Multiple sequence alignment - TraesCS1B01G306800

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 TraesCS1B01G306800 chr1B 100.000 2585 0 0 1 2585 529999682 529997098 0.000000e+00 4774.0
1 TraesCS1B01G306800 chr1D 91.123 2084 91 35 353 2373 392696248 392698300 0.000000e+00 2737.0
2 TraesCS1B01G306800 chr1D 85.468 406 47 9 1122 1526 392694199 392694593 1.850000e-111 412.0
3 TraesCS1B01G306800 chr1D 82.222 405 33 24 410 792 392695804 392695417 1.930000e-81 313.0
4 TraesCS1B01G306800 chr1D 96.154 52 1 1 2507 2558 392699245 392699295 1.650000e-12 84.2
5 TraesCS1B01G306800 chr1A 87.933 2279 140 56 353 2561 492653537 492651324 0.000000e+00 2560.0
6 TraesCS1B01G306800 chr1A 89.252 214 21 2 579 792 492654121 492654332 1.520000e-67 267.0
7 TraesCS1B01G306800 chr1A 90.647 139 13 0 1474 1612 492654809 492654671 4.390000e-43 185.0
8 TraesCS1B01G306800 chr1A 85.047 107 6 6 436 542 492653828 492653924 1.640000e-17 100.0
9 TraesCS1B01G306800 chr3D 86.914 512 49 8 1100 1593 454904079 454904590 2.250000e-155 558.0
10 TraesCS1B01G306800 chr3D 77.656 273 53 8 1182 1450 132275263 132275531 2.660000e-35 159.0
11 TraesCS1B01G306800 chr3A 86.719 512 50 8 1100 1593 597184318 597184829 1.050000e-153 553.0
12 TraesCS1B01G306800 chr3A 77.656 273 53 8 1182 1450 145667377 145667645 2.660000e-35 159.0
13 TraesCS1B01G306800 chr2B 96.418 335 9 3 1 334 787796807 787796475 1.350000e-152 549.0
14 TraesCS1B01G306800 chr2B 93.660 347 20 2 1 347 792776087 792775743 3.810000e-143 518.0
15 TraesCS1B01G306800 chr2B 93.084 347 23 1 1 347 324662281 324662626 8.250000e-140 507.0
16 TraesCS1B01G306800 chr2B 82.274 519 69 16 1096 1598 65883460 65882949 6.610000e-116 427.0
17 TraesCS1B01G306800 chr3B 95.549 337 12 3 1 337 283755554 283755221 1.050000e-148 536.0
18 TraesCS1B01G306800 chr3B 84.854 515 57 11 1100 1593 597816246 597816760 1.380000e-137 499.0
19 TraesCS1B01G306800 chr3B 78.022 273 52 8 1182 1450 188877359 188877627 5.720000e-37 165.0
20 TraesCS1B01G306800 chr6B 94.509 346 15 1 1 342 208567229 208567574 4.900000e-147 531.0
21 TraesCS1B01G306800 chr6B 92.241 348 25 2 1 347 136907357 136907703 2.310000e-135 492.0
22 TraesCS1B01G306800 chr7B 91.979 374 23 5 1 374 92339294 92339660 3.810000e-143 518.0
23 TraesCS1B01G306800 chr5B 92.507 347 25 1 1 347 102440047 102439702 1.790000e-136 496.0
24 TraesCS1B01G306800 chr4B 92.507 347 19 4 1 347 622059484 622059145 8.310000e-135 490.0
25 TraesCS1B01G306800 chr2D 82.432 518 70 15 1096 1598 37646329 37645818 1.420000e-117 433.0
26 TraesCS1B01G306800 chr2A 81.731 520 70 16 1096 1598 42495204 42494693 6.660000e-111 411.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G306800 chr1B 529997098 529999682 2584 True 4774.000000 4774 100.000 1 2585 1 chr1B.!!$R1 2584
1 TraesCS1B01G306800 chr1D 392694199 392699295 5096 False 1077.733333 2737 90.915 353 2558 3 chr1D.!!$F1 2205
2 TraesCS1B01G306800 chr1A 492651324 492654809 3485 True 1372.500000 2560 89.290 353 2561 2 chr1A.!!$R1 2208
3 TraesCS1B01G306800 chr3D 454904079 454904590 511 False 558.000000 558 86.914 1100 1593 1 chr3D.!!$F2 493
4 TraesCS1B01G306800 chr3A 597184318 597184829 511 False 553.000000 553 86.719 1100 1593 1 chr3A.!!$F2 493
5 TraesCS1B01G306800 chr2B 65882949 65883460 511 True 427.000000 427 82.274 1096 1598 1 chr2B.!!$R1 502
6 TraesCS1B01G306800 chr3B 597816246 597816760 514 False 499.000000 499 84.854 1100 1593 1 chr3B.!!$F2 493
7 TraesCS1B01G306800 chr2D 37645818 37646329 511 True 433.000000 433 82.432 1096 1598 1 chr2D.!!$R1 502
8 TraesCS1B01G306800 chr2A 42494693 42495204 511 True 411.000000 411 81.731 1096 1598 1 chr2A.!!$R1 502

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
731 2657 0.036875 CAACTCTCCCAAGTGACCCC 59.963 60.0 0.0 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1721 3716 0.320247 ATGATCAATCGCCTCCTCGC 60.32 55.0 0.0 0.0 0.0 5.03 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
115 116 9.546428 AAAAATTGCAAGTGAGCTTATAGTTTT 57.454 25.926 4.94 0.00 32.87 2.43
119 120 9.793252 ATTGCAAGTGAGCTTATAGTTTTATTG 57.207 29.630 4.94 0.00 32.87 1.90
120 121 8.335532 TGCAAGTGAGCTTATAGTTTTATTGT 57.664 30.769 0.00 0.00 32.87 2.71
121 122 9.443323 TGCAAGTGAGCTTATAGTTTTATTGTA 57.557 29.630 0.00 0.00 32.87 2.41
166 167 7.835634 TTGTACACGAAATGAAGTATGCATA 57.164 32.000 1.16 1.16 27.94 3.14
167 168 7.835634 TGTACACGAAATGAAGTATGCATAA 57.164 32.000 8.28 0.00 27.94 1.90
168 169 8.257830 TGTACACGAAATGAAGTATGCATAAA 57.742 30.769 8.28 0.00 27.94 1.40
169 170 8.722394 TGTACACGAAATGAAGTATGCATAAAA 58.278 29.630 8.28 0.00 27.94 1.52
170 171 9.716507 GTACACGAAATGAAGTATGCATAAAAT 57.283 29.630 8.28 0.00 27.94 1.82
174 175 9.897744 ACGAAATGAAGTATGCATAAAATATGG 57.102 29.630 8.28 0.00 27.94 2.74
175 176 9.897744 CGAAATGAAGTATGCATAAAATATGGT 57.102 29.630 8.28 0.00 27.94 3.55
242 243 9.855021 TCTTATATACTACATACTACGCGTACA 57.145 33.333 16.41 6.57 0.00 2.90
246 247 9.809096 ATATACTACATACTACGCGTACATACT 57.191 33.333 16.41 0.56 0.00 2.12
248 249 6.219473 ACTACATACTACGCGTACATACTCT 58.781 40.000 16.41 0.00 0.00 3.24
249 250 5.588568 ACATACTACGCGTACATACTCTC 57.411 43.478 16.41 0.00 0.00 3.20
250 251 4.450419 ACATACTACGCGTACATACTCTCC 59.550 45.833 16.41 0.00 0.00 3.71
251 252 1.863454 ACTACGCGTACATACTCTCCG 59.137 52.381 16.41 4.02 0.00 4.63
252 253 2.130395 CTACGCGTACATACTCTCCGA 58.870 52.381 16.41 0.00 0.00 4.55
254 255 2.759191 ACGCGTACATACTCTCCGATA 58.241 47.619 11.67 0.00 0.00 2.92
255 256 3.332919 ACGCGTACATACTCTCCGATAT 58.667 45.455 11.67 0.00 0.00 1.63
256 257 3.124806 ACGCGTACATACTCTCCGATATG 59.875 47.826 11.67 0.00 35.33 1.78
257 258 3.370061 CGCGTACATACTCTCCGATATGA 59.630 47.826 0.00 0.00 33.73 2.15
259 260 5.233689 CGCGTACATACTCTCCGATATGATA 59.766 44.000 0.00 0.00 33.73 2.15
260 261 6.562455 CGCGTACATACTCTCCGATATGATAG 60.562 46.154 0.00 0.00 33.73 2.08
261 262 6.479331 GCGTACATACTCTCCGATATGATAGA 59.521 42.308 0.00 0.00 33.73 1.98
262 263 7.171848 GCGTACATACTCTCCGATATGATAGAT 59.828 40.741 0.00 0.00 33.73 1.98
289 290 9.538508 ACTACTTAGAACGTATGAAACAAAAGT 57.461 29.630 0.00 0.00 0.00 2.66
290 291 9.793245 CTACTTAGAACGTATGAAACAAAAGTG 57.207 33.333 0.00 0.00 0.00 3.16
291 292 7.636326 ACTTAGAACGTATGAAACAAAAGTGG 58.364 34.615 0.00 0.00 0.00 4.00
292 293 5.432885 AGAACGTATGAAACAAAAGTGGG 57.567 39.130 0.00 0.00 0.00 4.61
293 294 5.127491 AGAACGTATGAAACAAAAGTGGGA 58.873 37.500 0.00 0.00 0.00 4.37
294 295 5.238650 AGAACGTATGAAACAAAAGTGGGAG 59.761 40.000 0.00 0.00 0.00 4.30
295 296 4.457466 ACGTATGAAACAAAAGTGGGAGT 58.543 39.130 0.00 0.00 0.00 3.85
296 297 5.613329 ACGTATGAAACAAAAGTGGGAGTA 58.387 37.500 0.00 0.00 0.00 2.59
297 298 6.056884 ACGTATGAAACAAAAGTGGGAGTAA 58.943 36.000 0.00 0.00 0.00 2.24
299 300 6.204108 CGTATGAAACAAAAGTGGGAGTAACT 59.796 38.462 0.00 0.00 0.00 2.24
302 303 6.416415 TGAAACAAAAGTGGGAGTAACTACA 58.584 36.000 0.00 0.00 0.00 2.74
303 304 6.316890 TGAAACAAAAGTGGGAGTAACTACAC 59.683 38.462 0.00 0.00 0.00 2.90
304 305 4.711399 ACAAAAGTGGGAGTAACTACACC 58.289 43.478 0.00 0.00 36.39 4.16
311 312 3.560105 GGGAGTAACTACACCCGATAGT 58.440 50.000 6.62 0.00 45.03 2.12
312 313 4.718961 GGGAGTAACTACACCCGATAGTA 58.281 47.826 6.62 0.00 45.03 1.82
314 315 4.759183 GGAGTAACTACACCCGATAGTAGG 59.241 50.000 11.12 0.00 41.49 3.18
315 316 5.455326 GGAGTAACTACACCCGATAGTAGGA 60.455 48.000 11.12 0.00 41.49 2.94
316 317 6.006275 AGTAACTACACCCGATAGTAGGAA 57.994 41.667 11.12 0.00 41.49 3.36
318 319 6.891908 AGTAACTACACCCGATAGTAGGAAAA 59.108 38.462 11.12 0.00 41.49 2.29
319 320 6.610075 AACTACACCCGATAGTAGGAAAAA 57.390 37.500 11.12 0.00 41.49 1.94
320 321 6.803366 ACTACACCCGATAGTAGGAAAAAT 57.197 37.500 11.12 0.00 41.49 1.82
322 323 7.627311 ACTACACCCGATAGTAGGAAAAATTT 58.373 34.615 11.12 0.00 41.49 1.82
323 324 6.753107 ACACCCGATAGTAGGAAAAATTTG 57.247 37.500 0.00 0.00 0.00 2.32
324 325 6.243148 ACACCCGATAGTAGGAAAAATTTGT 58.757 36.000 0.00 0.00 0.00 2.83
326 327 6.373216 CACCCGATAGTAGGAAAAATTTGTCA 59.627 38.462 10.53 0.00 0.00 3.58
327 328 7.067008 CACCCGATAGTAGGAAAAATTTGTCAT 59.933 37.037 10.53 5.73 0.00 3.06
328 329 8.269317 ACCCGATAGTAGGAAAAATTTGTCATA 58.731 33.333 10.53 4.69 0.00 2.15
329 330 9.284968 CCCGATAGTAGGAAAAATTTGTCATAT 57.715 33.333 10.53 3.26 0.00 1.78
413 2309 4.842574 ACCTCACAACCTTTTTGCAAAAT 58.157 34.783 24.39 8.04 0.00 1.82
473 2369 3.733709 CTCAAAAGGAGGCACTGGT 57.266 52.632 0.00 0.00 41.55 4.00
474 2370 2.859165 CTCAAAAGGAGGCACTGGTA 57.141 50.000 0.00 0.00 41.55 3.25
475 2371 3.140325 CTCAAAAGGAGGCACTGGTAA 57.860 47.619 0.00 0.00 41.55 2.85
515 2411 4.754322 AGCAACCAACCTTAACAACAAAG 58.246 39.130 0.00 0.00 0.00 2.77
566 2462 0.387622 CAACTGGGCGCATCACTTTG 60.388 55.000 10.83 7.36 0.00 2.77
567 2463 0.537143 AACTGGGCGCATCACTTTGA 60.537 50.000 10.83 0.00 0.00 2.69
568 2464 0.322816 ACTGGGCGCATCACTTTGAT 60.323 50.000 10.83 0.00 37.65 2.57
570 2466 2.016318 CTGGGCGCATCACTTTGATTA 58.984 47.619 10.83 0.00 34.28 1.75
571 2467 2.620115 CTGGGCGCATCACTTTGATTAT 59.380 45.455 10.83 0.00 34.28 1.28
575 2496 2.859806 GCGCATCACTTTGATTATGCCC 60.860 50.000 0.30 0.00 41.29 5.36
576 2497 2.358582 CGCATCACTTTGATTATGCCCA 59.641 45.455 0.00 0.00 41.29 5.36
592 2514 1.229145 CCAATGTCCCAAGCCCCAA 60.229 57.895 0.00 0.00 0.00 4.12
596 2518 0.625849 ATGTCCCAAGCCCCAACTAG 59.374 55.000 0.00 0.00 0.00 2.57
597 2519 1.303282 GTCCCAAGCCCCAACTAGG 59.697 63.158 0.00 0.00 37.03 3.02
632 2554 3.253955 CGGAAACAAGCACCGGAG 58.746 61.111 9.46 0.00 42.48 4.63
633 2555 2.954611 GGAAACAAGCACCGGAGC 59.045 61.111 16.88 16.88 0.00 4.70
637 2559 2.920076 AAACAAGCACCGGAGCCCAA 62.920 55.000 20.91 0.00 34.23 4.12
638 2560 2.597217 CAAGCACCGGAGCCCAAA 60.597 61.111 20.91 0.00 34.23 3.28
651 2573 1.530655 CCCAAACCGCCACCTTTCT 60.531 57.895 0.00 0.00 0.00 2.52
652 2574 1.524008 CCCAAACCGCCACCTTTCTC 61.524 60.000 0.00 0.00 0.00 2.87
654 2576 1.599797 AAACCGCCACCTTTCTCCG 60.600 57.895 0.00 0.00 0.00 4.63
655 2577 2.333701 AAACCGCCACCTTTCTCCGT 62.334 55.000 0.00 0.00 0.00 4.69
657 2579 3.423154 CGCCACCTTTCTCCGTGC 61.423 66.667 0.00 0.00 0.00 5.34
659 2581 1.295423 GCCACCTTTCTCCGTGCTA 59.705 57.895 0.00 0.00 0.00 3.49
676 2598 5.221342 CCGTGCTATCTCCTGAGAAAACTAT 60.221 44.000 0.20 0.00 41.36 2.12
731 2657 0.036875 CAACTCTCCCAAGTGACCCC 59.963 60.000 0.00 0.00 0.00 4.95
755 2689 3.629398 AGAAGTTGAGAAAACTGCACCTG 59.371 43.478 0.00 0.00 0.00 4.00
795 2729 1.615392 AGACAAATGGCCAAGTTGCTC 59.385 47.619 25.09 20.91 0.00 4.26
849 2783 2.066262 CCCAGGTGTATAATAAGCGCG 58.934 52.381 0.00 0.00 0.00 6.86
850 2784 1.459592 CCAGGTGTATAATAAGCGCGC 59.540 52.381 26.66 26.66 0.00 6.86
851 2785 1.124297 CAGGTGTATAATAAGCGCGCG 59.876 52.381 28.44 28.44 0.00 6.86
852 2786 0.179258 GGTGTATAATAAGCGCGCGC 60.179 55.000 45.10 45.10 42.33 6.86
914 2854 2.158928 CCAGCTAGCTCTCTCTGCAAAT 60.159 50.000 16.15 0.00 0.00 2.32
946 2886 4.954202 TCTACCATAAGCTCGGAAGAAGAA 59.046 41.667 3.92 0.00 41.32 2.52
950 2890 0.687354 AAGCTCGGAAGAAGAAGCCA 59.313 50.000 0.00 0.00 41.32 4.75
983 2923 2.284995 GGAGAGGGGCAGTGAGGT 60.285 66.667 0.00 0.00 0.00 3.85
984 2924 1.001760 GGAGAGGGGCAGTGAGGTA 59.998 63.158 0.00 0.00 0.00 3.08
985 2925 1.331399 GGAGAGGGGCAGTGAGGTAC 61.331 65.000 0.00 0.00 0.00 3.34
986 2926 0.614979 GAGAGGGGCAGTGAGGTACA 60.615 60.000 0.00 0.00 0.00 2.90
990 2930 2.646175 GGGCAGTGAGGTACAGCGA 61.646 63.158 0.00 0.00 42.21 4.93
992 2932 1.595993 GGCAGTGAGGTACAGCGAGA 61.596 60.000 0.00 0.00 42.21 4.04
1425 3369 0.978146 AGCACCGCCTCTCCAACTAT 60.978 55.000 0.00 0.00 0.00 2.12
1721 3716 1.561643 TCCTGACTAGTTGCCTCCAG 58.438 55.000 0.00 0.00 0.00 3.86
1758 3753 1.865340 CATGATCAGATCAGCGTGTGG 59.135 52.381 18.13 0.00 43.53 4.17
1812 3810 9.360093 CCATTTTTGACTACACAAAGTACAAAA 57.640 29.630 0.00 0.00 40.15 2.44
1835 3833 5.995565 TCATTGTGTTAGTGCTACTACCT 57.004 39.130 0.00 0.00 28.93 3.08
1861 3859 9.747898 TGATACTAACCCTTGTTCATAAACATT 57.252 29.630 0.00 0.00 44.59 2.71
1864 3862 7.882179 ACTAACCCTTGTTCATAAACATTCAC 58.118 34.615 0.00 0.00 44.59 3.18
1874 3873 6.249035 TCATAAACATTCACGTTTCTTCCC 57.751 37.500 0.00 0.00 39.70 3.97
1887 3886 4.504340 CGTTTCTTCCCCTTGTTCTCCTTA 60.504 45.833 0.00 0.00 0.00 2.69
1888 3887 5.382616 GTTTCTTCCCCTTGTTCTCCTTAA 58.617 41.667 0.00 0.00 0.00 1.85
1889 3888 5.860648 TTCTTCCCCTTGTTCTCCTTAAT 57.139 39.130 0.00 0.00 0.00 1.40
1890 3889 6.963117 TTCTTCCCCTTGTTCTCCTTAATA 57.037 37.500 0.00 0.00 0.00 0.98
1950 3949 6.019156 TGCAAATCGATCCTTTGTTTGAAAAC 60.019 34.615 10.70 0.00 36.26 2.43
1967 3967 3.756933 AAACCAGCAATGCAAATGTCT 57.243 38.095 8.35 0.00 0.00 3.41
1969 3969 3.308438 ACCAGCAATGCAAATGTCTTC 57.692 42.857 8.35 0.00 0.00 2.87
2021 4021 2.034221 GGGCAGAGTGGGTGGTTC 59.966 66.667 0.00 0.00 0.00 3.62
2079 4084 6.403418 CCAGTTAAGTTGTACCAAACGAAACA 60.403 38.462 13.75 0.00 34.61 2.83
2108 4113 0.682209 GGAGCTGTGGAACCATGCAT 60.682 55.000 18.17 0.00 34.36 3.96
2127 4139 1.303282 GGAGGGGTAGTGGCCAAAG 59.697 63.158 7.24 0.00 0.00 2.77
2289 4309 0.179073 AGCTTCCATATCACGCGCTT 60.179 50.000 5.73 0.00 0.00 4.68
2343 4364 1.280998 TCCCCCGAGACTTTGAATTCC 59.719 52.381 2.27 0.00 0.00 3.01
2348 4369 1.654105 CGAGACTTTGAATTCCCGTCG 59.346 52.381 2.27 0.00 0.00 5.12
2466 4494 2.827190 CATCCACGCTGCTGGCAT 60.827 61.111 11.70 5.68 41.91 4.40
2469 4497 3.818787 CCACGCTGCTGGCATTCC 61.819 66.667 0.00 0.00 41.91 3.01
2471 4499 4.393155 ACGCTGCTGGCATTCCGA 62.393 61.111 13.94 0.00 41.91 4.55
2497 4525 1.000283 GTGGATCTCGATGCCCTAGTG 60.000 57.143 0.00 0.00 0.00 2.74
2500 4528 2.427540 ATCTCGATGCCCTAGTGCGC 62.428 60.000 0.00 0.00 0.00 6.09
2501 4529 4.221422 TCGATGCCCTAGTGCGCC 62.221 66.667 4.18 0.00 0.00 6.53
2504 4532 3.482232 GATGCCCTAGTGCGCCCAT 62.482 63.158 4.18 0.00 0.00 4.00
2505 4533 3.779850 ATGCCCTAGTGCGCCCATG 62.780 63.158 4.18 0.00 0.00 3.66
2557 5429 5.562506 TCGTTCTCGTATCATGAAAGAGT 57.437 39.130 18.62 0.00 38.33 3.24
2558 5430 6.673154 TCGTTCTCGTATCATGAAAGAGTA 57.327 37.500 18.62 10.95 38.33 2.59
2559 5431 7.260558 TCGTTCTCGTATCATGAAAGAGTAT 57.739 36.000 18.62 0.00 38.33 2.12
2560 5432 8.374327 TCGTTCTCGTATCATGAAAGAGTATA 57.626 34.615 18.62 8.37 38.33 1.47
2561 5433 8.496751 TCGTTCTCGTATCATGAAAGAGTATAG 58.503 37.037 18.62 11.39 38.33 1.31
2562 5434 8.496751 CGTTCTCGTATCATGAAAGAGTATAGA 58.503 37.037 18.62 5.55 0.00 1.98
2570 5442 7.993821 TCATGAAAGAGTATAGAAAAGAGCG 57.006 36.000 0.00 0.00 0.00 5.03
2571 5443 7.548097 TCATGAAAGAGTATAGAAAAGAGCGT 58.452 34.615 0.00 0.00 0.00 5.07
2572 5444 8.683615 TCATGAAAGAGTATAGAAAAGAGCGTA 58.316 33.333 0.00 0.00 0.00 4.42
2573 5445 9.469807 CATGAAAGAGTATAGAAAAGAGCGTAT 57.530 33.333 0.00 0.00 0.00 3.06
2581 5453 9.843334 AGTATAGAAAAGAGCGTATAGTATTGC 57.157 33.333 0.00 0.00 0.00 3.56
2582 5454 9.843334 GTATAGAAAAGAGCGTATAGTATTGCT 57.157 33.333 8.78 8.78 41.11 3.91
2583 5455 8.749841 ATAGAAAAGAGCGTATAGTATTGCTG 57.250 34.615 12.72 0.00 37.91 4.41
2584 5456 5.986135 AGAAAAGAGCGTATAGTATTGCTGG 59.014 40.000 12.72 0.00 37.91 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 9.546428 AAAACTATAAGCTCACTTGCAATTTTT 57.454 25.926 0.00 0.00 36.57 1.94
93 94 9.793252 CAATAAAACTATAAGCTCACTTGCAAT 57.207 29.630 0.00 0.00 36.57 3.56
94 95 8.792633 ACAATAAAACTATAAGCTCACTTGCAA 58.207 29.630 0.00 0.00 36.57 4.08
95 96 8.335532 ACAATAAAACTATAAGCTCACTTGCA 57.664 30.769 0.00 0.00 36.57 4.08
137 138 9.158364 GCATACTTCATTTCGTGTACAAATATG 57.842 33.333 0.00 0.62 0.00 1.78
138 139 8.888716 TGCATACTTCATTTCGTGTACAAATAT 58.111 29.630 0.00 0.00 0.00 1.28
139 140 8.257830 TGCATACTTCATTTCGTGTACAAATA 57.742 30.769 0.00 0.00 0.00 1.40
140 141 7.139896 TGCATACTTCATTTCGTGTACAAAT 57.860 32.000 0.00 0.00 0.00 2.32
142 143 6.735678 ATGCATACTTCATTTCGTGTACAA 57.264 33.333 0.00 0.00 0.00 2.41
143 144 7.835634 TTATGCATACTTCATTTCGTGTACA 57.164 32.000 5.74 0.00 0.00 2.90
144 145 9.716507 ATTTTATGCATACTTCATTTCGTGTAC 57.283 29.630 5.74 0.00 0.00 2.90
148 149 9.897744 CCATATTTTATGCATACTTCATTTCGT 57.102 29.630 5.74 0.00 0.00 3.85
149 150 9.897744 ACCATATTTTATGCATACTTCATTTCG 57.102 29.630 5.74 0.00 0.00 3.46
216 217 9.855021 TGTACGCGTAGTATGTAGTATATAAGA 57.145 33.333 21.25 0.00 37.69 2.10
220 221 9.809096 AGTATGTACGCGTAGTATGTAGTATAT 57.191 33.333 21.25 2.43 37.69 0.86
221 222 9.290483 GAGTATGTACGCGTAGTATGTAGTATA 57.710 37.037 21.25 4.94 37.69 1.47
223 224 7.371159 AGAGTATGTACGCGTAGTATGTAGTA 58.629 38.462 21.25 0.00 37.69 1.82
224 225 6.219473 AGAGTATGTACGCGTAGTATGTAGT 58.781 40.000 21.25 10.64 37.69 2.73
225 226 6.183360 GGAGAGTATGTACGCGTAGTATGTAG 60.183 46.154 21.25 0.00 37.69 2.74
226 227 5.635280 GGAGAGTATGTACGCGTAGTATGTA 59.365 44.000 21.25 5.63 37.69 2.29
227 228 4.450419 GGAGAGTATGTACGCGTAGTATGT 59.550 45.833 21.25 9.14 37.69 2.29
228 229 4.433936 CGGAGAGTATGTACGCGTAGTATG 60.434 50.000 21.25 0.37 37.69 2.39
229 230 3.677121 CGGAGAGTATGTACGCGTAGTAT 59.323 47.826 21.25 18.64 37.69 2.12
230 231 3.052745 CGGAGAGTATGTACGCGTAGTA 58.947 50.000 21.25 12.49 0.00 1.82
231 232 1.863454 CGGAGAGTATGTACGCGTAGT 59.137 52.381 21.25 14.01 0.00 2.73
232 233 2.130395 TCGGAGAGTATGTACGCGTAG 58.870 52.381 21.25 3.74 0.00 3.51
233 234 2.223537 TCGGAGAGTATGTACGCGTA 57.776 50.000 16.41 16.41 0.00 4.42
235 236 3.370061 TCATATCGGAGAGTATGTACGCG 59.630 47.826 3.53 3.53 43.63 6.01
236 237 4.941325 TCATATCGGAGAGTATGTACGC 57.059 45.455 0.00 0.00 43.63 4.42
237 238 8.596271 ATCTATCATATCGGAGAGTATGTACG 57.404 38.462 0.00 0.00 43.63 3.67
264 265 9.793245 CACTTTTGTTTCATACGTTCTAAGTAG 57.207 33.333 0.00 0.00 0.00 2.57
265 266 8.767085 CCACTTTTGTTTCATACGTTCTAAGTA 58.233 33.333 0.00 0.00 0.00 2.24
266 267 7.255001 CCCACTTTTGTTTCATACGTTCTAAGT 60.255 37.037 0.00 0.00 0.00 2.24
267 268 7.041644 TCCCACTTTTGTTTCATACGTTCTAAG 60.042 37.037 0.00 0.00 0.00 2.18
268 269 6.766944 TCCCACTTTTGTTTCATACGTTCTAA 59.233 34.615 0.00 0.00 0.00 2.10
269 270 6.289834 TCCCACTTTTGTTTCATACGTTCTA 58.710 36.000 0.00 0.00 0.00 2.10
270 271 5.127491 TCCCACTTTTGTTTCATACGTTCT 58.873 37.500 0.00 0.00 0.00 3.01
271 272 5.008316 ACTCCCACTTTTGTTTCATACGTTC 59.992 40.000 0.00 0.00 0.00 3.95
272 273 4.885325 ACTCCCACTTTTGTTTCATACGTT 59.115 37.500 0.00 0.00 0.00 3.99
273 274 4.457466 ACTCCCACTTTTGTTTCATACGT 58.543 39.130 0.00 0.00 0.00 3.57
275 276 7.506328 AGTTACTCCCACTTTTGTTTCATAC 57.494 36.000 0.00 0.00 0.00 2.39
277 278 7.012989 GTGTAGTTACTCCCACTTTTGTTTCAT 59.987 37.037 7.55 0.00 0.00 2.57
278 279 6.316890 GTGTAGTTACTCCCACTTTTGTTTCA 59.683 38.462 7.55 0.00 0.00 2.69
280 281 5.591472 GGTGTAGTTACTCCCACTTTTGTTT 59.409 40.000 12.62 0.00 34.61 2.83
281 282 5.128205 GGTGTAGTTACTCCCACTTTTGTT 58.872 41.667 12.62 0.00 34.61 2.83
282 283 4.711399 GGTGTAGTTACTCCCACTTTTGT 58.289 43.478 12.62 0.00 34.61 2.83
291 292 4.759183 CCTACTATCGGGTGTAGTTACTCC 59.241 50.000 0.00 2.51 38.72 3.85
292 293 5.615289 TCCTACTATCGGGTGTAGTTACTC 58.385 45.833 0.00 0.00 35.62 2.59
293 294 5.636903 TCCTACTATCGGGTGTAGTTACT 57.363 43.478 0.00 0.00 35.62 2.24
294 295 6.699575 TTTCCTACTATCGGGTGTAGTTAC 57.300 41.667 0.00 0.00 35.62 2.50
295 296 7.716799 TTTTTCCTACTATCGGGTGTAGTTA 57.283 36.000 0.00 0.00 35.62 2.24
296 297 6.610075 TTTTTCCTACTATCGGGTGTAGTT 57.390 37.500 0.00 0.00 35.62 2.24
297 298 6.803366 ATTTTTCCTACTATCGGGTGTAGT 57.197 37.500 0.00 0.00 35.62 2.73
299 300 7.396418 ACAAATTTTTCCTACTATCGGGTGTA 58.604 34.615 0.00 0.00 0.00 2.90
302 303 6.478129 TGACAAATTTTTCCTACTATCGGGT 58.522 36.000 2.00 0.00 0.00 5.28
303 304 6.995511 TGACAAATTTTTCCTACTATCGGG 57.004 37.500 2.00 0.00 0.00 5.14
374 2270 5.693104 TGTGAGGTTAGATGTAACAAACGAC 59.307 40.000 14.11 4.51 40.46 4.34
424 2320 2.510382 TGACAACTTTTGTGGGGGTAGA 59.490 45.455 0.00 0.00 45.52 2.59
426 2322 3.226777 CATGACAACTTTTGTGGGGGTA 58.773 45.455 0.00 0.00 45.52 3.69
427 2323 2.038659 CATGACAACTTTTGTGGGGGT 58.961 47.619 0.00 0.00 45.52 4.95
428 2324 2.038659 ACATGACAACTTTTGTGGGGG 58.961 47.619 0.00 0.00 45.52 5.40
474 2370 9.953565 TGGTTGCTCTTGTTTACTAATACTATT 57.046 29.630 0.00 0.00 0.00 1.73
475 2371 9.953565 TTGGTTGCTCTTGTTTACTAATACTAT 57.046 29.630 0.00 0.00 0.00 2.12
566 2462 2.036346 GCTTGGGACATTGGGCATAATC 59.964 50.000 0.00 0.00 39.30 1.75
567 2463 2.041701 GCTTGGGACATTGGGCATAAT 58.958 47.619 0.00 0.00 39.30 1.28
568 2464 1.484038 GCTTGGGACATTGGGCATAA 58.516 50.000 0.00 0.00 39.30 1.90
570 2466 1.686800 GGCTTGGGACATTGGGCAT 60.687 57.895 0.00 0.00 39.30 4.40
571 2467 2.283821 GGCTTGGGACATTGGGCA 60.284 61.111 0.00 0.00 39.30 5.36
575 2496 0.542702 AGTTGGGGCTTGGGACATTG 60.543 55.000 0.00 0.00 39.30 2.82
576 2497 1.005924 CTAGTTGGGGCTTGGGACATT 59.994 52.381 0.00 0.00 39.30 2.71
592 2514 2.933834 AAACCAGGGCCGCCTAGT 60.934 61.111 9.86 1.38 0.00 2.57
612 2534 2.637025 CGGTGCTTGTTTCCGGTG 59.363 61.111 0.00 0.00 40.49 4.94
615 2537 2.966309 GCTCCGGTGCTTGTTTCCG 61.966 63.158 20.97 0.00 43.30 4.30
616 2538 2.626780 GGCTCCGGTGCTTGTTTCC 61.627 63.158 26.25 5.73 0.00 3.13
618 2540 2.597510 GGGCTCCGGTGCTTGTTT 60.598 61.111 26.25 0.00 0.00 2.83
619 2541 2.920076 TTTGGGCTCCGGTGCTTGTT 62.920 55.000 26.25 0.00 0.00 2.83
620 2542 3.429372 TTTGGGCTCCGGTGCTTGT 62.429 57.895 26.25 0.00 0.00 3.16
623 2545 4.660938 GGTTTGGGCTCCGGTGCT 62.661 66.667 26.25 0.00 0.00 4.40
632 2554 3.220999 GAAAGGTGGCGGTTTGGGC 62.221 63.158 0.00 0.00 0.00 5.36
633 2555 1.524008 GAGAAAGGTGGCGGTTTGGG 61.524 60.000 0.00 0.00 0.00 4.12
637 2559 2.032071 CGGAGAAAGGTGGCGGTT 59.968 61.111 0.00 0.00 0.00 4.44
638 2560 3.239253 ACGGAGAAAGGTGGCGGT 61.239 61.111 0.00 0.00 0.00 5.68
641 2563 0.107654 ATAGCACGGAGAAAGGTGGC 60.108 55.000 0.00 0.00 34.76 5.01
651 2573 2.437085 TTCTCAGGAGATAGCACGGA 57.563 50.000 0.00 0.00 37.29 4.69
652 2574 3.118956 AGTTTTCTCAGGAGATAGCACGG 60.119 47.826 0.00 0.00 37.29 4.94
654 2576 6.220201 GGATAGTTTTCTCAGGAGATAGCAC 58.780 44.000 0.00 0.00 37.29 4.40
655 2577 5.305644 GGGATAGTTTTCTCAGGAGATAGCA 59.694 44.000 0.00 0.00 37.29 3.49
657 2579 5.841237 TGGGGATAGTTTTCTCAGGAGATAG 59.159 44.000 0.00 0.00 37.29 2.08
659 2581 4.635473 TGGGGATAGTTTTCTCAGGAGAT 58.365 43.478 0.00 0.00 37.29 2.75
676 2598 0.104672 TCAGTTGGGAGAGTTGGGGA 60.105 55.000 0.00 0.00 0.00 4.81
731 2657 5.049818 CAGGTGCAGTTTTCTCAACTTCTAG 60.050 44.000 0.00 0.00 0.00 2.43
755 2689 0.595825 GCTGTGGTTGAGCAAGTTGC 60.596 55.000 20.44 20.44 45.46 4.17
795 2729 0.600255 GGTGGTCACTCACAACTCGG 60.600 60.000 0.93 0.00 39.27 4.63
864 2798 4.426313 GGTCCTTTGGCGAGGGGG 62.426 72.222 2.62 0.00 37.41 5.40
865 2799 2.893682 GATGGTCCTTTGGCGAGGGG 62.894 65.000 2.62 0.00 37.41 4.79
914 2854 3.961408 GAGCTTATGGTAGACAAGGGAGA 59.039 47.826 0.00 0.00 0.00 3.71
968 2908 0.616111 CTGTACCTCACTGCCCCTCT 60.616 60.000 0.00 0.00 0.00 3.69
983 2923 3.304458 CGGCATTATACACTCTCGCTGTA 60.304 47.826 0.00 0.00 0.00 2.74
984 2924 2.543861 CGGCATTATACACTCTCGCTGT 60.544 50.000 0.00 0.00 0.00 4.40
985 2925 2.054363 CGGCATTATACACTCTCGCTG 58.946 52.381 0.00 0.00 0.00 5.18
986 2926 1.681793 ACGGCATTATACACTCTCGCT 59.318 47.619 0.00 0.00 0.00 4.93
990 2930 3.961182 CGTGTACGGCATTATACACTCT 58.039 45.455 11.53 0.00 45.92 3.24
1721 3716 0.320247 ATGATCAATCGCCTCCTCGC 60.320 55.000 0.00 0.00 0.00 5.03
1758 3753 4.386954 GGGTAAACGTACACAAGCTAGAAC 59.613 45.833 0.00 0.00 33.44 3.01
1812 3810 6.154534 TCAGGTAGTAGCACTAACACAATGAT 59.845 38.462 12.07 0.00 40.80 2.45
1861 3859 2.171870 AGAACAAGGGGAAGAAACGTGA 59.828 45.455 0.00 0.00 0.00 4.35
1864 3862 2.152016 GGAGAACAAGGGGAAGAAACG 58.848 52.381 0.00 0.00 0.00 3.60
1950 3949 3.306917 TGAAGACATTTGCATTGCTGG 57.693 42.857 10.49 0.00 0.00 4.85
1967 3967 5.279406 CCAACTTGGCTGTGGATTTAATGAA 60.279 40.000 0.00 0.00 0.00 2.57
1969 3969 4.497300 CCAACTTGGCTGTGGATTTAATG 58.503 43.478 0.00 0.00 0.00 1.90
2001 4001 4.087892 CCACCCACTCTGCCCTCG 62.088 72.222 0.00 0.00 0.00 4.63
2021 4021 8.139350 TGACTATTGTATGTATCCCACTAAACG 58.861 37.037 0.00 0.00 0.00 3.60
2108 4113 1.464395 TTTGGCCACTACCCCTCCA 60.464 57.895 3.88 0.00 0.00 3.86
2127 4139 4.999950 CCAGTTCATCATTAGCTATGGTCC 59.000 45.833 0.00 0.00 34.85 4.46
2343 4364 5.225334 CGATCGATCTCAATTATAACGACGG 59.775 44.000 22.43 0.00 0.00 4.79
2348 4369 6.517597 GCACACGATCGATCTCAATTATAAC 58.482 40.000 24.34 0.00 0.00 1.89
2429 4457 5.337250 GGATGGTTTGTAAAATCTGTTCCCC 60.337 44.000 0.00 0.00 0.00 4.81
2466 4494 4.137872 GATCCACGGGCGTCGGAA 62.138 66.667 0.00 0.00 44.45 4.30
2469 4497 4.907034 CGAGATCCACGGGCGTCG 62.907 72.222 2.56 0.00 45.88 5.12
2471 4499 2.833582 ATCGAGATCCACGGGCGT 60.834 61.111 9.43 0.00 0.00 5.68
2497 4525 4.994201 CGATGCATGCATGGGCGC 62.994 66.667 36.73 20.48 45.35 6.53
2500 4528 0.803117 GAGATCGATGCATGCATGGG 59.197 55.000 36.73 26.15 36.70 4.00
2501 4529 0.803117 GGAGATCGATGCATGCATGG 59.197 55.000 36.73 33.27 36.70 3.66
2504 4532 0.883370 GCTGGAGATCGATGCATGCA 60.883 55.000 25.04 25.04 0.00 3.96
2505 4533 0.603172 AGCTGGAGATCGATGCATGC 60.603 55.000 11.82 11.82 0.00 4.06
2557 5429 9.841880 CAGCAATACTATACGCTCTTTTCTATA 57.158 33.333 0.00 0.00 30.72 1.31
2558 5430 7.815068 CCAGCAATACTATACGCTCTTTTCTAT 59.185 37.037 0.00 0.00 30.72 1.98
2559 5431 7.145985 CCAGCAATACTATACGCTCTTTTCTA 58.854 38.462 0.00 0.00 30.72 2.10
2560 5432 5.986135 CCAGCAATACTATACGCTCTTTTCT 59.014 40.000 0.00 0.00 30.72 2.52
2561 5433 6.216750 CCAGCAATACTATACGCTCTTTTC 57.783 41.667 0.00 0.00 30.72 2.29


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

AutoCloner maintained by Alex Coulton.