Multiple sequence alignment - TraesCS4A01G342100

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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 TraesCS4A01G342100 chr4A 100.000 4070 0 0 1 4070 622176400 622172331 0.000000e+00 7516
1 TraesCS4A01G342100 chr4A 89.706 408 40 2 3500 3907 53767606 53767201 1.680000e-143 520
2 TraesCS4A01G342100 chr4A 78.235 510 56 39 316 792 622247772 622248259 4.010000e-70 276
3 TraesCS4A01G342100 chr4A 84.112 214 19 3 231 444 622245899 622246097 4.150000e-45 193
4 TraesCS4A01G342100 chr5D 93.752 3857 183 14 1 3838 546824489 546828306 0.000000e+00 5734
5 TraesCS4A01G342100 chr5D 76.433 471 38 33 330 791 546683017 546682611 1.930000e-43 187
6 TraesCS4A01G342100 chr5B 93.692 3852 199 20 1 3838 689901866 689898045 0.000000e+00 5727
7 TraesCS4A01G342100 chr5B 85.586 111 14 2 344 453 689882120 689882011 9.240000e-22 115
8 TraesCS4A01G342100 chr3D 90.998 411 35 2 3497 3907 97984604 97985012 1.650000e-153 553
9 TraesCS4A01G342100 chr2D 91.542 402 32 2 3506 3907 411766120 411765721 1.650000e-153 553
10 TraesCS4A01G342100 chr6D 91.045 402 33 2 3506 3907 38963688 38963290 1.290000e-149 540
11 TraesCS4A01G342100 chr5A 90.756 238 19 3 3670 3907 147102573 147102339 8.490000e-82 315
12 TraesCS4A01G342100 chr5A 90.336 238 20 3 3670 3907 147123657 147123423 3.950000e-80 309
13 TraesCS4A01G342100 chr6A 90.336 238 20 3 3670 3907 276755482 276755716 3.950000e-80 309


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 TraesCS4A01G342100 chr4A 622172331 622176400 4069 True 7516.0 7516 100.0000 1 4070 1 chr4A.!!$R2 4069
1 TraesCS4A01G342100 chr4A 622245899 622248259 2360 False 234.5 276 81.1735 231 792 2 chr4A.!!$F1 561
2 TraesCS4A01G342100 chr5D 546824489 546828306 3817 False 5734.0 5734 93.7520 1 3838 1 chr5D.!!$F1 3837
3 TraesCS4A01G342100 chr5B 689898045 689901866 3821 True 5727.0 5727 93.6920 1 3838 1 chr5B.!!$R2 3837

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
48 49 1.024579 CAAAACCGGCAGGCGTAGAT 61.025 55.000 16.17 0.0 42.76 1.98 F
218 222 1.283613 ACCCTACGATGCCCAAATGAA 59.716 47.619 0.00 0.0 0.00 2.57 F
820 2665 1.336755 CCCTTCTCTCTCTAGCTTCGC 59.663 57.143 0.00 0.0 0.00 4.70 F
2241 4098 0.038744 CATTGCTGGACCAAGGGAGT 59.961 55.000 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 3585 0.321346 TCTTTGCCATGTCGAGCTCA 59.679 50.000 15.4 0.0 0.00 4.26 R
1743 3600 0.878961 GGCTGTCGAACACCGTCTTT 60.879 55.000 0.0 0.0 39.75 2.52 R
2436 4293 0.037326 TCTCGCTGAACGCCTTCAAT 60.037 50.000 0.0 0.0 43.23 2.57 R
3460 5322 1.208293 CCTGGAGTACTTGAGAAGGCC 59.792 57.143 0.0 0.0 0.00 5.19 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
48 49 1.024579 CAAAACCGGCAGGCGTAGAT 61.025 55.000 16.17 0.00 42.76 1.98
122 123 2.076100 CTGCCTCGCATTGTTAGTCAA 58.924 47.619 0.00 0.00 38.13 3.18
218 222 1.283613 ACCCTACGATGCCCAAATGAA 59.716 47.619 0.00 0.00 0.00 2.57
358 362 4.504916 CTGGCCGAGGAGCACGAG 62.505 72.222 0.00 0.00 0.00 4.18
731 2576 4.521062 AGCAGCGGCAGGATCGAC 62.521 66.667 12.44 0.00 44.61 4.20
820 2665 1.336755 CCCTTCTCTCTCTAGCTTCGC 59.663 57.143 0.00 0.00 0.00 4.70
864 2709 2.294791 TGTGTATTCTTTTGTTGGGCCG 59.705 45.455 0.00 0.00 0.00 6.13
962 2813 2.515979 TTGGTTCCTCTGCGGCTCA 61.516 57.895 0.00 0.00 0.00 4.26
964 2815 1.743252 GGTTCCTCTGCGGCTCAAG 60.743 63.158 0.00 0.00 0.00 3.02
965 2816 2.046892 TTCCTCTGCGGCTCAAGC 60.047 61.111 0.00 0.00 41.14 4.01
966 2817 2.587247 TTCCTCTGCGGCTCAAGCT 61.587 57.895 0.00 0.00 41.70 3.74
967 2818 2.511145 CCTCTGCGGCTCAAGCTC 60.511 66.667 0.00 0.00 41.70 4.09
968 2819 2.578128 CTCTGCGGCTCAAGCTCT 59.422 61.111 0.00 0.00 41.70 4.09
969 2820 1.519013 CTCTGCGGCTCAAGCTCTC 60.519 63.158 0.00 0.00 41.70 3.20
970 2821 1.947597 CTCTGCGGCTCAAGCTCTCT 61.948 60.000 0.00 0.00 41.70 3.10
971 2822 1.810441 CTGCGGCTCAAGCTCTCTG 60.810 63.158 0.00 0.00 41.70 3.35
972 2823 3.194308 GCGGCTCAAGCTCTCTGC 61.194 66.667 1.46 0.00 41.70 4.26
1182 3033 4.072088 CGCAAGAACGTCGTGGCC 62.072 66.667 0.00 0.00 43.02 5.36
1256 3107 1.766143 GAGATGTTCGCGGACATGGC 61.766 60.000 36.57 22.78 40.21 4.40
1529 3386 4.735132 CCGGAGCGGCGAGTTCAA 62.735 66.667 12.98 0.00 41.17 2.69
1532 3389 3.843240 GAGCGGCGAGTTCAAGCG 61.843 66.667 12.98 0.00 0.00 4.68
1533 3390 4.357947 AGCGGCGAGTTCAAGCGA 62.358 61.111 12.98 0.00 0.00 4.93
1536 3393 2.738521 GGCGAGTTCAAGCGAGCA 60.739 61.111 0.00 0.00 0.00 4.26
1743 3600 1.902765 ATGGTGAGCTCGACATGGCA 61.903 55.000 18.70 8.20 0.00 4.92
1760 3617 0.232303 GCAAAGACGGTGTTCGACAG 59.768 55.000 0.00 0.00 42.43 3.51
1821 3678 0.910338 AGCTGCACATCAGAGATGGT 59.090 50.000 11.29 0.00 45.72 3.55
1875 3732 0.911769 TGATCTCGGAGGGCATTGTT 59.088 50.000 4.96 0.00 0.00 2.83
1962 3819 2.297033 GCTTCACTCTTTGGCCATCAAA 59.703 45.455 6.09 0.00 42.50 2.69
2004 3861 1.675641 GGTGTCGAATGCCCTGCTT 60.676 57.895 0.00 0.00 0.00 3.91
2190 4047 1.904287 TGCCAAACGACTATGCCTTT 58.096 45.000 0.00 0.00 0.00 3.11
2241 4098 0.038744 CATTGCTGGACCAAGGGAGT 59.961 55.000 0.00 0.00 0.00 3.85
2256 4113 1.559682 GGGAGTCAGTTCCATTGCCTA 59.440 52.381 0.00 0.00 39.09 3.93
2285 4142 1.202580 GCTAGGGTGCGACATGAAGAT 60.203 52.381 0.00 0.00 0.00 2.40
2292 4149 0.299895 GCGACATGAAGATCTGCACG 59.700 55.000 5.22 6.69 0.00 5.34
2436 4293 2.756400 GGTGAGGTGGACATGGCA 59.244 61.111 0.00 0.00 0.00 4.92
2465 4322 2.350522 GTTCAGCGAGATGTGTTCCAT 58.649 47.619 0.00 0.00 36.13 3.41
2612 4469 2.176273 CCTCACACTATGCCTGCGC 61.176 63.158 0.00 0.00 0.00 6.09
2687 4544 0.392998 GAGATGCCTTTTGAGCCCGA 60.393 55.000 0.00 0.00 0.00 5.14
2888 4745 3.319198 GGACGAGGCTGGGGTGAA 61.319 66.667 0.51 0.00 0.00 3.18
2889 4746 2.266055 GACGAGGCTGGGGTGAAG 59.734 66.667 0.51 0.00 0.00 3.02
2902 4759 2.121832 TGAAGAAGGAGGCCGGGA 59.878 61.111 2.18 0.00 0.00 5.14
2903 4760 1.306997 TGAAGAAGGAGGCCGGGAT 60.307 57.895 2.18 0.00 0.00 3.85
2985 4842 2.124612 TCGCCGTCCATCTACCGA 60.125 61.111 0.00 0.00 0.00 4.69
3004 4861 3.432186 CCGAATGCTCTGGGAATTGTCTA 60.432 47.826 0.00 0.00 0.00 2.59
3030 4887 3.118847 CCATGCGAGATACAGCCTATGAT 60.119 47.826 0.00 0.00 0.00 2.45
3104 4961 6.011481 AGTAGTGCATATCCTACTAGGTTCC 58.989 44.000 11.83 0.00 41.51 3.62
3109 4966 5.026790 GCATATCCTACTAGGTTCCTCCAT 58.973 45.833 1.83 0.00 36.53 3.41
3115 4972 4.962995 CCTACTAGGTTCCTCCATTTCTGA 59.037 45.833 0.00 0.00 39.02 3.27
3149 5006 7.340487 ACTGAGTCTTTCTTCTTTTCCAATTGT 59.660 33.333 4.43 0.00 0.00 2.71
3243 5100 6.541278 ATGCTATGTAGGCATGTAGCAATATG 59.459 38.462 15.00 0.00 44.78 1.78
3374 5231 6.783708 TTATTTACTTACCCCATTTGGCAG 57.216 37.500 0.00 0.00 0.00 4.85
3460 5322 2.103771 ACTCAGGTATGGCTGTAGCATG 59.896 50.000 6.18 0.00 44.36 4.06
3531 5393 3.057456 ACAGAACAGACACTTAGCTACGG 60.057 47.826 1.95 0.00 0.00 4.02
3540 5402 3.192212 ACACTTAGCTACGGGTTACACTC 59.808 47.826 0.00 0.00 0.00 3.51
3609 5471 9.995003 CCAAATGAGCTAATTTCTCTAGATAGT 57.005 33.333 6.03 0.00 0.00 2.12
3698 5560 8.663167 AGAAGATTGGTGATACATATGATGGAA 58.337 33.333 10.38 0.00 33.60 3.53
3704 5566 6.942005 TGGTGATACATATGATGGAATTGTCC 59.058 38.462 10.38 0.00 45.21 4.02
3726 5588 3.740115 GTTCAGTGTTCCACTATGGTGT 58.260 45.455 8.53 0.00 43.43 4.16
3746 5608 5.296748 GTGTATTGGTTCACCTGCAATTTT 58.703 37.500 0.00 0.00 36.82 1.82
3805 5667 8.783093 TGTTGTAAATATTCCAGAGTTTGACAG 58.217 33.333 0.00 0.00 0.00 3.51
3806 5668 7.377766 TGTAAATATTCCAGAGTTTGACAGC 57.622 36.000 0.00 0.00 0.00 4.40
3809 5671 7.472334 AAATATTCCAGAGTTTGACAGCAAT 57.528 32.000 0.00 0.00 33.25 3.56
3810 5672 4.778534 ATTCCAGAGTTTGACAGCAATG 57.221 40.909 0.00 0.00 33.25 2.82
3860 5722 9.072375 TCTTACTGATCTTGTACATATCTCTGG 57.928 37.037 15.78 8.74 0.00 3.86
3861 5723 6.662865 ACTGATCTTGTACATATCTCTGGG 57.337 41.667 15.78 7.13 0.00 4.45
3862 5724 6.377080 ACTGATCTTGTACATATCTCTGGGA 58.623 40.000 15.78 0.00 0.00 4.37
3863 5725 7.015680 ACTGATCTTGTACATATCTCTGGGAT 58.984 38.462 15.78 0.00 38.38 3.85
3864 5726 7.178274 ACTGATCTTGTACATATCTCTGGGATC 59.822 40.741 15.78 9.81 35.98 3.36
3865 5727 7.244558 TGATCTTGTACATATCTCTGGGATCT 58.755 38.462 15.78 0.00 35.98 2.75
3866 5728 7.395772 TGATCTTGTACATATCTCTGGGATCTC 59.604 40.741 15.78 0.00 35.98 2.75
3867 5729 6.857848 TCTTGTACATATCTCTGGGATCTCT 58.142 40.000 0.00 0.00 35.98 3.10
3868 5730 7.301420 TCTTGTACATATCTCTGGGATCTCTT 58.699 38.462 0.00 0.00 35.98 2.85
3869 5731 6.907853 TGTACATATCTCTGGGATCTCTTG 57.092 41.667 0.00 0.00 35.98 3.02
3870 5732 5.777223 TGTACATATCTCTGGGATCTCTTGG 59.223 44.000 0.00 0.00 35.98 3.61
3871 5733 4.825445 ACATATCTCTGGGATCTCTTGGT 58.175 43.478 0.00 0.00 35.98 3.67
3872 5734 5.970289 ACATATCTCTGGGATCTCTTGGTA 58.030 41.667 0.00 0.00 35.98 3.25
3873 5735 6.569737 ACATATCTCTGGGATCTCTTGGTAT 58.430 40.000 0.00 0.00 35.98 2.73
3874 5736 6.667414 ACATATCTCTGGGATCTCTTGGTATC 59.333 42.308 0.00 0.00 35.98 2.24
3875 5737 4.823364 TCTCTGGGATCTCTTGGTATCT 57.177 45.455 0.00 0.00 0.00 1.98
3876 5738 5.149584 TCTCTGGGATCTCTTGGTATCTT 57.850 43.478 0.00 0.00 0.00 2.40
3877 5739 4.898265 TCTCTGGGATCTCTTGGTATCTTG 59.102 45.833 0.00 0.00 0.00 3.02
3878 5740 4.624913 TCTGGGATCTCTTGGTATCTTGT 58.375 43.478 0.00 0.00 0.00 3.16
3879 5741 4.651503 TCTGGGATCTCTTGGTATCTTGTC 59.348 45.833 0.00 0.00 0.00 3.18
3880 5742 3.711704 TGGGATCTCTTGGTATCTTGTCC 59.288 47.826 0.00 0.00 0.00 4.02
3881 5743 3.711704 GGGATCTCTTGGTATCTTGTCCA 59.288 47.826 0.00 0.00 0.00 4.02
3882 5744 4.164221 GGGATCTCTTGGTATCTTGTCCAA 59.836 45.833 0.00 0.00 40.77 3.53
3899 5761 8.359642 TCTTGTCCAAGATTTTGTAAATGAAGG 58.640 33.333 5.64 0.00 42.06 3.46
3900 5762 7.595819 TGTCCAAGATTTTGTAAATGAAGGT 57.404 32.000 0.00 0.00 32.21 3.50
3901 5763 7.432869 TGTCCAAGATTTTGTAAATGAAGGTG 58.567 34.615 0.00 0.00 32.21 4.00
3902 5764 7.286546 TGTCCAAGATTTTGTAAATGAAGGTGA 59.713 33.333 0.00 0.00 32.21 4.02
3903 5765 8.306761 GTCCAAGATTTTGTAAATGAAGGTGAT 58.693 33.333 0.00 0.00 32.21 3.06
3904 5766 9.527157 TCCAAGATTTTGTAAATGAAGGTGATA 57.473 29.630 0.00 0.00 32.21 2.15
3905 5767 9.793252 CCAAGATTTTGTAAATGAAGGTGATAG 57.207 33.333 0.00 0.00 32.21 2.08
3906 5768 9.294030 CAAGATTTTGTAAATGAAGGTGATAGC 57.706 33.333 0.00 0.00 0.00 2.97
3907 5769 8.579850 AGATTTTGTAAATGAAGGTGATAGCA 57.420 30.769 0.00 0.00 0.00 3.49
3908 5770 9.193806 AGATTTTGTAAATGAAGGTGATAGCAT 57.806 29.630 0.00 0.00 0.00 3.79
3909 5771 9.455847 GATTTTGTAAATGAAGGTGATAGCATC 57.544 33.333 0.00 0.00 0.00 3.91
3910 5772 7.936496 TTTGTAAATGAAGGTGATAGCATCA 57.064 32.000 0.00 0.00 36.84 3.07
3911 5773 7.936496 TTGTAAATGAAGGTGATAGCATCAA 57.064 32.000 0.00 0.00 41.69 2.57
3912 5774 7.558161 TGTAAATGAAGGTGATAGCATCAAG 57.442 36.000 0.00 0.00 41.69 3.02
3913 5775 7.337938 TGTAAATGAAGGTGATAGCATCAAGA 58.662 34.615 0.00 0.00 41.69 3.02
3914 5776 7.994911 TGTAAATGAAGGTGATAGCATCAAGAT 59.005 33.333 0.00 0.00 41.69 2.40
3915 5777 7.507733 AAATGAAGGTGATAGCATCAAGATC 57.492 36.000 0.00 0.00 41.69 2.75
3916 5778 5.619132 TGAAGGTGATAGCATCAAGATCA 57.381 39.130 0.00 0.00 41.69 2.92
3917 5779 5.993055 TGAAGGTGATAGCATCAAGATCAA 58.007 37.500 0.00 0.00 41.69 2.57
3918 5780 6.053650 TGAAGGTGATAGCATCAAGATCAAG 58.946 40.000 0.00 0.00 41.69 3.02
3919 5781 5.883685 AGGTGATAGCATCAAGATCAAGA 57.116 39.130 0.00 0.00 41.69 3.02
3920 5782 6.436738 AGGTGATAGCATCAAGATCAAGAT 57.563 37.500 0.00 0.00 41.69 2.40
3921 5783 6.465948 AGGTGATAGCATCAAGATCAAGATC 58.534 40.000 1.81 1.81 41.69 2.75
3922 5784 6.042897 AGGTGATAGCATCAAGATCAAGATCA 59.957 38.462 12.21 0.00 41.69 2.92
3923 5785 6.879993 GGTGATAGCATCAAGATCAAGATCAT 59.120 38.462 12.21 0.00 41.69 2.45
3924 5786 8.039538 GGTGATAGCATCAAGATCAAGATCATA 58.960 37.037 12.21 0.00 41.69 2.15
3925 5787 9.602568 GTGATAGCATCAAGATCAAGATCATAT 57.397 33.333 12.21 0.00 41.69 1.78
3952 5814 9.078990 TGATATGTAAGTGTCAAGGTATCTAGG 57.921 37.037 0.00 0.00 0.00 3.02
3953 5815 9.080097 GATATGTAAGTGTCAAGGTATCTAGGT 57.920 37.037 0.00 0.00 0.00 3.08
3954 5816 6.525578 TGTAAGTGTCAAGGTATCTAGGTG 57.474 41.667 0.00 0.00 0.00 4.00
3955 5817 6.250711 TGTAAGTGTCAAGGTATCTAGGTGA 58.749 40.000 0.00 0.00 0.00 4.02
3956 5818 6.895756 TGTAAGTGTCAAGGTATCTAGGTGAT 59.104 38.462 0.00 0.00 39.11 3.06
3957 5819 6.472686 AAGTGTCAAGGTATCTAGGTGATC 57.527 41.667 0.00 0.00 36.65 2.92
3958 5820 5.519808 AGTGTCAAGGTATCTAGGTGATCA 58.480 41.667 0.00 0.00 36.65 2.92
3959 5821 5.958380 AGTGTCAAGGTATCTAGGTGATCAA 59.042 40.000 0.00 0.00 36.65 2.57
3960 5822 6.440647 AGTGTCAAGGTATCTAGGTGATCAAA 59.559 38.462 0.00 0.00 36.65 2.69
3961 5823 7.126421 AGTGTCAAGGTATCTAGGTGATCAAAT 59.874 37.037 0.00 0.00 36.65 2.32
3962 5824 8.421784 GTGTCAAGGTATCTAGGTGATCAAATA 58.578 37.037 0.00 0.00 36.65 1.40
3963 5825 9.159254 TGTCAAGGTATCTAGGTGATCAAATAT 57.841 33.333 0.00 0.00 36.65 1.28
4004 5866 9.793259 AGAACATTTTCTAGATTCTACAAACCA 57.207 29.630 4.12 0.00 40.54 3.67
4018 5880 9.636789 ATTCTACAAACCAAAAGTAGTTAAGGT 57.363 29.630 0.00 1.70 37.20 3.50
4022 5884 8.400184 ACAAACCAAAAGTAGTTAAGGTATCC 57.600 34.615 6.93 0.00 29.91 2.59
4023 5885 8.000127 ACAAACCAAAAGTAGTTAAGGTATCCA 59.000 33.333 6.93 0.00 29.91 3.41
4024 5886 8.512138 CAAACCAAAAGTAGTTAAGGTATCCAG 58.488 37.037 6.93 0.00 29.91 3.86
4025 5887 6.718294 ACCAAAAGTAGTTAAGGTATCCAGG 58.282 40.000 5.10 0.00 0.00 4.45
4026 5888 6.502863 ACCAAAAGTAGTTAAGGTATCCAGGA 59.497 38.462 0.00 0.00 0.00 3.86
4027 5889 7.048512 CCAAAAGTAGTTAAGGTATCCAGGAG 58.951 42.308 0.00 0.00 0.00 3.69
4028 5890 7.311109 CCAAAAGTAGTTAAGGTATCCAGGAGT 60.311 40.741 0.00 0.00 0.00 3.85
4029 5891 8.755977 CAAAAGTAGTTAAGGTATCCAGGAGTA 58.244 37.037 0.00 0.00 0.00 2.59
4030 5892 9.503369 AAAAGTAGTTAAGGTATCCAGGAGTAT 57.497 33.333 0.00 0.00 0.00 2.12
4031 5893 8.480133 AAGTAGTTAAGGTATCCAGGAGTATG 57.520 38.462 0.00 0.00 0.00 2.39
4032 5894 7.593653 AGTAGTTAAGGTATCCAGGAGTATGT 58.406 38.462 0.00 0.00 0.00 2.29
4033 5895 6.732896 AGTTAAGGTATCCAGGAGTATGTG 57.267 41.667 0.00 0.00 0.00 3.21
4034 5896 6.203072 AGTTAAGGTATCCAGGAGTATGTGT 58.797 40.000 0.00 0.00 0.00 3.72
4035 5897 6.672657 AGTTAAGGTATCCAGGAGTATGTGTT 59.327 38.462 0.00 0.00 0.00 3.32
4036 5898 7.182206 AGTTAAGGTATCCAGGAGTATGTGTTT 59.818 37.037 0.00 0.00 0.00 2.83
4037 5899 6.388619 AAGGTATCCAGGAGTATGTGTTTT 57.611 37.500 0.00 0.00 0.00 2.43
4038 5900 5.990668 AGGTATCCAGGAGTATGTGTTTTC 58.009 41.667 0.00 0.00 0.00 2.29
4039 5901 5.726793 AGGTATCCAGGAGTATGTGTTTTCT 59.273 40.000 0.00 0.00 0.00 2.52
4040 5902 6.049790 GGTATCCAGGAGTATGTGTTTTCTC 58.950 44.000 0.00 0.00 0.00 2.87
4041 5903 4.553330 TCCAGGAGTATGTGTTTTCTCC 57.447 45.455 0.00 0.00 44.61 3.71
4045 5907 4.553330 GGAGTATGTGTTTTCTCCTGGA 57.447 45.455 0.00 0.00 42.02 3.86
4046 5908 4.906618 GGAGTATGTGTTTTCTCCTGGAA 58.093 43.478 0.00 0.00 42.02 3.53
4047 5909 5.313712 GGAGTATGTGTTTTCTCCTGGAAA 58.686 41.667 0.00 0.00 42.02 3.13
4048 5910 5.946377 GGAGTATGTGTTTTCTCCTGGAAAT 59.054 40.000 0.00 0.00 42.63 2.17
4049 5911 6.434340 GGAGTATGTGTTTTCTCCTGGAAATT 59.566 38.462 0.00 0.00 42.63 1.82
4050 5912 7.610305 GGAGTATGTGTTTTCTCCTGGAAATTA 59.390 37.037 0.00 0.00 42.63 1.40
4051 5913 9.178758 GAGTATGTGTTTTCTCCTGGAAATTAT 57.821 33.333 0.00 0.00 42.63 1.28
4052 5914 9.533831 AGTATGTGTTTTCTCCTGGAAATTATT 57.466 29.630 0.00 0.00 42.63 1.40
4055 5917 8.934023 TGTGTTTTCTCCTGGAAATTATTAGT 57.066 30.769 0.00 0.00 42.63 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 0.976641 ATTTCGAGAGGGTGACTGCA 59.023 50.000 0.00 0.00 0.00 4.41
122 123 0.630673 TCTATGGTTTGGCAGGGCAT 59.369 50.000 0.00 0.00 0.00 4.40
204 208 0.808125 TTCGGTTCATTTGGGCATCG 59.192 50.000 0.00 0.00 0.00 3.84
218 222 2.872245 CTCGTATGCCATCAATTTCGGT 59.128 45.455 0.00 0.00 0.00 4.69
879 2724 4.473520 AATGCTCTCGTGGGCCGG 62.474 66.667 6.92 0.00 37.11 6.13
889 2734 1.683365 AATTGGGCCGCAATGCTCT 60.683 52.632 17.06 2.68 31.16 4.09
910 2755 2.012673 GATAAGCTTCAGCCCAGTGTG 58.987 52.381 0.00 0.00 43.38 3.82
942 2791 2.281484 GCCGCAGAGGAACCAACA 60.281 61.111 0.00 0.00 45.00 3.33
964 2815 2.516460 CCCATGGCAGCAGAGAGC 60.516 66.667 6.09 0.00 46.19 4.09
965 2816 1.146485 CTCCCATGGCAGCAGAGAG 59.854 63.158 6.09 1.55 0.00 3.20
966 2817 1.614525 ACTCCCATGGCAGCAGAGA 60.615 57.895 18.51 3.62 0.00 3.10
967 2818 1.451567 CACTCCCATGGCAGCAGAG 60.452 63.158 6.09 9.81 0.00 3.35
968 2819 2.672908 CACTCCCATGGCAGCAGA 59.327 61.111 6.09 0.00 0.00 4.26
969 2820 2.439701 CCACTCCCATGGCAGCAG 60.440 66.667 6.09 0.00 31.52 4.24
970 2821 2.934932 TCCACTCCCATGGCAGCA 60.935 61.111 6.09 0.00 39.85 4.41
971 2822 2.439156 GTCCACTCCCATGGCAGC 60.439 66.667 6.09 0.00 39.85 5.25
972 2823 1.377725 GTGTCCACTCCCATGGCAG 60.378 63.158 6.09 2.72 39.85 4.85
1182 3033 4.436998 GACACGGCCGAGGTCCAG 62.437 72.222 35.90 13.98 0.00 3.86
1224 3075 4.031719 ATCTCGATCGCGGCCTCG 62.032 66.667 9.35 9.35 38.28 4.63
1532 3389 4.074526 TGAGTGCCTCCGCTGCTC 62.075 66.667 0.00 0.00 37.84 4.26
1533 3390 4.079850 CTGAGTGCCTCCGCTGCT 62.080 66.667 0.00 0.00 35.36 4.24
1545 3402 0.469070 GCTCCATCATCTGGCTGAGT 59.531 55.000 0.00 0.00 45.52 3.41
1549 3406 2.815945 CCCGCTCCATCATCTGGCT 61.816 63.158 0.00 0.00 45.52 4.75
1558 3415 2.765807 CTCCACTCCCCGCTCCAT 60.766 66.667 0.00 0.00 0.00 3.41
1694 3551 2.152013 GAAATCGATCAGCGCGCTCC 62.152 60.000 34.28 21.62 40.61 4.70
1728 3585 0.321346 TCTTTGCCATGTCGAGCTCA 59.679 50.000 15.40 0.00 0.00 4.26
1743 3600 0.878961 GGCTGTCGAACACCGTCTTT 60.879 55.000 0.00 0.00 39.75 2.52
1760 3617 1.598130 ACGTTCTTGCACTGGAGGC 60.598 57.895 0.00 0.00 0.00 4.70
1821 3678 2.041922 AGTGCATCCTCCGGCCTA 60.042 61.111 0.00 0.00 0.00 3.93
1962 3819 2.214181 GATCACTCGCCAGGTCACGT 62.214 60.000 0.00 0.00 0.00 4.49
2055 3912 1.006805 GTCTGGATCCTCGATGCCG 60.007 63.158 14.23 0.00 29.18 5.69
2190 4047 1.079127 GGAGCTTAGCACGCTGGAA 60.079 57.895 7.07 0.00 37.96 3.53
2241 4098 0.255890 GGGCTAGGCAATGGAACTGA 59.744 55.000 19.14 0.00 0.00 3.41
2292 4149 1.231958 TGTTGATCAACGCGTTCCCC 61.232 55.000 28.55 13.79 43.94 4.81
2302 4159 4.455533 GCACTTGGAGTACATGTTGATCAA 59.544 41.667 2.30 3.38 35.49 2.57
2436 4293 0.037326 TCTCGCTGAACGCCTTCAAT 60.037 50.000 0.00 0.00 43.23 2.57
2527 4384 0.323725 GCCACACCTTCATCCACCAT 60.324 55.000 0.00 0.00 0.00 3.55
2535 4392 2.106338 TCTGAAGAATGCCACACCTTCA 59.894 45.455 0.00 0.00 41.62 3.02
2687 4544 0.879765 CGTCTTCCACACTAGGACGT 59.120 55.000 0.00 0.00 42.85 4.34
2707 4564 2.703798 GCCTGCATGACGCCAACAT 61.704 57.895 0.00 0.00 41.33 2.71
2865 4722 2.503061 CCAGCCTCGTCCATCCTG 59.497 66.667 0.00 0.00 0.00 3.86
2888 4745 1.764054 CTGATCCCGGCCTCCTTCT 60.764 63.158 0.00 0.00 0.00 2.85
2889 4746 2.825264 CTGATCCCGGCCTCCTTC 59.175 66.667 0.00 0.00 0.00 3.46
2902 4759 1.229625 TGACCTCCACCCAGCTGAT 60.230 57.895 17.39 0.00 0.00 2.90
2903 4760 1.915266 CTGACCTCCACCCAGCTGA 60.915 63.158 17.39 0.00 0.00 4.26
2985 4842 4.340381 GCATTAGACAATTCCCAGAGCATT 59.660 41.667 0.00 0.00 0.00 3.56
3004 4861 1.233019 GCTGTATCTCGCATGGCATT 58.767 50.000 0.00 0.00 0.00 3.56
3030 4887 6.653526 ACATCCAACAATTCAACATCTTCA 57.346 33.333 0.00 0.00 0.00 3.02
3081 4938 6.011481 AGGAACCTAGTAGGATATGCACTAC 58.989 44.000 23.50 4.46 37.67 2.73
3104 4961 5.551233 TCAGTTACCTTGTCAGAAATGGAG 58.449 41.667 0.00 0.00 0.00 3.86
3109 4966 5.871396 AGACTCAGTTACCTTGTCAGAAA 57.129 39.130 0.00 0.00 0.00 2.52
3115 4972 6.487299 AGAAGAAAGACTCAGTTACCTTGT 57.513 37.500 0.00 0.00 0.00 3.16
3134 4991 5.350633 TGCAAGTGACAATTGGAAAAGAAG 58.649 37.500 16.65 0.00 0.00 2.85
3149 5006 5.356751 ACAAAGAACAGTGTAATGCAAGTGA 59.643 36.000 0.00 0.00 0.00 3.41
3365 5222 5.078411 ACTAGTGAGTCTACTGCCAAATG 57.922 43.478 0.00 0.00 32.19 2.32
3374 5231 6.587206 AACCCAGTTTACTAGTGAGTCTAC 57.413 41.667 5.39 0.00 37.10 2.59
3460 5322 1.208293 CCTGGAGTACTTGAGAAGGCC 59.792 57.143 0.00 0.00 0.00 5.19
3531 5393 3.560068 CAGTCCAAACTGTGAGTGTAACC 59.440 47.826 0.00 0.00 46.52 2.85
3609 5471 4.074970 GCTTCTTCCCTCATTCACTTCAA 58.925 43.478 0.00 0.00 0.00 2.69
3642 5504 9.278978 GAACTTGTTAAGAAAATTCTCTCCTCT 57.721 33.333 0.00 0.00 36.28 3.69
3660 5522 6.122277 TCACCAATCTTCTTGAGAACTTGTT 58.878 36.000 9.00 0.00 38.06 2.83
3698 5560 2.631160 TGGAACACTGAACGGACAAT 57.369 45.000 0.00 0.00 0.00 2.71
3726 5588 5.538053 TCAGAAAATTGCAGGTGAACCAATA 59.462 36.000 1.62 0.00 38.89 1.90
3838 5700 6.377080 TCCCAGAGATATGTACAAGATCAGT 58.623 40.000 18.39 0.00 0.00 3.41
3839 5701 6.907853 TCCCAGAGATATGTACAAGATCAG 57.092 41.667 18.39 10.44 0.00 2.90
3840 5702 7.244558 AGATCCCAGAGATATGTACAAGATCA 58.755 38.462 18.39 2.88 34.42 2.92
3841 5703 7.615365 AGAGATCCCAGAGATATGTACAAGATC 59.385 40.741 0.00 6.33 34.42 2.75
3842 5704 7.477864 AGAGATCCCAGAGATATGTACAAGAT 58.522 38.462 0.00 0.00 34.42 2.40
3843 5705 6.857848 AGAGATCCCAGAGATATGTACAAGA 58.142 40.000 0.00 0.00 34.42 3.02
3844 5706 7.377398 CAAGAGATCCCAGAGATATGTACAAG 58.623 42.308 0.00 0.00 34.42 3.16
3845 5707 6.268617 CCAAGAGATCCCAGAGATATGTACAA 59.731 42.308 0.00 0.00 34.42 2.41
3846 5708 5.777223 CCAAGAGATCCCAGAGATATGTACA 59.223 44.000 0.00 0.00 34.42 2.90
3847 5709 5.777732 ACCAAGAGATCCCAGAGATATGTAC 59.222 44.000 0.00 0.00 34.42 2.90
3848 5710 5.970289 ACCAAGAGATCCCAGAGATATGTA 58.030 41.667 0.00 0.00 34.42 2.29
3849 5711 4.825445 ACCAAGAGATCCCAGAGATATGT 58.175 43.478 0.00 0.00 34.42 2.29
3850 5712 6.896860 AGATACCAAGAGATCCCAGAGATATG 59.103 42.308 0.00 0.00 34.42 1.78
3851 5713 7.055314 AGATACCAAGAGATCCCAGAGATAT 57.945 40.000 0.00 0.00 34.42 1.63
3852 5714 6.476409 AGATACCAAGAGATCCCAGAGATA 57.524 41.667 0.00 0.00 34.42 1.98
3853 5715 5.352700 AGATACCAAGAGATCCCAGAGAT 57.647 43.478 0.00 0.00 38.17 2.75
3854 5716 4.823364 AGATACCAAGAGATCCCAGAGA 57.177 45.455 0.00 0.00 0.00 3.10
3855 5717 4.653341 ACAAGATACCAAGAGATCCCAGAG 59.347 45.833 0.00 0.00 0.00 3.35
3856 5718 4.624913 ACAAGATACCAAGAGATCCCAGA 58.375 43.478 0.00 0.00 0.00 3.86
3857 5719 4.202305 GGACAAGATACCAAGAGATCCCAG 60.202 50.000 0.00 0.00 0.00 4.45
3858 5720 3.711704 GGACAAGATACCAAGAGATCCCA 59.288 47.826 0.00 0.00 0.00 4.37
3859 5721 3.711704 TGGACAAGATACCAAGAGATCCC 59.288 47.826 0.00 0.00 32.93 3.85
3860 5722 5.359194 TTGGACAAGATACCAAGAGATCC 57.641 43.478 0.00 0.00 40.59 3.36
3874 5736 8.143835 ACCTTCATTTACAAAATCTTGGACAAG 58.856 33.333 5.72 5.72 36.82 3.16
3875 5737 7.925483 CACCTTCATTTACAAAATCTTGGACAA 59.075 33.333 0.00 0.00 36.82 3.18
3876 5738 7.286546 TCACCTTCATTTACAAAATCTTGGACA 59.713 33.333 0.00 0.00 36.82 4.02
3877 5739 7.657336 TCACCTTCATTTACAAAATCTTGGAC 58.343 34.615 0.00 0.00 36.82 4.02
3878 5740 7.831691 TCACCTTCATTTACAAAATCTTGGA 57.168 32.000 0.00 0.00 36.82 3.53
3879 5741 9.793252 CTATCACCTTCATTTACAAAATCTTGG 57.207 33.333 0.00 0.00 36.82 3.61
3880 5742 9.294030 GCTATCACCTTCATTTACAAAATCTTG 57.706 33.333 0.00 0.00 38.61 3.02
3881 5743 9.023962 TGCTATCACCTTCATTTACAAAATCTT 57.976 29.630 0.00 0.00 0.00 2.40
3882 5744 8.579850 TGCTATCACCTTCATTTACAAAATCT 57.420 30.769 0.00 0.00 0.00 2.40
3883 5745 9.455847 GATGCTATCACCTTCATTTACAAAATC 57.544 33.333 0.00 0.00 0.00 2.17
3884 5746 8.970020 TGATGCTATCACCTTCATTTACAAAAT 58.030 29.630 0.00 0.00 33.59 1.82
3885 5747 8.347004 TGATGCTATCACCTTCATTTACAAAA 57.653 30.769 0.00 0.00 33.59 2.44
3886 5748 7.936496 TGATGCTATCACCTTCATTTACAAA 57.064 32.000 0.00 0.00 33.59 2.83
3887 5749 7.828717 TCTTGATGCTATCACCTTCATTTACAA 59.171 33.333 0.00 0.00 39.39 2.41
3888 5750 7.337938 TCTTGATGCTATCACCTTCATTTACA 58.662 34.615 0.00 0.00 39.39 2.41
3889 5751 7.792374 TCTTGATGCTATCACCTTCATTTAC 57.208 36.000 0.00 0.00 39.39 2.01
3890 5752 8.212995 TGATCTTGATGCTATCACCTTCATTTA 58.787 33.333 0.00 0.00 39.39 1.40
3891 5753 7.058525 TGATCTTGATGCTATCACCTTCATTT 58.941 34.615 0.00 0.00 39.39 2.32
3892 5754 6.598503 TGATCTTGATGCTATCACCTTCATT 58.401 36.000 0.00 0.00 39.39 2.57
3893 5755 6.183810 TGATCTTGATGCTATCACCTTCAT 57.816 37.500 0.00 0.00 39.39 2.57
3894 5756 5.619132 TGATCTTGATGCTATCACCTTCA 57.381 39.130 0.00 0.00 39.39 3.02
3895 5757 6.286758 TCTTGATCTTGATGCTATCACCTTC 58.713 40.000 0.00 0.00 39.39 3.46
3896 5758 6.244552 TCTTGATCTTGATGCTATCACCTT 57.755 37.500 0.00 0.00 39.39 3.50
3897 5759 5.883685 TCTTGATCTTGATGCTATCACCT 57.116 39.130 0.00 0.00 39.39 4.00
3898 5760 6.228995 TGATCTTGATCTTGATGCTATCACC 58.771 40.000 11.31 0.00 39.39 4.02
3899 5761 7.908827 ATGATCTTGATCTTGATGCTATCAC 57.091 36.000 11.31 0.00 39.39 3.06
3926 5788 9.078990 CCTAGATACCTTGACACTTACATATCA 57.921 37.037 0.00 0.00 0.00 2.15
3927 5789 9.080097 ACCTAGATACCTTGACACTTACATATC 57.920 37.037 0.00 0.00 0.00 1.63
3928 5790 8.861086 CACCTAGATACCTTGACACTTACATAT 58.139 37.037 0.00 0.00 0.00 1.78
3929 5791 8.057011 TCACCTAGATACCTTGACACTTACATA 58.943 37.037 0.00 0.00 0.00 2.29
3930 5792 6.895756 TCACCTAGATACCTTGACACTTACAT 59.104 38.462 0.00 0.00 0.00 2.29
3931 5793 6.250711 TCACCTAGATACCTTGACACTTACA 58.749 40.000 0.00 0.00 0.00 2.41
3932 5794 6.770746 TCACCTAGATACCTTGACACTTAC 57.229 41.667 0.00 0.00 0.00 2.34
3933 5795 7.123383 TGATCACCTAGATACCTTGACACTTA 58.877 38.462 0.00 0.00 37.00 2.24
3934 5796 5.958380 TGATCACCTAGATACCTTGACACTT 59.042 40.000 0.00 0.00 37.00 3.16
3935 5797 5.519808 TGATCACCTAGATACCTTGACACT 58.480 41.667 0.00 0.00 37.00 3.55
3936 5798 5.854010 TGATCACCTAGATACCTTGACAC 57.146 43.478 0.00 0.00 37.00 3.67
3937 5799 6.867519 TTTGATCACCTAGATACCTTGACA 57.132 37.500 0.00 0.00 37.00 3.58
3978 5840 9.793259 TGGTTTGTAGAATCTAGAAAATGTTCT 57.207 29.630 13.18 3.06 46.18 3.01
3992 5854 9.636789 ACCTTAACTACTTTTGGTTTGTAGAAT 57.363 29.630 0.00 0.00 37.62 2.40
3996 5858 9.506018 GGATACCTTAACTACTTTTGGTTTGTA 57.494 33.333 0.00 0.00 0.00 2.41
3997 5859 8.000127 TGGATACCTTAACTACTTTTGGTTTGT 59.000 33.333 0.00 0.00 0.00 2.83
3998 5860 8.398878 TGGATACCTTAACTACTTTTGGTTTG 57.601 34.615 0.00 0.00 0.00 2.93
3999 5861 7.668469 CCTGGATACCTTAACTACTTTTGGTTT 59.332 37.037 0.00 0.00 0.00 3.27
4000 5862 7.017850 TCCTGGATACCTTAACTACTTTTGGTT 59.982 37.037 0.00 0.00 0.00 3.67
4001 5863 6.502863 TCCTGGATACCTTAACTACTTTTGGT 59.497 38.462 0.00 0.00 0.00 3.67
4002 5864 6.954232 TCCTGGATACCTTAACTACTTTTGG 58.046 40.000 0.00 0.00 0.00 3.28
4003 5865 7.621796 ACTCCTGGATACCTTAACTACTTTTG 58.378 38.462 0.00 0.00 0.00 2.44
4004 5866 7.809880 ACTCCTGGATACCTTAACTACTTTT 57.190 36.000 0.00 0.00 0.00 2.27
4005 5867 8.925338 CATACTCCTGGATACCTTAACTACTTT 58.075 37.037 0.00 0.00 0.00 2.66
4006 5868 8.066247 ACATACTCCTGGATACCTTAACTACTT 58.934 37.037 0.00 0.00 0.00 2.24
4007 5869 7.506261 CACATACTCCTGGATACCTTAACTACT 59.494 40.741 0.00 0.00 0.00 2.57
4008 5870 7.287235 ACACATACTCCTGGATACCTTAACTAC 59.713 40.741 0.00 0.00 0.00 2.73
4009 5871 7.359849 ACACATACTCCTGGATACCTTAACTA 58.640 38.462 0.00 0.00 0.00 2.24
4010 5872 6.203072 ACACATACTCCTGGATACCTTAACT 58.797 40.000 0.00 0.00 0.00 2.24
4011 5873 6.481434 ACACATACTCCTGGATACCTTAAC 57.519 41.667 0.00 0.00 0.00 2.01
4012 5874 7.504926 AAACACATACTCCTGGATACCTTAA 57.495 36.000 0.00 0.00 0.00 1.85
4013 5875 7.402071 AGAAAACACATACTCCTGGATACCTTA 59.598 37.037 0.00 0.00 0.00 2.69
4014 5876 6.215636 AGAAAACACATACTCCTGGATACCTT 59.784 38.462 0.00 0.00 0.00 3.50
4015 5877 5.726793 AGAAAACACATACTCCTGGATACCT 59.273 40.000 0.00 0.00 0.00 3.08
4016 5878 5.990668 AGAAAACACATACTCCTGGATACC 58.009 41.667 0.00 0.00 0.00 2.73
4017 5879 6.049790 GGAGAAAACACATACTCCTGGATAC 58.950 44.000 0.00 0.00 43.64 2.24
4018 5880 6.235231 GGAGAAAACACATACTCCTGGATA 57.765 41.667 0.00 0.00 43.64 2.59
4019 5881 5.104259 GGAGAAAACACATACTCCTGGAT 57.896 43.478 0.00 0.00 43.64 3.41
4020 5882 4.553330 GGAGAAAACACATACTCCTGGA 57.447 45.455 0.00 0.00 43.64 3.86
4024 5886 4.553330 TCCAGGAGAAAACACATACTCC 57.447 45.455 0.00 0.00 46.28 3.85


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

AutoCloner maintained by Alex Coulton.