Multiple sequence alignment - TraesCS3D01G186000

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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 TraesCS3D01G186000 chr3D 100.000 5374 0 0 1 5374 171336117 171330744 0.000000e+00 9925.0
1 TraesCS3D01G186000 chr3D 80.088 683 114 20 2198 2867 340701163 340700490 6.260000e-134 488.0
2 TraesCS3D01G186000 chr3A 93.270 4829 240 42 23 4818 208805789 208801013 0.000000e+00 7038.0
3 TraesCS3D01G186000 chr3A 90.526 95 9 0 5278 5372 208800403 208800309 5.650000e-25 126.0
4 TraesCS3D01G186000 chr3B 95.408 2853 105 21 1 2839 250279433 250276593 0.000000e+00 4519.0
5 TraesCS3D01G186000 chr3B 96.066 1881 45 6 2831 4700 250275907 250274045 0.000000e+00 3037.0
6 TraesCS3D01G186000 chr3B 93.281 253 15 2 5061 5312 250272795 250272544 6.570000e-99 372.0
7 TraesCS3D01G186000 chr3B 93.798 129 8 0 4934 5062 250272962 250272834 1.530000e-45 195.0
8 TraesCS3D01G186000 chr3B 89.130 138 7 3 4738 4867 250273140 250273003 1.200000e-36 165.0
9 TraesCS3D01G186000 chr4D 86.706 677 68 9 1989 2646 369260421 369261094 0.000000e+00 732.0
10 TraesCS3D01G186000 chr4A 84.741 675 83 9 1989 2646 95186234 95185563 0.000000e+00 658.0
11 TraesCS3D01G186000 chr4A 85.938 192 17 4 2676 2866 95185357 95185175 4.250000e-46 196.0
12 TraesCS3D01G186000 chr4B 84.226 672 79 15 1989 2646 454697979 454698637 3.530000e-176 628.0
13 TraesCS3D01G186000 chr4B 88.318 214 15 4 2654 2866 454698726 454698930 1.160000e-61 248.0
14 TraesCS3D01G186000 chr4B 94.737 38 2 0 4872 4909 375390502 375390539 5.810000e-05 60.2
15 TraesCS3D01G186000 chr7A 80.723 830 129 19 1995 2800 252713297 252712475 7.650000e-173 617.0
16 TraesCS3D01G186000 chr7A 100.000 34 0 0 4872 4905 708810579 708810612 4.490000e-06 63.9
17 TraesCS3D01G186000 chr7D 80.845 710 106 18 2117 2806 237408291 237407592 1.020000e-146 531.0
18 TraesCS3D01G186000 chr7D 78.960 404 74 6 2401 2797 611170890 611170491 1.150000e-66 265.0
19 TraesCS3D01G186000 chr7D 82.063 223 15 7 4976 5173 6790483 6790705 3.330000e-37 167.0
20 TraesCS3D01G186000 chr5D 81.051 628 90 24 2191 2810 560450980 560451586 1.750000e-129 473.0
21 TraesCS3D01G186000 chr2B 82.989 435 63 9 2315 2743 3411297 3410868 3.040000e-102 383.0
22 TraesCS3D01G186000 chr2B 76.800 625 104 20 2205 2811 556969557 556968956 4.040000e-81 313.0
23 TraesCS3D01G186000 chr2B 89.333 75 6 2 2794 2867 410162555 410162482 5.730000e-15 93.5
24 TraesCS3D01G186000 chr2B 97.368 38 1 0 4863 4900 66373835 66373872 1.250000e-06 65.8
25 TraesCS3D01G186000 chr2A 85.398 226 24 6 2587 2810 182912980 182913198 5.420000e-55 226.0
26 TraesCS3D01G186000 chr1A 79.828 233 22 7 4976 5183 78947576 78947344 4.340000e-31 147.0
27 TraesCS3D01G186000 chr1A 100.000 34 0 0 4872 4905 321398979 321399012 4.490000e-06 63.9
28 TraesCS3D01G186000 chr5B 79.747 237 19 16 4976 5186 669421667 669421434 1.560000e-30 145.0
29 TraesCS3D01G186000 chr2D 86.486 74 10 0 2794 2867 344948933 344948860 1.240000e-11 82.4
30 TraesCS3D01G186000 chr2D 97.727 44 1 0 4863 4906 37904918 37904961 5.770000e-10 76.8
31 TraesCS3D01G186000 chr2D 97.727 44 1 0 4863 4906 37950433 37950476 5.770000e-10 76.8
32 TraesCS3D01G186000 chr5A 97.436 39 1 0 4867 4905 26810954 26810916 3.470000e-07 67.6
33 TraesCS3D01G186000 chr5A 97.368 38 1 0 4868 4905 139933894 139933857 1.250000e-06 65.8
34 TraesCS3D01G186000 chr1B 92.857 42 0 2 4872 4911 630468778 630468818 2.090000e-04 58.4


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 TraesCS3D01G186000 chr3D 171330744 171336117 5373 True 9925.0 9925 100.0000 1 5374 1 chr3D.!!$R1 5373
1 TraesCS3D01G186000 chr3D 340700490 340701163 673 True 488.0 488 80.0880 2198 2867 1 chr3D.!!$R2 669
2 TraesCS3D01G186000 chr3A 208800309 208805789 5480 True 3582.0 7038 91.8980 23 5372 2 chr3A.!!$R1 5349
3 TraesCS3D01G186000 chr3B 250272544 250279433 6889 True 1657.6 4519 93.5366 1 5312 5 chr3B.!!$R1 5311
4 TraesCS3D01G186000 chr4D 369260421 369261094 673 False 732.0 732 86.7060 1989 2646 1 chr4D.!!$F1 657
5 TraesCS3D01G186000 chr4A 95185175 95186234 1059 True 427.0 658 85.3395 1989 2866 2 chr4A.!!$R1 877
6 TraesCS3D01G186000 chr4B 454697979 454698930 951 False 438.0 628 86.2720 1989 2866 2 chr4B.!!$F2 877
7 TraesCS3D01G186000 chr7A 252712475 252713297 822 True 617.0 617 80.7230 1995 2800 1 chr7A.!!$R1 805
8 TraesCS3D01G186000 chr7D 237407592 237408291 699 True 531.0 531 80.8450 2117 2806 1 chr7D.!!$R1 689
9 TraesCS3D01G186000 chr5D 560450980 560451586 606 False 473.0 473 81.0510 2191 2810 1 chr5D.!!$F1 619
10 TraesCS3D01G186000 chr2B 556968956 556969557 601 True 313.0 313 76.8000 2205 2811 1 chr2B.!!$R3 606

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
177 178 0.109723 CCCGGTTCCTCCTGTTTGAA 59.890 55.0 0.00 0.0 0.00 2.69 F
934 942 0.307453 TTATGCGCATTCATCCGTGC 59.693 50.0 30.42 0.0 39.10 5.34 F
1736 1746 0.977395 AGGGCTGACTACAAGGACAC 59.023 55.0 0.00 0.0 0.00 3.67 F
2763 2998 0.240411 GCAGTACGGACTATAGCGGG 59.760 60.0 0.00 0.0 33.32 6.13 F
2772 3008 2.694109 GGACTATAGCGGGTCTGTTCTT 59.306 50.0 0.00 0.0 33.46 2.52 F
4178 5118 0.969149 ACATGGACAAGCTCGACTCA 59.031 50.0 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 1972 1.270571 TGGTTCGCAGTTGCTATGTCA 60.271 47.619 2.29 0.0 39.32 3.58 R
2763 2998 0.685660 AAGGTCCCGGAAGAACAGAC 59.314 55.000 0.73 0.0 0.00 3.51 R
2772 3008 1.980772 GGAACTCGAAGGTCCCGGA 60.981 63.158 0.73 0.0 46.52 5.14 R
4178 5118 2.122768 AGATTCCTTCCTCCGAATGCT 58.877 47.619 0.00 0.0 0.00 3.79 R
4330 5270 2.279120 CGCCGTGCTCTCCATCTC 60.279 66.667 0.00 0.0 0.00 2.75 R
5268 7136 1.274703 CCTCAGCCCACTGGGTATGT 61.275 60.000 16.03 0.0 43.50 2.29 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
175 176 0.328258 ATCCCGGTTCCTCCTGTTTG 59.672 55.000 0.00 0.00 0.00 2.93
177 178 0.109723 CCCGGTTCCTCCTGTTTGAA 59.890 55.000 0.00 0.00 0.00 2.69
192 193 1.522668 TTGAATGGTTCAGGCAGACG 58.477 50.000 0.00 0.00 41.38 4.18
254 259 3.001330 GCCGGTTCGATTGTAGATTTCTG 59.999 47.826 1.90 0.00 0.00 3.02
256 261 3.555956 CGGTTCGATTGTAGATTTCTGGG 59.444 47.826 0.00 0.00 0.00 4.45
302 307 2.616842 GTCTGGTGTTGTTTTGGACGAT 59.383 45.455 0.00 0.00 0.00 3.73
337 342 6.038714 GGAAATTTGGTAGATTTCGATCTGCT 59.961 38.462 0.00 0.00 41.95 4.24
340 345 3.300388 TGGTAGATTTCGATCTGCTCCT 58.700 45.455 4.46 0.00 34.36 3.69
353 358 3.034635 TCTGCTCCTCCTGGAATTCTAC 58.965 50.000 5.23 0.00 42.66 2.59
413 419 2.614481 CGCAGGTAGTTTTTAGCCTGGA 60.614 50.000 10.86 0.00 46.23 3.86
446 452 1.338020 CTGTTTGTTCTTCAGCCCACC 59.662 52.381 0.00 0.00 0.00 4.61
447 453 0.310854 GTTTGTTCTTCAGCCCACCG 59.689 55.000 0.00 0.00 0.00 4.94
449 455 0.534203 TTGTTCTTCAGCCCACCGAC 60.534 55.000 0.00 0.00 0.00 4.79
460 466 2.246739 CCACCGACAGCTGTGTGTG 61.247 63.158 27.27 27.11 36.88 3.82
481 487 4.342378 GTGGCATCAGTAGATCCAGTTCTA 59.658 45.833 0.00 0.00 34.38 2.10
487 493 2.941480 GTAGATCCAGTTCTACGGGGA 58.059 52.381 0.00 0.00 38.91 4.81
498 504 0.824759 CTACGGGGAGAAAGGGACAG 59.175 60.000 0.00 0.00 0.00 3.51
503 509 0.693049 GGGAGAAAGGGACAGCTGAA 59.307 55.000 23.35 0.00 0.00 3.02
504 510 1.339535 GGGAGAAAGGGACAGCTGAAG 60.340 57.143 23.35 0.00 0.00 3.02
523 529 8.251750 GCTGAAGCGTATATAAATATTCCACA 57.748 34.615 0.00 0.00 0.00 4.17
524 530 8.383619 GCTGAAGCGTATATAAATATTCCACAG 58.616 37.037 0.00 0.00 0.00 3.66
525 531 8.251750 TGAAGCGTATATAAATATTCCACAGC 57.748 34.615 0.00 0.00 0.00 4.40
530 536 8.814235 GCGTATATAAATATTCCACAGCGTTAT 58.186 33.333 0.00 0.00 0.00 1.89
545 551 2.632228 CGTTATCGCGTCTTGATCGTA 58.368 47.619 5.77 0.00 0.00 3.43
575 581 5.865085 TCCATCAGGCACCAGTATTATAAC 58.135 41.667 0.00 0.00 33.74 1.89
603 609 3.508845 ACAGTGGAATTAGTGCCTTGT 57.491 42.857 0.00 0.00 0.00 3.16
638 644 0.695924 TCCTCCCATTTCCTTTCGCA 59.304 50.000 0.00 0.00 0.00 5.10
639 645 1.074727 TCCTCCCATTTCCTTTCGCAA 59.925 47.619 0.00 0.00 0.00 4.85
934 942 0.307453 TTATGCGCATTCATCCGTGC 59.693 50.000 30.42 0.00 39.10 5.34
994 1003 1.900486 AGAGTCGTCCCCCTTTAGTTG 59.100 52.381 0.00 0.00 0.00 3.16
1084 1093 4.006319 ACAGCAAGAGAAAGTAAGATGCC 58.994 43.478 0.00 0.00 32.95 4.40
1160 1169 5.913137 CCATTTGGCTGTTCTATTTACCA 57.087 39.130 0.00 0.00 0.00 3.25
1204 1213 2.833794 CAACTTGAAGAACCCTCGTCA 58.166 47.619 0.00 0.00 38.16 4.35
1349 1358 3.381590 GCCAGAAATGATTTCCTGGGTAC 59.618 47.826 24.46 13.00 40.54 3.34
1446 1455 6.967767 AGTGTAATTAAGACATCGACGAGAAG 59.032 38.462 3.01 0.00 0.00 2.85
1461 1470 2.548920 CGAGAAGTTGGAAGAGCAGGTT 60.549 50.000 0.00 0.00 0.00 3.50
1508 1518 7.497773 AAGTTTAGTGTAGGAGGAATAAGCT 57.502 36.000 0.00 0.00 0.00 3.74
1552 1562 5.298527 ACCACTGTGCTGATTGAATGATATG 59.701 40.000 1.29 0.00 0.00 1.78
1586 1596 7.592938 TGAACTGTTGGCTGAAAACATTATAG 58.407 34.615 0.00 0.00 36.95 1.31
1736 1746 0.977395 AGGGCTGACTACAAGGACAC 59.023 55.000 0.00 0.00 0.00 3.67
1770 1780 1.140312 TTCTTGTTCTGAGGCCAGGT 58.860 50.000 5.01 0.00 40.76 4.00
1946 1956 8.806429 TTGGAGTTGCTTGATCTGAATAAATA 57.194 30.769 0.00 0.00 0.00 1.40
2305 2342 4.077184 GTGGCGTCCATGTCGGGA 62.077 66.667 9.04 0.00 35.28 5.14
2763 2998 0.240411 GCAGTACGGACTATAGCGGG 59.760 60.000 0.00 0.00 33.32 6.13
2772 3008 2.694109 GGACTATAGCGGGTCTGTTCTT 59.306 50.000 0.00 0.00 33.46 2.52
3556 4490 6.169094 ACCTCAATCATTACTCTGTGAACAG 58.831 40.000 3.98 3.98 45.08 3.16
3684 4618 5.450818 TTAGCTATCCCACCAATTTGTCT 57.549 39.130 0.00 0.00 0.00 3.41
3767 4703 4.593206 TGATATTTGGCGGTCTCCTCTAAT 59.407 41.667 0.00 0.00 0.00 1.73
3768 4704 5.778241 TGATATTTGGCGGTCTCCTCTAATA 59.222 40.000 0.00 0.00 0.00 0.98
3769 4705 6.440647 TGATATTTGGCGGTCTCCTCTAATAT 59.559 38.462 0.00 0.00 0.00 1.28
3770 4706 7.618117 TGATATTTGGCGGTCTCCTCTAATATA 59.382 37.037 0.00 0.00 0.00 0.86
3771 4707 6.875972 ATTTGGCGGTCTCCTCTAATATAT 57.124 37.500 0.00 0.00 0.00 0.86
3772 4708 5.916661 TTGGCGGTCTCCTCTAATATATC 57.083 43.478 0.00 0.00 0.00 1.63
3773 4709 5.194473 TGGCGGTCTCCTCTAATATATCT 57.806 43.478 0.00 0.00 0.00 1.98
3774 4710 4.950475 TGGCGGTCTCCTCTAATATATCTG 59.050 45.833 0.00 0.00 0.00 2.90
3775 4711 4.951094 GGCGGTCTCCTCTAATATATCTGT 59.049 45.833 0.00 0.00 0.00 3.41
3776 4712 5.419471 GGCGGTCTCCTCTAATATATCTGTT 59.581 44.000 0.00 0.00 0.00 3.16
3777 4713 6.071278 GGCGGTCTCCTCTAATATATCTGTTT 60.071 42.308 0.00 0.00 0.00 2.83
3778 4714 7.379750 GCGGTCTCCTCTAATATATCTGTTTT 58.620 38.462 0.00 0.00 0.00 2.43
3779 4715 8.521176 GCGGTCTCCTCTAATATATCTGTTTTA 58.479 37.037 0.00 0.00 0.00 1.52
3781 4717 9.863845 GGTCTCCTCTAATATATCTGTTTTAGC 57.136 37.037 0.00 0.00 0.00 3.09
3782 4718 9.562583 GTCTCCTCTAATATATCTGTTTTAGCG 57.437 37.037 0.00 0.00 0.00 4.26
3798 4735 8.481974 TGTTTTAGCGTATATCTGTTTTAGCA 57.518 30.769 0.00 0.00 0.00 3.49
3958 4898 6.577103 TCTCTTAGATAGATTGCAGTGGTTG 58.423 40.000 0.00 0.00 30.92 3.77
4178 5118 0.969149 ACATGGACAAGCTCGACTCA 59.031 50.000 0.00 0.00 0.00 3.41
4349 5289 4.819761 GATGGAGAGCACGGCGCA 62.820 66.667 10.83 0.00 46.13 6.09
4490 5431 4.069304 CACATTTTCGGGTCCAAGACTTA 58.931 43.478 0.00 0.00 32.47 2.24
4495 5436 6.363167 TTTTCGGGTCCAAGACTTAGAATA 57.637 37.500 0.00 0.00 32.47 1.75
4639 5584 8.653338 GGCGCTTCTATACGAAATAATTTGATA 58.347 33.333 7.64 0.00 0.00 2.15
4679 5631 6.216801 TGACTAACCGATGCACTTTACTAT 57.783 37.500 0.00 0.00 0.00 2.12
4695 5647 8.826710 CACTTTACTATTTGAGTGTTGTTCTGA 58.173 33.333 0.00 0.00 39.39 3.27
4725 6313 2.107378 TGATGGCTGTTACTTTGTGGGA 59.893 45.455 0.00 0.00 0.00 4.37
4728 6316 2.152016 GGCTGTTACTTTGTGGGACTC 58.848 52.381 0.00 0.00 0.00 3.36
4729 6317 2.224548 GGCTGTTACTTTGTGGGACTCT 60.225 50.000 0.00 0.00 0.00 3.24
4730 6318 2.808543 GCTGTTACTTTGTGGGACTCTG 59.191 50.000 0.00 0.00 0.00 3.35
4731 6319 3.494398 GCTGTTACTTTGTGGGACTCTGA 60.494 47.826 0.00 0.00 0.00 3.27
4732 6320 4.804261 GCTGTTACTTTGTGGGACTCTGAT 60.804 45.833 0.00 0.00 0.00 2.90
4733 6321 4.641396 TGTTACTTTGTGGGACTCTGATG 58.359 43.478 0.00 0.00 0.00 3.07
4735 6323 3.409026 ACTTTGTGGGACTCTGATGAC 57.591 47.619 0.00 0.00 0.00 3.06
4736 6324 2.705658 ACTTTGTGGGACTCTGATGACA 59.294 45.455 0.00 0.00 0.00 3.58
4828 6647 5.297029 GGAGTAGTATTTTCATGAACCAGGC 59.703 44.000 7.89 0.00 0.00 4.85
4861 6688 3.186613 GCTTCTTCCAAAGTGTAGGAACG 59.813 47.826 0.00 0.00 38.91 3.95
4869 6696 2.249844 AGTGTAGGAACGGGTTGTTG 57.750 50.000 0.00 0.00 42.09 3.33
4873 6700 3.566742 GTGTAGGAACGGGTTGTTGATTT 59.433 43.478 0.00 0.00 42.09 2.17
4874 6701 4.037089 GTGTAGGAACGGGTTGTTGATTTT 59.963 41.667 0.00 0.00 42.09 1.82
4876 6703 4.053469 AGGAACGGGTTGTTGATTTTTG 57.947 40.909 0.00 0.00 42.09 2.44
4877 6704 3.702045 AGGAACGGGTTGTTGATTTTTGA 59.298 39.130 0.00 0.00 42.09 2.69
4878 6705 4.048504 GGAACGGGTTGTTGATTTTTGAG 58.951 43.478 0.00 0.00 42.09 3.02
4880 6707 5.508994 GGAACGGGTTGTTGATTTTTGAGAT 60.509 40.000 0.00 0.00 42.09 2.75
4882 6709 6.254281 ACGGGTTGTTGATTTTTGAGATAG 57.746 37.500 0.00 0.00 0.00 2.08
4883 6710 5.095490 CGGGTTGTTGATTTTTGAGATAGC 58.905 41.667 0.00 0.00 0.00 2.97
4886 6713 7.361713 CGGGTTGTTGATTTTTGAGATAGCTTA 60.362 37.037 0.00 0.00 0.00 3.09
4888 6715 7.755373 GGTTGTTGATTTTTGAGATAGCTTACC 59.245 37.037 0.00 0.00 0.00 2.85
4889 6716 7.994425 TGTTGATTTTTGAGATAGCTTACCA 57.006 32.000 0.00 0.00 0.00 3.25
4891 6718 7.121168 TGTTGATTTTTGAGATAGCTTACCAGG 59.879 37.037 0.00 0.00 0.00 4.45
4892 6719 5.590259 TGATTTTTGAGATAGCTTACCAGGC 59.410 40.000 0.00 0.00 0.00 4.85
4895 6722 3.827008 TGAGATAGCTTACCAGGCTTG 57.173 47.619 0.00 0.00 40.74 4.01
4897 6724 3.133003 TGAGATAGCTTACCAGGCTTGAC 59.867 47.826 0.00 0.00 40.74 3.18
4898 6725 2.101582 AGATAGCTTACCAGGCTTGACG 59.898 50.000 0.00 0.00 40.74 4.35
4908 6735 3.876300 GCTTGACGCCTGGTGTAG 58.124 61.111 13.78 9.29 0.00 2.74
4918 6745 3.226884 CTGGTGTAGGAACGGGTTG 57.773 57.895 0.00 0.00 0.00 3.77
4919 6746 0.953960 CTGGTGTAGGAACGGGTTGC 60.954 60.000 0.00 0.00 0.00 4.17
4920 6747 1.673337 GGTGTAGGAACGGGTTGCC 60.673 63.158 0.00 0.00 0.00 4.52
4921 6748 1.673337 GTGTAGGAACGGGTTGCCC 60.673 63.158 0.00 0.00 41.09 5.36
4922 6749 2.148052 TGTAGGAACGGGTTGCCCA 61.148 57.895 4.96 0.00 45.83 5.36
4923 6750 1.376812 GTAGGAACGGGTTGCCCAG 60.377 63.158 4.96 0.33 45.83 4.45
4924 6751 3.262448 TAGGAACGGGTTGCCCAGC 62.262 63.158 4.96 0.00 45.83 4.85
4925 6752 4.966787 GGAACGGGTTGCCCAGCA 62.967 66.667 4.96 0.00 45.83 4.41
4926 6753 3.670377 GAACGGGTTGCCCAGCAC 61.670 66.667 4.96 0.00 45.83 4.40
4930 6757 3.134127 GGGTTGCCCAGCACGATC 61.134 66.667 0.00 0.00 44.65 3.69
4931 6758 2.359850 GGTTGCCCAGCACGATCA 60.360 61.111 0.00 0.00 38.71 2.92
4932 6759 1.750399 GGTTGCCCAGCACGATCAT 60.750 57.895 0.00 0.00 38.71 2.45
4945 6772 4.271049 AGCACGATCATCTTAAATTGACCG 59.729 41.667 0.00 0.66 0.00 4.79
4979 6806 3.241067 ACACGCGTGGATATTTGTAGT 57.759 42.857 39.21 14.19 34.19 2.73
4994 6821 5.782893 TTTGTAGTGGCAGCTATTTTTGT 57.217 34.783 0.00 0.00 0.00 2.83
5023 6850 0.449388 CAATCTGGCTTGCGAGTTCC 59.551 55.000 2.14 0.00 0.00 3.62
5027 6854 2.347490 GGCTTGCGAGTTCCCTCA 59.653 61.111 2.14 0.00 37.59 3.86
5071 6937 7.439157 AATAGATTAGCAAATGCGCTATGAA 57.561 32.000 9.73 0.00 43.77 2.57
5111 6977 2.433446 GATGATGCCCCGCCAGAT 59.567 61.111 0.00 0.00 0.00 2.90
5173 7039 5.890752 AGCTAATAAAGGGAGGGAAGTAC 57.109 43.478 0.00 0.00 0.00 2.73
5174 7040 4.659368 AGCTAATAAAGGGAGGGAAGTACC 59.341 45.833 0.00 0.00 38.08 3.34
5275 7143 4.254492 GGACTCTGAAAAGTCACATACCC 58.746 47.826 6.40 0.00 46.15 3.69
5314 7430 6.877611 TTGAGTTTTCAGTGAGATTAACCC 57.122 37.500 0.00 0.00 34.15 4.11
5317 7433 7.004086 TGAGTTTTCAGTGAGATTAACCCATT 58.996 34.615 0.00 0.00 0.00 3.16
5318 7434 7.505585 TGAGTTTTCAGTGAGATTAACCCATTT 59.494 33.333 0.00 0.00 0.00 2.32
5319 7435 8.934023 AGTTTTCAGTGAGATTAACCCATTTA 57.066 30.769 0.00 0.00 0.00 1.40
5322 7438 5.437060 TCAGTGAGATTAACCCATTTAGCC 58.563 41.667 0.00 0.00 0.00 3.93
5368 7484 6.866248 ACAATGTTAACAAAATTAAGAGGGCG 59.134 34.615 13.23 0.00 0.00 6.13
5372 7488 4.514781 AACAAAATTAAGAGGGCGTTCC 57.485 40.909 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 156 0.328258 AAACAGGAGGAACCGGGATG 59.672 55.000 6.32 0.00 44.74 3.51
164 165 3.754965 CTGAACCATTCAAACAGGAGGA 58.245 45.455 0.00 0.00 39.58 3.71
175 176 1.796796 GCGTCTGCCTGAACCATTC 59.203 57.895 0.00 0.00 33.98 2.67
177 178 2.434884 CGCGTCTGCCTGAACCAT 60.435 61.111 0.00 0.00 38.08 3.55
192 193 0.589729 CACACAGCAACAGTTCACGC 60.590 55.000 0.00 0.00 0.00 5.34
254 259 1.330234 GACGAGGGATCTAGAACCCC 58.670 60.000 29.48 24.69 46.64 4.95
256 261 0.953003 CCGACGAGGGATCTAGAACC 59.047 60.000 10.54 10.54 35.97 3.62
302 307 5.886609 TCTACCAAATTTCCTCACATCCAA 58.113 37.500 0.00 0.00 0.00 3.53
337 342 2.840640 TCGGTAGAATTCCAGGAGGA 57.159 50.000 0.65 0.00 43.93 3.71
362 367 2.571757 CAGGAGCGTAACCAGCGA 59.428 61.111 0.00 0.00 40.04 4.93
373 378 0.542333 GGTTCCTACCTTCCAGGAGC 59.458 60.000 0.00 0.00 43.05 4.70
404 409 2.427453 GTCGAGATCAAGTCCAGGCTAA 59.573 50.000 0.00 0.00 0.00 3.09
406 411 0.820871 GTCGAGATCAAGTCCAGGCT 59.179 55.000 0.00 0.00 0.00 4.58
411 417 2.996621 CAAACAGGTCGAGATCAAGTCC 59.003 50.000 0.00 0.00 0.00 3.85
413 419 3.753294 ACAAACAGGTCGAGATCAAGT 57.247 42.857 0.00 0.00 0.00 3.16
446 452 1.904852 GATGCCACACACAGCTGTCG 61.905 60.000 18.64 13.89 0.00 4.35
447 453 0.886043 TGATGCCACACACAGCTGTC 60.886 55.000 18.64 5.08 0.00 3.51
449 455 0.887836 ACTGATGCCACACACAGCTG 60.888 55.000 13.48 13.48 33.37 4.24
460 466 4.557695 CGTAGAACTGGATCTACTGATGCC 60.558 50.000 16.02 0.00 46.25 4.40
481 487 2.593956 GCTGTCCCTTTCTCCCCGT 61.594 63.158 0.00 0.00 0.00 5.28
483 489 1.201429 TCAGCTGTCCCTTTCTCCCC 61.201 60.000 14.67 0.00 0.00 4.81
487 493 0.321122 CGCTTCAGCTGTCCCTTTCT 60.321 55.000 14.67 0.00 39.32 2.52
498 504 8.251750 TGTGGAATATTTATATACGCTTCAGC 57.748 34.615 0.00 0.00 37.78 4.26
503 509 6.395629 ACGCTGTGGAATATTTATATACGCT 58.604 36.000 0.00 0.00 0.00 5.07
504 510 6.642683 ACGCTGTGGAATATTTATATACGC 57.357 37.500 0.00 0.00 0.00 4.42
525 531 1.463805 ACGATCAAGACGCGATAACG 58.536 50.000 15.93 11.32 42.93 3.18
530 536 0.806868 ACCTTACGATCAAGACGCGA 59.193 50.000 15.93 0.00 0.00 5.87
575 581 2.159282 ACTAATTCCACTGTAGCGTCGG 60.159 50.000 0.00 0.00 0.00 4.79
603 609 3.577919 GGAGGAGAGGAACCTATAAGCA 58.422 50.000 0.00 0.00 37.93 3.91
646 653 3.274095 CTCTGAAATGGGAGGAACCTC 57.726 52.381 11.97 11.97 42.04 3.85
994 1003 6.633856 ACTTCCATAGAAATGACATTTTGCC 58.366 36.000 14.46 2.80 34.84 4.52
1084 1093 8.655092 CAAATAGAGCTCTAAAGTTGAAGAGTG 58.345 37.037 26.62 7.69 41.13 3.51
1160 1169 5.294552 GCTTTCGTACCTCATTTATCTGCTT 59.705 40.000 0.00 0.00 0.00 3.91
1204 1213 4.929146 AAGGAAACCCTGTATTGCTAGT 57.071 40.909 0.00 0.00 33.44 2.57
1446 1455 3.067833 GAGTACAACCTGCTCTTCCAAC 58.932 50.000 0.00 0.00 0.00 3.77
1461 1470 1.818674 TCTGCATGCTTCTCGAGTACA 59.181 47.619 20.33 9.61 0.00 2.90
1508 1518 3.936453 GGTGTGTTACTGTCACTGACAAA 59.064 43.478 12.92 3.06 42.26 2.83
1552 1562 4.947388 TCAGCCAACAGTTCATTAATACCC 59.053 41.667 0.00 0.00 0.00 3.69
1586 1596 8.078596 AGTATCAAGAACAATCTTCTTTTGCAC 58.921 33.333 0.00 0.00 44.11 4.57
1736 1746 5.567138 AACAAGAACAGTTCTTCCAAGTG 57.433 39.130 23.41 15.31 46.62 3.16
1770 1780 5.178797 GCAGTGAATGAGCTAACCTCTAAA 58.821 41.667 0.00 0.00 41.35 1.85
1946 1956 7.611770 TGCTATGTCACTTTCACACTATTACT 58.388 34.615 0.00 0.00 0.00 2.24
1962 1972 1.270571 TGGTTCGCAGTTGCTATGTCA 60.271 47.619 2.29 0.00 39.32 3.58
2083 2094 5.391312 AAATTATGTGCTGGTGGACTTTC 57.609 39.130 0.00 0.00 35.45 2.62
2763 2998 0.685660 AAGGTCCCGGAAGAACAGAC 59.314 55.000 0.73 0.00 0.00 3.51
2772 3008 1.980772 GGAACTCGAAGGTCCCGGA 60.981 63.158 0.73 0.00 46.52 5.14
2990 3923 6.426327 TGTATGATTCACAAACAAACGTGAG 58.574 36.000 0.00 0.00 42.73 3.51
3099 4033 5.904750 AGGCATCCCCATAATTTACACAATT 59.095 36.000 0.00 0.00 35.39 2.32
3163 4097 4.019858 CTCCAGACTTCCAGAGTGATGTA 58.980 47.826 0.00 0.00 39.19 2.29
3556 4490 3.876320 TGGAAAACAAAAGGCAGAAATGC 59.124 39.130 0.00 0.00 0.00 3.56
3724 4660 4.253685 TCAGGAAGCAATACAGCTAACAC 58.746 43.478 0.00 0.00 45.89 3.32
3771 4707 8.814235 GCTAAAACAGATATACGCTAAAACAGA 58.186 33.333 0.00 0.00 0.00 3.41
3772 4708 8.600625 TGCTAAAACAGATATACGCTAAAACAG 58.399 33.333 0.00 0.00 0.00 3.16
3773 4709 8.481974 TGCTAAAACAGATATACGCTAAAACA 57.518 30.769 0.00 0.00 0.00 2.83
3774 4710 9.370126 CATGCTAAAACAGATATACGCTAAAAC 57.630 33.333 0.00 0.00 0.00 2.43
3775 4711 9.320352 TCATGCTAAAACAGATATACGCTAAAA 57.680 29.630 0.00 0.00 0.00 1.52
3776 4712 8.880878 TCATGCTAAAACAGATATACGCTAAA 57.119 30.769 0.00 0.00 0.00 1.85
3777 4713 8.880878 TTCATGCTAAAACAGATATACGCTAA 57.119 30.769 0.00 0.00 0.00 3.09
3778 4714 9.140286 GATTCATGCTAAAACAGATATACGCTA 57.860 33.333 0.00 0.00 0.00 4.26
3779 4715 7.657354 TGATTCATGCTAAAACAGATATACGCT 59.343 33.333 0.00 0.00 0.00 5.07
3780 4716 7.796838 TGATTCATGCTAAAACAGATATACGC 58.203 34.615 0.00 0.00 0.00 4.42
3781 4717 9.586150 GTTGATTCATGCTAAAACAGATATACG 57.414 33.333 0.00 0.00 0.00 3.06
3782 4718 9.884465 GGTTGATTCATGCTAAAACAGATATAC 57.116 33.333 0.00 0.00 0.00 1.47
4178 5118 2.122768 AGATTCCTTCCTCCGAATGCT 58.877 47.619 0.00 0.00 0.00 3.79
4330 5270 2.279120 CGCCGTGCTCTCCATCTC 60.279 66.667 0.00 0.00 0.00 2.75
4349 5289 3.050275 GCGCAGGCCTTCTTCGTT 61.050 61.111 0.00 0.00 34.68 3.85
4490 5431 5.833667 TGATACCACGGACAGAGAATATTCT 59.166 40.000 17.96 17.96 41.00 2.40
4495 5436 5.386060 TCTATGATACCACGGACAGAGAAT 58.614 41.667 0.00 0.00 29.72 2.40
4656 5608 4.530710 AGTAAAGTGCATCGGTTAGTCA 57.469 40.909 0.00 0.00 0.00 3.41
4679 5631 9.299963 CAAACATAAATCAGAACAACACTCAAA 57.700 29.630 0.00 0.00 0.00 2.69
4695 5647 8.367156 ACAAAGTAACAGCCATCAAACATAAAT 58.633 29.630 0.00 0.00 0.00 1.40
4725 6313 7.497249 GCTAATTTCCATACTTGTCATCAGAGT 59.503 37.037 0.00 0.00 0.00 3.24
4728 6316 7.798596 AGCTAATTTCCATACTTGTCATCAG 57.201 36.000 0.00 0.00 0.00 2.90
4729 6317 8.486210 AGTAGCTAATTTCCATACTTGTCATCA 58.514 33.333 0.00 0.00 0.00 3.07
4730 6318 8.894768 AGTAGCTAATTTCCATACTTGTCATC 57.105 34.615 0.00 0.00 0.00 2.92
4731 6319 8.709308 AGAGTAGCTAATTTCCATACTTGTCAT 58.291 33.333 0.00 0.00 0.00 3.06
4732 6320 7.981789 CAGAGTAGCTAATTTCCATACTTGTCA 59.018 37.037 0.00 0.00 0.00 3.58
4733 6321 8.198109 TCAGAGTAGCTAATTTCCATACTTGTC 58.802 37.037 0.00 0.00 0.00 3.18
4735 6323 8.948631 TTCAGAGTAGCTAATTTCCATACTTG 57.051 34.615 0.00 0.00 0.00 3.16
4799 6618 5.531122 TCATGAAAATACTACTCCCTCCG 57.469 43.478 0.00 0.00 0.00 4.63
4828 6647 0.250081 GGAAGAAGCCGCCCAGATAG 60.250 60.000 0.00 0.00 0.00 2.08
4836 6655 1.464997 CTACACTTTGGAAGAAGCCGC 59.535 52.381 0.00 0.00 0.00 6.53
4837 6656 2.076863 CCTACACTTTGGAAGAAGCCG 58.923 52.381 0.00 0.00 0.00 5.52
4861 6688 6.272822 AGCTATCTCAAAAATCAACAACCC 57.727 37.500 0.00 0.00 0.00 4.11
4869 6696 5.825151 AGCCTGGTAAGCTATCTCAAAAATC 59.175 40.000 0.00 0.00 39.29 2.17
4873 6700 4.225042 TCAAGCCTGGTAAGCTATCTCAAA 59.775 41.667 0.00 0.00 40.49 2.69
4874 6701 3.774766 TCAAGCCTGGTAAGCTATCTCAA 59.225 43.478 0.00 0.00 40.49 3.02
4876 6703 3.723260 GTCAAGCCTGGTAAGCTATCTC 58.277 50.000 0.00 0.00 40.49 2.75
4877 6704 2.101582 CGTCAAGCCTGGTAAGCTATCT 59.898 50.000 0.00 0.00 40.49 1.98
4878 6705 2.474816 CGTCAAGCCTGGTAAGCTATC 58.525 52.381 0.00 0.00 40.49 2.08
4880 6707 0.108329 GCGTCAAGCCTGGTAAGCTA 60.108 55.000 0.00 0.00 40.49 3.32
4882 6709 3.178539 GCGTCAAGCCTGGTAAGC 58.821 61.111 0.00 0.00 40.81 3.09
4891 6718 2.167398 TCCTACACCAGGCGTCAAGC 62.167 60.000 0.00 0.00 45.10 4.01
4892 6719 0.320374 TTCCTACACCAGGCGTCAAG 59.680 55.000 0.00 0.00 45.10 3.02
4895 6722 1.445582 CGTTCCTACACCAGGCGTC 60.446 63.158 0.00 0.00 45.10 5.19
4897 6724 2.125673 CCGTTCCTACACCAGGCG 60.126 66.667 0.00 0.00 45.10 5.52
4898 6725 2.120737 AACCCGTTCCTACACCAGGC 62.121 60.000 0.00 0.00 45.10 4.85
4901 6728 1.071814 GCAACCCGTTCCTACACCA 59.928 57.895 0.00 0.00 0.00 4.17
4902 6729 1.673337 GGCAACCCGTTCCTACACC 60.673 63.158 0.00 0.00 0.00 4.16
4903 6730 3.976758 GGCAACCCGTTCCTACAC 58.023 61.111 0.00 0.00 0.00 2.90
4915 6742 0.745845 AGATGATCGTGCTGGGCAAC 60.746 55.000 0.00 0.00 41.47 4.17
4916 6743 0.035152 AAGATGATCGTGCTGGGCAA 60.035 50.000 0.00 0.00 41.47 4.52
4917 6744 0.829990 TAAGATGATCGTGCTGGGCA 59.170 50.000 0.00 0.00 35.60 5.36
4918 6745 1.953559 TTAAGATGATCGTGCTGGGC 58.046 50.000 0.00 0.00 0.00 5.36
4919 6746 4.576053 TCAATTTAAGATGATCGTGCTGGG 59.424 41.667 0.00 0.00 0.00 4.45
4920 6747 5.504665 GGTCAATTTAAGATGATCGTGCTGG 60.505 44.000 0.00 0.00 0.00 4.85
4921 6748 5.505286 GGTCAATTTAAGATGATCGTGCTG 58.495 41.667 0.00 0.00 0.00 4.41
4922 6749 4.271049 CGGTCAATTTAAGATGATCGTGCT 59.729 41.667 13.90 0.00 43.36 4.40
4923 6750 4.518217 CGGTCAATTTAAGATGATCGTGC 58.482 43.478 13.90 0.00 43.36 5.34
4924 6751 4.570772 ACCGGTCAATTTAAGATGATCGTG 59.429 41.667 18.21 13.72 46.07 4.35
4925 6752 4.766375 ACCGGTCAATTTAAGATGATCGT 58.234 39.130 18.21 8.46 46.07 3.73
4926 6753 5.405571 CCTACCGGTCAATTTAAGATGATCG 59.594 44.000 12.40 14.75 46.83 3.69
4927 6754 5.179555 GCCTACCGGTCAATTTAAGATGATC 59.820 44.000 12.40 0.00 0.00 2.92
4928 6755 5.063880 GCCTACCGGTCAATTTAAGATGAT 58.936 41.667 12.40 0.00 0.00 2.45
4929 6756 4.448210 GCCTACCGGTCAATTTAAGATGA 58.552 43.478 12.40 0.00 0.00 2.92
4930 6757 3.564225 GGCCTACCGGTCAATTTAAGATG 59.436 47.826 12.40 0.00 34.11 2.90
4931 6758 3.201266 TGGCCTACCGGTCAATTTAAGAT 59.799 43.478 12.40 0.00 43.26 2.40
4932 6759 2.572556 TGGCCTACCGGTCAATTTAAGA 59.427 45.455 12.40 0.00 43.26 2.10
4945 6772 1.296727 GCGTGTTAAGATGGCCTACC 58.703 55.000 3.32 0.00 0.00 3.18
4979 6806 6.100404 AGAAATCAACAAAAATAGCTGCCA 57.900 33.333 0.00 0.00 0.00 4.92
4994 6821 4.142622 CGCAAGCCAGATTGTAGAAATCAA 60.143 41.667 0.00 0.00 32.56 2.57
5071 6937 2.641815 ACCCAGAGAGAAGAATGTGCTT 59.358 45.455 0.00 0.00 0.00 3.91
5087 6953 2.196776 GGGGCATCATCCACCCAG 59.803 66.667 0.00 0.00 46.21 4.45
5111 6977 6.373005 TCATTCAACAAGAGAGGGACAATA 57.627 37.500 0.00 0.00 0.00 1.90
5249 7117 4.963318 TGTGACTTTTCAGAGTCCATCT 57.037 40.909 2.89 0.00 44.29 2.90
5268 7136 1.274703 CCTCAGCCCACTGGGTATGT 61.275 60.000 16.03 0.00 43.50 2.29
5322 7438 4.022935 TGTTTGCAGATAAGTCAAGCTTGG 60.023 41.667 25.73 8.53 38.05 3.61


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

AutoCloner maintained by Alex Coulton.