 0.00 5.34
281 282 2.280186 CTCCCCTATTCGGCGTGC 60.280 66.667 6.85 0.00 0.00 5.34
282 283 4.215742 TCCCCTATTCGGCGTGCG 62.216 66.667 6.85 0.00 0.00 5.34
295 296 4.840005 GTGCGGGCCAGCCTAGTC 62.840 72.222 25.66 6.86 36.02 2.59
300 301 3.851128 GGCCAGCCTAGTCGGGTC 61.851 72.222 0.00 0.00 42.98 4.46
301 302 4.208686 GCCAGCCTAGTCGGGTCG 62.209 72.222 0.00 0.00 42.98 4.79
302 303 4.208686 CCAGCCTAGTCGGGTCGC 62.209 72.222 0.00 0.00 42.98 5.19
303 304 4.554363 CAGCCTAGTCGGGTCGCG 62.554 72.222 0.00 0.00 42.98 5.87
306 307 3.823330 CCTAGTCGGGTCGCGCTT 61.823 66.667 5.56 0.00 0.00 4.68
307 308 2.181021 CTAGTCGGGTCGCGCTTT 59.819 61.111 5.56 0.00 0.00 3.51
308 309 1.872679 CTAGTCGGGTCGCGCTTTC 60.873 63.158 5.56 0.00 0.00 2.62
309 310 2.267681 CTAGTCGGGTCGCGCTTTCT 62.268 60.000 5.56 3.46 0.00 2.52
310 311 2.262471 TAGTCGGGTCGCGCTTTCTC 62.262 60.000 5.56 0.00 0.00 2.87
311 312 3.371063 TCGGGTCGCGCTTTCTCT 61.371 61.111 5.56 0.00 0.00 3.10
312 313 2.432628 CGGGTCGCGCTTTCTCTT 60.433 61.111 5.56 0.00 0.00 2.85
313 314 2.730672 CGGGTCGCGCTTTCTCTTG 61.731 63.158 5.56 0.00 0.00 3.02
314 315 1.374252 GGGTCGCGCTTTCTCTTGA 60.374 57.895 5.56 0.00 0.00 3.02
315 316 0.741221 GGGTCGCGCTTTCTCTTGAT 60.741 55.000 5.56 0.00 0.00 2.57
316 317 0.647925 GGTCGCGCTTTCTCTTGATC 59.352 55.000 5.56 0.00 0.00 2.92
317 318 0.296056 GTCGCGCTTTCTCTTGATCG 59.704 55.000 5.56 0.00 0.00 3.69
318 319 1.012889 CGCGCTTTCTCTTGATCGC 60.013 57.895 5.56 0.00 39.26 4.58
319 320 1.349973 GCGCTTTCTCTTGATCGCC 59.650 57.895 0.00 0.00 37.02 5.54
320 321 1.633171 CGCTTTCTCTTGATCGCCG 59.367 57.895 0.00 0.00 0.00 6.46
321 322 1.756375 CGCTTTCTCTTGATCGCCGG 61.756 60.000 0.00 0.00 0.00 6.13
322 323 0.741221 GCTTTCTCTTGATCGCCGGT 60.741 55.000 1.90 0.00 0.00 5.28
323 324 1.726853 CTTTCTCTTGATCGCCGGTT 58.273 50.000 1.90 0.00 0.00 4.44
324 325 1.661112 CTTTCTCTTGATCGCCGGTTC 59.339 52.381 1.90 0.00 0.00 3.62
325 326 0.108329 TTCTCTTGATCGCCGGTTCC 60.108 55.000 1.90 0.00 0.00 3.62
326 327 1.878522 CTCTTGATCGCCGGTTCCG 60.879 63.158 1.90 4.08 0.00 4.30
327 328 2.125673 CTTGATCGCCGGTTCCGT 60.126 61.111 1.90 0.00 0.00 4.69
328 329 1.140161 CTTGATCGCCGGTTCCGTA 59.860 57.895 1.90 0.00 0.00 4.02
329 330 1.143969 CTTGATCGCCGGTTCCGTAC 61.144 60.000 1.90 1.45 0.00 3.67
330 331 1.875420 TTGATCGCCGGTTCCGTACA 61.875 55.000 1.90 0.84 0.00 2.90
331 332 1.588139 GATCGCCGGTTCCGTACAG 60.588 63.158 1.90 0.00 0.00 2.74
332 333 2.948840 GATCGCCGGTTCCGTACAGG 62.949 65.000 1.90 0.00 44.10 4.00
340 341 2.273123 TCCGTACAGGAGGCGCTA 59.727 61.111 7.64 0.00 45.98 4.26
341 342 2.117156 TCCGTACAGGAGGCGCTAC 61.117 63.158 7.64 0.00 45.98 3.58
342 343 2.119655 CCGTACAGGAGGCGCTACT 61.120 63.158 7.64 0.00 45.00 2.57
344 345 1.437986 GTACAGGAGGCGCTACTGG 59.562 63.158 23.11 8.83 46.09 4.00
345 346 1.000019 TACAGGAGGCGCTACTGGT 60.000 57.895 23.11 13.30 46.09 4.00
346 347 1.320344 TACAGGAGGCGCTACTGGTG 61.320 60.000 23.11 10.97 46.09 4.17
347 348 3.077556 AGGAGGCGCTACTGGTGG 61.078 66.667 7.64 0.00 0.00 4.61
354 355 3.221222 GCTACTGGTGGCGAGGAT 58.779 61.111 0.00 0.00 0.00 3.24
355 356 1.068250 GCTACTGGTGGCGAGGATC 59.932 63.158 0.00 0.00 0.00 3.36
356 357 1.395826 GCTACTGGTGGCGAGGATCT 61.396 60.000 0.00 0.00 0.00 2.75
357 358 1.982660 CTACTGGTGGCGAGGATCTA 58.017 55.000 0.00 0.00 0.00 1.98
358 359 1.883275 CTACTGGTGGCGAGGATCTAG 59.117 57.143 0.00 0.00 0.00 2.43
359 360 0.033011 ACTGGTGGCGAGGATCTAGT 60.033 55.000 0.00 0.00 0.00 2.57
360 361 1.115467 CTGGTGGCGAGGATCTAGTT 58.885 55.000 0.00 0.00 0.00 2.24
361 362 1.067821 CTGGTGGCGAGGATCTAGTTC 59.932 57.143 0.00 0.00 0.00 3.01
362 363 0.030908 GGTGGCGAGGATCTAGTTCG 59.969 60.000 0.00 0.00 37.40 3.95
363 364 1.022735 GTGGCGAGGATCTAGTTCGA 58.977 55.000 11.59 0.00 36.49 3.71
364 365 1.002251 GTGGCGAGGATCTAGTTCGAG 60.002 57.143 11.59 0.72 36.49 4.04
365 366 0.039888 GGCGAGGATCTAGTTCGAGC 60.040 60.000 11.59 0.00 36.49 5.03
366 367 0.384974 GCGAGGATCTAGTTCGAGCG 60.385 60.000 11.59 7.95 36.49 5.03
367 368 1.218763 CGAGGATCTAGTTCGAGCGA 58.781 55.000 0.00 0.00 36.49 4.93
368 369 1.598132 CGAGGATCTAGTTCGAGCGAA 59.402 52.381 0.55 0.55 36.49 4.70
369 370 2.031807 CGAGGATCTAGTTCGAGCGAAA 59.968 50.000 6.91 0.00 36.49 3.46
370 371 3.304123 CGAGGATCTAGTTCGAGCGAAAT 60.304 47.826 10.42 10.42 36.49 2.17
371 372 4.223659 GAGGATCTAGTTCGAGCGAAATC 58.776 47.826 8.90 7.50 35.75 2.17
372 373 3.004944 AGGATCTAGTTCGAGCGAAATCC 59.995 47.826 19.05 19.05 37.74 3.01
373 374 2.865343 TCTAGTTCGAGCGAAATCCC 57.135 50.000 8.90 0.00 35.75 3.85
374 375 2.376109 TCTAGTTCGAGCGAAATCCCT 58.624 47.619 8.90 4.10 35.75 4.20
375 376 2.099263 TCTAGTTCGAGCGAAATCCCTG 59.901 50.000 8.90 0.18 35.75 4.45
376 377 0.108138 AGTTCGAGCGAAATCCCTGG 60.108 55.000 6.91 0.00 35.75 4.45
377 378 1.449601 TTCGAGCGAAATCCCTGGC 60.450 57.895 2.42 0.00 0.00 4.85
378 379 2.869503 TTCGAGCGAAATCCCTGGCC 62.870 60.000 2.42 0.00 0.00 5.36
379 380 2.897350 GAGCGAAATCCCTGGCCG 60.897 66.667 0.00 0.00 0.00 6.13
380 381 4.489771 AGCGAAATCCCTGGCCGG 62.490 66.667 3.88 3.88 0.00 6.13
383 384 4.440829 GAAATCCCTGGCCGGCCA 62.441 66.667 44.03 44.03 45.02 5.36
384 385 3.738745 GAAATCCCTGGCCGGCCAT 62.739 63.158 46.65 32.12 46.15 4.40
385 386 4.528039 AATCCCTGGCCGGCCATG 62.528 66.667 46.65 40.94 46.15 3.66
415 416 3.839432 GACGGCCCCTCCTTCGAG 61.839 72.222 0.00 0.00 35.72 4.04
423 424 3.441290 CTCCTTCGAGGCGTCGGT 61.441 66.667 26.64 0.00 46.80 4.69
424 425 2.987547 TCCTTCGAGGCGTCGGTT 60.988 61.111 26.64 0.00 46.80 4.44
425 426 2.048503 CCTTCGAGGCGTCGGTTT 60.049 61.111 26.64 0.00 46.80 3.27
426 427 2.092882 CCTTCGAGGCGTCGGTTTC 61.093 63.158 26.64 0.00 46.80 2.78
446 447 1.936547 CGTGCCTATGGAAAAGCTCTC 59.063 52.381 0.00 0.00 0.00 3.20
448 449 1.134401 TGCCTATGGAAAAGCTCTCGG 60.134 52.381 0.00 0.00 0.00 4.63
453 454 0.973632 TGGAAAAGCTCTCGGCACTA 59.026 50.000 0.00 0.00 44.79 2.74
470 471 2.096980 CACTATCGTAGACTTGTGCGGA 59.903 50.000 0.01 0.00 42.51 5.54
474 475 1.421410 CGTAGACTTGTGCGGATGGC 61.421 60.000 0.00 0.00 43.96 4.40
480 481 2.191354 CTTGTGCGGATGGCTGTGTG 62.191 60.000 0.00 0.00 44.05 3.82
548 556 7.161773 AGAAAACATGATACTTGGTTGATGG 57.838 36.000 0.00 0.00 0.00 3.51
589 597 3.057526 TGCTCGATGGATATGTTACCGAG 60.058 47.826 0.00 0.00 43.14 4.63
611 619 7.664567 CGAGTCCTCGTAAACTAAGATTTTTC 58.335 38.462 8.50 0.00 46.99 2.29
633 641 3.812262 TGTCTGACCAATATGGCATCTG 58.188 45.455 1.65 2.60 42.67 2.90
780 792 4.713792 AAGAAATCAAGGTCCAGTCACT 57.286 40.909 0.00 0.00 0.00 3.41
822 834 3.562567 AAGCTTGTACTCTCACGACTC 57.437 47.619 0.00 0.00 0.00 3.36
839 851 2.816672 GACTCTTTTCTTTGGGAGCAGG 59.183 50.000 0.00 0.00 0.00 4.85
857 871 3.756117 CAGGAAAACTAAGGGCTCAGTT 58.244 45.455 0.00 0.00 36.56 3.16
951 1029 0.832135 TTGGTCGTCTCCCTGAGCTT 60.832 55.000 0.00 0.00 33.88 3.74
1023 1101 2.666190 GCTGTGGTGAGCGCTTCA 60.666 61.111 13.26 8.56 0.00 3.02
1353 1434 2.231478 TCGTCTGAAGACACTTGGATCC 59.769 50.000 4.20 4.20 44.99 3.36
1407 1488 3.508402 TCAAGGCTCGTGTTATGTCAGTA 59.492 43.478 0.00 0.00 0.00 2.74
1473 1554 2.225019 CACTTCTGGTCATGCAGTTGTC 59.775 50.000 0.00 0.00 0.00 3.18
1583 1664 1.286880 CGGAAAACAGCTTGGGCAG 59.713 57.895 0.00 0.00 41.70 4.85
1763 1844 1.303561 AAGTGCCATGCCACGATGT 60.304 52.632 0.46 0.00 40.59 3.06
1913 1994 7.490962 TTGAATGTATACCTAATTTCTGCCG 57.509 36.000 0.00 0.00 0.00 5.69
1919 2000 2.987232 ACCTAATTTCTGCCGAACTCC 58.013 47.619 0.00 0.00 0.00 3.85
1963 2044 3.829886 AATCCAGCGTGTTTGTATGTG 57.170 42.857 0.00 0.00 0.00 3.21
2074 2156 2.076100 ACCATTGTATGTGTCTGTGCG 58.924 47.619 0.00 0.00 0.00 5.34
2115 2206 0.371301 CGTGTGTGATCGCCATTCTG 59.629 55.000 3.31 0.00 0.00 3.02
2496 2592 3.243168 GCAAGCTCATGTTGTCAAGTTGA 60.243 43.478 0.08 0.08 0.00 3.18
2702 2798 6.166982 AGTAGACCAGCTGTAAGAAATGAAC 58.833 40.000 13.81 0.00 34.07 3.18
2740 2836 3.569701 AGTCGATTGGTTTTGCACTTGAT 59.430 39.130 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.302344 CTTGGCACCCCGGGTTTG 61.302 66.667 21.85 17.34 31.02 2.93
37 38 4.614036 CCTTGGCACCCCGGGTTT 62.614 66.667 21.85 2.04 31.02 3.27
40 41 4.820744 CATCCTTGGCACCCCGGG 62.821 72.222 15.80 15.80 0.00 5.73
41 42 4.820744 CCATCCTTGGCACCCCGG 62.821 72.222 0.00 0.00 35.85 5.73
81 82 4.020617 TTCCCCACGCAGAGGCAG 62.021 66.667 0.00 0.00 41.24 4.85
82 83 4.329545 GTTCCCCACGCAGAGGCA 62.330 66.667 0.00 0.00 41.24 4.75
84 85 4.410400 GGGTTCCCCACGCAGAGG 62.410 72.222 0.00 0.00 44.65 3.69
93 94 3.489513 CCAGATCCGGGGTTCCCC 61.490 72.222 16.52 16.52 41.57 4.81
94 95 2.366435 TCCAGATCCGGGGTTCCC 60.366 66.667 0.00 0.00 41.09 3.97
95 96 3.108288 GCTCCAGATCCGGGGTTCC 62.108 68.421 0.00 0.00 0.00 3.62
96 97 2.317149 CTGCTCCAGATCCGGGGTTC 62.317 65.000 0.00 0.00 32.44 3.62
97 98 2.285368 TGCTCCAGATCCGGGGTT 60.285 61.111 0.00 0.00 0.00 4.11
98 99 2.765807 CTGCTCCAGATCCGGGGT 60.766 66.667 0.00 0.00 32.44 4.95
99 100 4.247380 GCTGCTCCAGATCCGGGG 62.247 72.222 0.00 0.00 32.44 5.73
100 101 4.598894 CGCTGCTCCAGATCCGGG 62.599 72.222 0.00 0.00 32.44 5.73
101 102 4.598894 CCGCTGCTCCAGATCCGG 62.599 72.222 0.00 0.00 32.44 5.14
113 114 3.515286 CTGCCAATGGAGCCGCTG 61.515 66.667 2.05 0.00 0.00 5.18
114 115 4.809496 CCTGCCAATGGAGCCGCT 62.809 66.667 2.05 0.00 0.00 5.52
117 118 4.764771 TGCCCTGCCAATGGAGCC 62.765 66.667 2.05 0.00 0.00 4.70
118 119 3.455469 GTGCCCTGCCAATGGAGC 61.455 66.667 2.05 0.00 0.00 4.70
119 120 3.136123 CGTGCCCTGCCAATGGAG 61.136 66.667 2.05 0.00 0.00 3.86
120 121 4.738998 CCGTGCCCTGCCAATGGA 62.739 66.667 2.05 0.00 0.00 3.41
158 159 4.530857 GGGACGCCAGATCCACCG 62.531 72.222 0.00 0.00 38.06 4.94
191 192 1.227556 CCAACGACCATCGGATCCC 60.228 63.158 6.06 0.00 45.59 3.85
192 193 1.887707 GCCAACGACCATCGGATCC 60.888 63.158 0.00 0.00 45.59 3.36
193 194 2.237751 CGCCAACGACCATCGGATC 61.238 63.158 2.97 0.00 45.59 3.36
194 195 2.202878 CGCCAACGACCATCGGAT 60.203 61.111 2.97 0.00 45.59 4.18
195 196 4.444838 CCGCCAACGACCATCGGA 62.445 66.667 2.97 0.00 45.59 4.55
233 234 4.796231 AGATCACGCGCACCGACC 62.796 66.667 5.73 0.00 41.02 4.79
234 235 3.545481 CAGATCACGCGCACCGAC 61.545 66.667 5.73 0.00 41.02 4.79
235 236 4.794439 CCAGATCACGCGCACCGA 62.794 66.667 5.73 0.00 41.02 4.69
243 244 2.892425 GGAAGGCGCCAGATCACG 60.892 66.667 31.54 0.00 0.00 4.35
244 245 2.514824 GGGAAGGCGCCAGATCAC 60.515 66.667 31.54 20.89 0.00 3.06
245 246 2.688666 AGGGAAGGCGCCAGATCA 60.689 61.111 31.54 0.00 0.00 2.92
246 247 2.110006 GAGGGAAGGCGCCAGATC 59.890 66.667 31.54 22.57 0.00 2.75
247 248 3.483869 GGAGGGAAGGCGCCAGAT 61.484 66.667 31.54 14.90 0.00 2.90
248 249 4.722535 AGGAGGGAAGGCGCCAGA 62.723 66.667 31.54 0.00 0.00 3.86
249 250 4.168291 GAGGAGGGAAGGCGCCAG 62.168 72.222 31.54 0.00 0.00 4.85
253 254 2.681273 ATAGGGGAGGAGGGAAGGCG 62.681 65.000 0.00 0.00 0.00 5.52
254 255 0.402126 AATAGGGGAGGAGGGAAGGC 60.402 60.000 0.00 0.00 0.00 4.35
255 256 1.735926 GAATAGGGGAGGAGGGAAGG 58.264 60.000 0.00 0.00 0.00 3.46
256 257 1.343069 CGAATAGGGGAGGAGGGAAG 58.657 60.000 0.00 0.00 0.00 3.46
257 258 0.105142 CCGAATAGGGGAGGAGGGAA 60.105 60.000 0.00 0.00 35.97 3.97
258 259 1.547248 CCGAATAGGGGAGGAGGGA 59.453 63.158 0.00 0.00 35.97 4.20
259 260 2.217745 GCCGAATAGGGGAGGAGGG 61.218 68.421 0.00 0.00 41.48 4.30
260 261 3.472809 GCCGAATAGGGGAGGAGG 58.527 66.667 0.00 0.00 41.48 4.30
278 279 4.840005 GACTAGGCTGGCCCGCAC 62.840 72.222 21.51 10.26 39.21 5.34
283 284 3.851128 GACCCGACTAGGCTGGCC 61.851 72.222 5.85 3.00 39.21 5.36
284 285 4.208686 CGACCCGACTAGGCTGGC 62.209 72.222 5.85 0.00 39.21 4.85
285 286 4.208686 GCGACCCGACTAGGCTGG 62.209 72.222 4.14 4.14 39.21 4.85
286 287 4.554363 CGCGACCCGACTAGGCTG 62.554 72.222 0.00 0.00 40.02 4.85
289 290 3.352338 AAAGCGCGACCCGACTAGG 62.352 63.158 12.10 0.00 40.02 3.02
290 291 1.872679 GAAAGCGCGACCCGACTAG 60.873 63.158 12.10 0.00 40.02 2.57
291 292 2.180017 GAAAGCGCGACCCGACTA 59.820 61.111 12.10 0.00 40.02 2.59
292 293 3.628280 GAGAAAGCGCGACCCGACT 62.628 63.158 12.10 0.00 40.02 4.18
293 294 3.179939 GAGAAAGCGCGACCCGAC 61.180 66.667 12.10 0.00 40.02 4.79
294 295 2.927580 AAGAGAAAGCGCGACCCGA 61.928 57.895 12.10 0.00 40.02 5.14
295 296 2.432628 AAGAGAAAGCGCGACCCG 60.433 61.111 12.10 0.00 40.75 5.28
296 297 0.741221 ATCAAGAGAAAGCGCGACCC 60.741 55.000 12.10 0.00 0.00 4.46
297 298 0.647925 GATCAAGAGAAAGCGCGACC 59.352 55.000 12.10 0.00 0.00 4.79
298 299 0.296056 CGATCAAGAGAAAGCGCGAC 59.704 55.000 12.10 0.04 0.00 5.19
299 300 1.413767 GCGATCAAGAGAAAGCGCGA 61.414 55.000 12.10 0.00 34.77 5.87
300 301 1.012889 GCGATCAAGAGAAAGCGCG 60.013 57.895 0.00 0.00 34.77 6.86
301 302 1.349973 GGCGATCAAGAGAAAGCGC 59.650 57.895 0.00 0.00 40.08 5.92
302 303 1.633171 CGGCGATCAAGAGAAAGCG 59.367 57.895 0.00 0.00 33.00 4.68
303 304 0.741221 ACCGGCGATCAAGAGAAAGC 60.741 55.000 9.30 0.00 0.00 3.51
304 305 1.661112 GAACCGGCGATCAAGAGAAAG 59.339 52.381 9.30 0.00 0.00 2.62
305 306 1.674817 GGAACCGGCGATCAAGAGAAA 60.675 52.381 9.30 0.00 0.00 2.52
306 307 0.108329 GGAACCGGCGATCAAGAGAA 60.108 55.000 9.30 0.00 0.00 2.87
307 308 1.515954 GGAACCGGCGATCAAGAGA 59.484 57.895 9.30 0.00 0.00 3.10
308 309 1.878522 CGGAACCGGCGATCAAGAG 60.879 63.158 9.30 0.00 35.56 2.85
309 310 1.314534 TACGGAACCGGCGATCAAGA 61.315 55.000 9.30 0.00 44.69 3.02
310 311 1.140161 TACGGAACCGGCGATCAAG 59.860 57.895 9.30 7.10 44.69 3.02
311 312 1.153784 GTACGGAACCGGCGATCAA 60.154 57.895 9.30 0.00 44.69 2.57
312 313 2.274232 CTGTACGGAACCGGCGATCA 62.274 60.000 9.30 1.84 44.69 2.92
313 314 1.588139 CTGTACGGAACCGGCGATC 60.588 63.158 9.30 6.26 44.69 3.69
314 315 2.493030 CTGTACGGAACCGGCGAT 59.507 61.111 9.30 0.00 44.69 4.58
315 316 3.751246 CCTGTACGGAACCGGCGA 61.751 66.667 9.30 0.00 44.69 5.54
316 317 3.695022 CTCCTGTACGGAACCGGCG 62.695 68.421 17.44 0.00 42.53 6.46
317 318 2.183555 CTCCTGTACGGAACCGGC 59.816 66.667 17.44 10.06 42.53 6.13
318 319 2.890371 CCTCCTGTACGGAACCGG 59.110 66.667 17.44 0.00 42.53 5.28
319 320 2.183555 GCCTCCTGTACGGAACCG 59.816 66.667 11.83 11.83 42.53 4.44
320 321 2.183555 CGCCTCCTGTACGGAACC 59.816 66.667 2.31 0.00 42.53 3.62
321 322 1.660560 TAGCGCCTCCTGTACGGAAC 61.661 60.000 2.29 0.58 42.53 3.62
322 323 1.378911 TAGCGCCTCCTGTACGGAA 60.379 57.895 2.29 0.00 42.53 4.30
323 324 2.117156 GTAGCGCCTCCTGTACGGA 61.117 63.158 2.29 4.78 40.30 4.69
324 325 2.119655 AGTAGCGCCTCCTGTACGG 61.120 63.158 2.29 0.00 0.00 4.02
325 326 1.064296 CAGTAGCGCCTCCTGTACG 59.936 63.158 2.29 0.00 0.00 3.67
326 327 1.321074 ACCAGTAGCGCCTCCTGTAC 61.321 60.000 2.29 0.00 0.00 2.90
327 328 1.000019 ACCAGTAGCGCCTCCTGTA 60.000 57.895 2.29 0.00 0.00 2.74
328 329 2.283966 ACCAGTAGCGCCTCCTGT 60.284 61.111 2.29 0.00 0.00 4.00
329 330 2.185350 CACCAGTAGCGCCTCCTG 59.815 66.667 2.29 7.75 0.00 3.86
330 331 3.077556 CCACCAGTAGCGCCTCCT 61.078 66.667 2.29 0.00 0.00 3.69
331 332 4.840005 GCCACCAGTAGCGCCTCC 62.840 72.222 2.29 0.00 0.00 4.30
337 338 1.068250 GATCCTCGCCACCAGTAGC 59.932 63.158 0.00 0.00 0.00 3.58
338 339 1.883275 CTAGATCCTCGCCACCAGTAG 59.117 57.143 0.00 0.00 0.00 2.57
339 340 1.214673 ACTAGATCCTCGCCACCAGTA 59.785 52.381 0.00 0.00 0.00 2.74
340 341 0.033011 ACTAGATCCTCGCCACCAGT 60.033 55.000 0.00 0.00 0.00 4.00
341 342 1.067821 GAACTAGATCCTCGCCACCAG 59.932 57.143 0.00 0.00 0.00 4.00
342 343 1.112113 GAACTAGATCCTCGCCACCA 58.888 55.000 0.00 0.00 0.00 4.17
343 344 0.030908 CGAACTAGATCCTCGCCACC 59.969 60.000 0.00 0.00 0.00 4.61
344 345 1.002251 CTCGAACTAGATCCTCGCCAC 60.002 57.143 0.00 0.00 32.66 5.01
345 346 1.309950 CTCGAACTAGATCCTCGCCA 58.690 55.000 0.00 0.00 32.66 5.69
346 347 0.039888 GCTCGAACTAGATCCTCGCC 60.040 60.000 0.00 0.00 32.66 5.54
347 348 0.384974 CGCTCGAACTAGATCCTCGC 60.385 60.000 0.00 0.00 32.66 5.03
348 349 1.218763 TCGCTCGAACTAGATCCTCG 58.781 55.000 0.00 0.00 0.00 4.63
349 350 3.694535 TTTCGCTCGAACTAGATCCTC 57.305 47.619 4.01 0.00 33.41 3.71
350 351 3.004944 GGATTTCGCTCGAACTAGATCCT 59.995 47.826 18.73 0.00 36.03 3.24
351 352 3.310246 GGATTTCGCTCGAACTAGATCC 58.690 50.000 14.05 14.05 33.44 3.36
352 353 3.004944 AGGGATTTCGCTCGAACTAGATC 59.995 47.826 4.01 5.27 33.57 2.75
353 354 2.959707 AGGGATTTCGCTCGAACTAGAT 59.040 45.455 4.01 0.00 33.57 1.98
354 355 2.099263 CAGGGATTTCGCTCGAACTAGA 59.901 50.000 4.01 0.00 37.00 2.43
355 356 2.464865 CAGGGATTTCGCTCGAACTAG 58.535 52.381 4.01 0.00 37.00 2.57
356 357 1.136305 CCAGGGATTTCGCTCGAACTA 59.864 52.381 4.01 0.00 37.00 2.24
357 358 0.108138 CCAGGGATTTCGCTCGAACT 60.108 55.000 4.01 0.00 37.00 3.01
358 359 1.706287 GCCAGGGATTTCGCTCGAAC 61.706 60.000 4.01 0.00 37.00 3.95
359 360 1.449601 GCCAGGGATTTCGCTCGAA 60.450 57.895 0.02 0.02 37.00 3.71
360 361 2.186903 GCCAGGGATTTCGCTCGA 59.813 61.111 0.00 0.00 37.00 4.04
361 362 2.897350 GGCCAGGGATTTCGCTCG 60.897 66.667 0.00 0.00 37.00 5.03
362 363 2.897350 CGGCCAGGGATTTCGCTC 60.897 66.667 2.24 0.00 37.00 5.03
363 364 4.489771 CCGGCCAGGGATTTCGCT 62.490 66.667 2.24 0.00 39.95 4.93
366 367 4.440829 TGGCCGGCCAGGGATTTC 62.441 66.667 44.23 15.73 41.89 2.17
398 399 3.839432 CTCGAAGGAGGGGCCGTC 61.839 72.222 17.79 17.79 43.43 4.79
406 407 2.488087 AAACCGACGCCTCGAAGGAG 62.488 60.000 6.68 4.46 43.06 3.69
407 408 2.482296 GAAACCGACGCCTCGAAGGA 62.482 60.000 6.68 0.00 43.06 3.36
408 409 2.048503 AAACCGACGCCTCGAAGG 60.049 61.111 6.68 0.00 43.06 3.46
409 410 2.434134 CGAAACCGACGCCTCGAAG 61.434 63.158 6.68 0.00 43.06 3.79
410 411 2.429571 CGAAACCGACGCCTCGAA 60.430 61.111 6.68 0.00 43.06 3.71
411 412 3.663176 ACGAAACCGACGCCTCGA 61.663 61.111 15.36 0.00 43.06 4.04
412 413 3.467119 CACGAAACCGACGCCTCG 61.467 66.667 9.11 9.11 39.83 4.63
413 414 3.774702 GCACGAAACCGACGCCTC 61.775 66.667 0.00 0.00 0.00 4.70
415 416 3.919973 TAGGCACGAAACCGACGCC 62.920 63.158 12.50 12.50 43.87 5.68
416 417 1.808390 ATAGGCACGAAACCGACGC 60.808 57.895 0.00 0.00 0.00 5.19
417 418 1.418342 CCATAGGCACGAAACCGACG 61.418 60.000 0.00 0.00 0.00 5.12
418 419 0.108520 TCCATAGGCACGAAACCGAC 60.109 55.000 0.00 0.00 0.00 4.79
419 420 0.609151 TTCCATAGGCACGAAACCGA 59.391 50.000 0.00 0.00 0.00 4.69
420 421 1.444836 TTTCCATAGGCACGAAACCG 58.555 50.000 0.00 0.00 0.00 4.44
421 422 2.415491 GCTTTTCCATAGGCACGAAACC 60.415 50.000 0.00 0.00 0.00 3.27
422 423 2.488153 AGCTTTTCCATAGGCACGAAAC 59.512 45.455 0.00 0.00 0.00 2.78
423 424 2.747446 GAGCTTTTCCATAGGCACGAAA 59.253 45.455 0.00 0.00 0.00 3.46
424 425 2.027192 AGAGCTTTTCCATAGGCACGAA 60.027 45.455 0.00 0.00 0.00 3.85
425 426 1.555075 AGAGCTTTTCCATAGGCACGA 59.445 47.619 0.00 0.00 0.00 4.35
426 427 1.936547 GAGAGCTTTTCCATAGGCACG 59.063 52.381 0.00 0.00 0.00 5.34
432 433 1.555075 AGTGCCGAGAGCTTTTCCATA 59.445 47.619 0.00 0.00 44.23 2.74
453 454 1.202417 CCATCCGCACAAGTCTACGAT 60.202 52.381 0.00 0.00 0.00 3.73
470 471 4.558496 CGTTGGAAAAATACACACAGCCAT 60.558 41.667 0.00 0.00 0.00 4.40
474 475 2.970609 CGCGTTGGAAAAATACACACAG 59.029 45.455 0.00 0.00 0.00 3.66
503 504 3.575965 ATGGGAAACGCTTTAGCTTTG 57.424 42.857 0.00 0.00 39.32 2.77
522 530 8.906867 CCATCAACCAAGTATCATGTTTTCTAT 58.093 33.333 0.00 0.00 0.00 1.98
524 532 6.721208 ACCATCAACCAAGTATCATGTTTTCT 59.279 34.615 0.00 0.00 0.00 2.52
589 597 8.307921 ACAGAAAAATCTTAGTTTACGAGGAC 57.692 34.615 0.00 0.00 0.00 3.85
606 614 5.076182 TGCCATATTGGTCAGACAGAAAAA 58.924 37.500 2.17 0.00 40.46 1.94
611 619 3.813724 CAGATGCCATATTGGTCAGACAG 59.186 47.826 2.17 0.00 40.46 3.51
663 671 2.936202 TCTTTTGAAAGAGCAGCCTGT 58.064 42.857 2.16 0.00 39.95 4.00
719 727 2.900122 GTACGTACGACCAAGCTGTA 57.100 50.000 24.41 0.00 0.00 2.74
780 792 4.734398 TTTCTTTCTTTTCAAGCAGCCA 57.266 36.364 0.00 0.00 0.00 4.75
822 834 4.100035 AGTTTTCCTGCTCCCAAAGAAAAG 59.900 41.667 0.00 0.00 35.59 2.27
839 851 5.767816 TTGAAACTGAGCCCTTAGTTTTC 57.232 39.130 16.20 11.30 45.46 2.29
927 944 0.457851 CAGGGAGACGACCAAGCTAG 59.542 60.000 0.00 0.00 0.00 3.42
1407 1488 6.629291 GCTTGTAGCTAGTCCTCTGATCTTTT 60.629 42.308 0.00 0.00 38.45 2.27
1563 1644 2.855514 GCCCAAGCTGTTTTCCGCA 61.856 57.895 0.00 0.00 35.50 5.69
1583 1664 0.102300 AGACAAAAACCTGCAACGCC 59.898 50.000 0.00 0.00 0.00 5.68
1594 1675 7.500559 CCCACCAAATCCAAAAATAGACAAAAA 59.499 33.333 0.00 0.00 0.00 1.94
1763 1844 9.717942 CCCAAAATTGAATGTCCTTTGTAAATA 57.282 29.630 0.00 0.00 0.00 1.40
2150 2241 8.548721 ACACTTCTGAAATAAGAACTTTACACG 58.451 33.333 0.00 0.00 32.75 4.49
2205 2296 7.939386 GCAATTTTATCGCTGCGTAAAATTATC 59.061 33.333 34.43 29.26 43.34 1.75
2702 2798 1.534175 CGACTTCCGAATCTTCTCCCG 60.534 57.143 0.00 0.00 41.76 5.14
2740 2836 5.818678 TGCCCTCTAGACTTTGACTTTTA 57.181 39.130 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.