Multiple sequence alignment - TraesCS5B01G449800

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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 TraesCS5B01G449800 chr5B 100.000 4313 0 0 1 4313 622069335 622065023 0.000000e+00 7965.0
1 TraesCS5B01G449800 chr5B 77.097 310 48 12 3389 3678 622380902 622380596 1.610000e-34 158.0
2 TraesCS5B01G449800 chr5D 97.280 3861 71 10 1 3853 500676945 500673111 0.000000e+00 6517.0
3 TraesCS5B01G449800 chr5D 98.599 357 3 1 3957 4313 500673113 500672759 7.870000e-177 630.0
4 TraesCS5B01G449800 chr5A 79.630 216 25 13 4099 4303 624801567 624801774 2.090000e-28 137.0
5 TraesCS5B01G449800 chr2A 79.487 195 39 1 2368 2562 16668139 16667946 2.090000e-28 137.0
6 TraesCS5B01G449800 chr7A 71.360 625 143 21 1999 2592 320060 320679 3.500000e-26 130.0
7 TraesCS5B01G449800 chr1D 93.617 47 3 0 1445 1491 192569780 192569826 2.150000e-08 71.3
8 TraesCS5B01G449800 chr1A 93.617 47 3 0 1445 1491 238678433 238678479 2.150000e-08 71.3


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 TraesCS5B01G449800 chr5B 622065023 622069335 4312 True 7965.0 7965 100.0000 1 4313 1 chr5B.!!$R1 4312
1 TraesCS5B01G449800 chr5D 500672759 500676945 4186 True 3573.5 6517 97.9395 1 4313 2 chr5D.!!$R1 4312

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
467 468 0.106708 GTGGATATGCCTGCCGAAGA 59.893 55.0 0.0 0.0 37.63 2.87 F
468 469 0.106708 TGGATATGCCTGCCGAAGAC 59.893 55.0 0.0 0.0 37.63 3.01 F
1125 1126 0.246635 CCAATCTGGTTCTCGACGGT 59.753 55.0 0.0 0.0 31.35 4.83 F
2754 2755 0.101759 GGCTGCATGGCAACTATGTG 59.898 55.0 0.5 0.0 38.41 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 1719 0.108472 TGCTGCTGACGAGAATCCAG 60.108 55.000 0.00 0.0 0.0 3.86 R
2427 2428 1.154016 ATCGTCGAGGAGCACGTTG 60.154 57.895 13.85 0.0 37.3 4.10 R
2903 2904 0.252479 CTGCATCAAGGCCAGAGTCT 59.748 55.000 5.01 0.0 0.0 3.24 R
3950 3958 0.036388 GGTGCTCTTGGATCGGTGAA 60.036 55.000 0.00 0.0 0.0 3.18 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
56 57 1.546476 ACGAAAGACGCAGAGAAGGAT 59.454 47.619 0.00 0.00 46.94 3.24
62 63 1.140589 CGCAGAGAAGGATCGCACT 59.859 57.895 0.00 0.00 0.00 4.40
73 74 1.412710 GGATCGCACTCTACCATTGGA 59.587 52.381 10.37 0.00 0.00 3.53
158 159 0.112606 TCACCTTGAGGAGTCCGTCT 59.887 55.000 2.76 0.00 38.94 4.18
169 170 1.664965 GTCCGTCTGCTGTGACCAC 60.665 63.158 0.00 0.00 33.70 4.16
279 280 1.488393 CCAAGCTAAGGAAGAGGAGGG 59.512 57.143 0.00 0.00 0.00 4.30
373 374 0.173708 GTGCTCGGTAGACCTCCAAG 59.826 60.000 0.00 0.00 0.00 3.61
420 421 0.251916 TGGCTAACTGGCAGCGTATT 59.748 50.000 15.89 3.68 46.76 1.89
421 422 1.483004 TGGCTAACTGGCAGCGTATTA 59.517 47.619 15.89 4.77 46.76 0.98
440 441 2.982339 ATCTACTCGCCATCTAGGGT 57.018 50.000 0.00 0.00 38.09 4.34
466 467 0.179048 TGTGGATATGCCTGCCGAAG 60.179 55.000 0.00 0.00 37.63 3.79
467 468 0.106708 GTGGATATGCCTGCCGAAGA 59.893 55.000 0.00 0.00 37.63 2.87
468 469 0.106708 TGGATATGCCTGCCGAAGAC 59.893 55.000 0.00 0.00 37.63 3.01
469 470 0.394565 GGATATGCCTGCCGAAGACT 59.605 55.000 0.00 0.00 0.00 3.24
470 471 1.202698 GGATATGCCTGCCGAAGACTT 60.203 52.381 0.00 0.00 0.00 3.01
471 472 1.869767 GATATGCCTGCCGAAGACTTG 59.130 52.381 0.00 0.00 0.00 3.16
472 473 0.613260 TATGCCTGCCGAAGACTTGT 59.387 50.000 0.00 0.00 0.00 3.16
473 474 0.674895 ATGCCTGCCGAAGACTTGTC 60.675 55.000 0.00 0.00 0.00 3.18
474 475 1.301716 GCCTGCCGAAGACTTGTCA 60.302 57.895 3.49 0.00 0.00 3.58
475 476 0.884704 GCCTGCCGAAGACTTGTCAA 60.885 55.000 3.49 0.00 0.00 3.18
476 477 0.868406 CCTGCCGAAGACTTGTCAAC 59.132 55.000 3.49 0.00 0.00 3.18
482 483 2.471743 CCGAAGACTTGTCAACGACTTC 59.528 50.000 16.18 12.55 33.15 3.01
594 595 2.222027 GGCATAAATCTTCTGGTCCCG 58.778 52.381 0.00 0.00 0.00 5.14
634 635 7.072562 TCATAATACCAAGGGCCACATAATTT 58.927 34.615 6.18 0.00 0.00 1.82
775 776 3.947910 ATTGGGTGCACAATTGAAGAG 57.052 42.857 20.43 0.13 37.81 2.85
805 806 0.463654 TCATGTAGGCGCCCATCAAC 60.464 55.000 26.15 14.34 0.00 3.18
829 830 6.260050 ACAAATGTCGTTTCTGTTGTCACTAT 59.740 34.615 0.00 0.00 0.00 2.12
846 847 3.873361 CACTATCGTTGAATGGCACTCAT 59.127 43.478 0.00 0.00 37.79 2.90
861 862 5.713792 GCACTCATGCCTAGACTAAGATA 57.286 43.478 0.00 0.00 46.97 1.98
862 863 6.090483 GCACTCATGCCTAGACTAAGATAA 57.910 41.667 0.00 0.00 46.97 1.75
863 864 5.923684 GCACTCATGCCTAGACTAAGATAAC 59.076 44.000 0.00 0.00 46.97 1.89
864 865 6.461648 GCACTCATGCCTAGACTAAGATAACA 60.462 42.308 0.00 0.00 46.97 2.41
865 866 7.665690 CACTCATGCCTAGACTAAGATAACAT 58.334 38.462 0.00 0.00 0.00 2.71
874 875 5.431765 AGACTAAGATAACATGCTTGTGGG 58.568 41.667 5.94 0.00 35.83 4.61
879 880 5.121380 AGATAACATGCTTGTGGGAAGAT 57.879 39.130 5.94 0.00 35.83 2.40
1024 1025 2.496817 CTCTGCCCTGGCTCGTAC 59.503 66.667 9.97 0.00 42.51 3.67
1057 1058 4.770010 TCCTTGGCCTTAACCAACAAATAG 59.230 41.667 3.32 0.00 44.80 1.73
1099 1100 3.196469 CCAGTTCATCTACTCTGGCTTCA 59.804 47.826 0.00 0.00 40.43 3.02
1125 1126 0.246635 CCAATCTGGTTCTCGACGGT 59.753 55.000 0.00 0.00 31.35 4.83
1175 1176 1.282157 GGACCTAACCAATGGCTCTGT 59.718 52.381 0.00 0.00 0.00 3.41
1227 1228 3.071479 TCCATTACGCTTCCACAAGTTC 58.929 45.455 0.00 0.00 31.45 3.01
1228 1229 3.074412 CCATTACGCTTCCACAAGTTCT 58.926 45.455 0.00 0.00 31.45 3.01
1229 1230 3.125316 CCATTACGCTTCCACAAGTTCTC 59.875 47.826 0.00 0.00 31.45 2.87
1343 1344 2.551459 CACCAAGCAAGAACTTCTCAGG 59.449 50.000 0.00 0.00 0.00 3.86
1380 1381 1.227674 CATGGGCCTCCTTAGCGAC 60.228 63.158 4.53 0.00 0.00 5.19
1544 1545 6.314896 GGCTTCTATGATGATAAGCATGGTAC 59.685 42.308 0.00 0.00 44.81 3.34
1664 1665 3.387609 TTGCCAAACCAGCCAGGGT 62.388 57.895 0.00 0.00 45.04 4.34
1665 1666 2.991540 GCCAAACCAGCCAGGGTC 60.992 66.667 0.00 0.00 41.32 4.46
1718 1719 3.497640 GTCCTCACAGAATCAGCATATGC 59.502 47.826 20.36 20.36 42.49 3.14
1884 1885 7.050377 CCAAGTTTCTAGAGATAATTCTGCCA 58.950 38.462 0.00 0.00 30.30 4.92
1917 1918 0.599728 CAGCAGGAGCGCTAATCCTC 60.600 60.000 11.50 7.63 44.05 3.71
1935 1936 2.400399 CTCGTGGTTTTTCTGCTCGTA 58.600 47.619 0.00 0.00 0.00 3.43
2164 2165 4.883585 CGAATCAAGGGATGAAGGAATTCA 59.116 41.667 7.93 0.00 42.54 2.57
2219 2220 1.135402 CCGCAATCTTGTGCCCTTAAC 60.135 52.381 0.00 0.00 41.73 2.01
2239 2240 2.740826 GCTACTGCCGGCGAAACA 60.741 61.111 23.90 1.77 0.00 2.83
2270 2271 8.543774 ACTCCTTCTAGTGTATGAATTCATGTT 58.456 33.333 27.59 13.87 37.15 2.71
2427 2428 2.223203 CCATCGAGACATCAAAGCAAGC 60.223 50.000 0.00 0.00 0.00 4.01
2586 2587 1.377856 GAAGGCAAGCCCTCTCACC 60.378 63.158 7.62 0.00 45.62 4.02
2611 2612 3.810941 TGTATTTTCTTTCGGCGTGTTCT 59.189 39.130 6.85 0.00 0.00 3.01
2754 2755 0.101759 GGCTGCATGGCAACTATGTG 59.898 55.000 0.50 0.00 38.41 3.21
2805 2806 2.301296 AGGATTGATATGCTCTCACCCG 59.699 50.000 0.00 0.00 0.00 5.28
2973 2974 3.005897 CCTCGTATCCTTCATCGATGGTT 59.994 47.826 24.61 7.25 0.00 3.67
2982 2983 3.961480 TCATCGATGGTTAGCTATGGG 57.039 47.619 24.61 0.00 0.00 4.00
2986 2987 2.628178 TCGATGGTTAGCTATGGGTCAG 59.372 50.000 0.00 0.00 0.00 3.51
2990 2991 3.990369 TGGTTAGCTATGGGTCAGTACT 58.010 45.455 0.00 0.00 0.00 2.73
3120 3121 1.360852 AGGGAGTGGACTGATCAGACT 59.639 52.381 29.27 20.87 0.00 3.24
3121 3122 1.480137 GGGAGTGGACTGATCAGACTG 59.520 57.143 29.27 3.73 0.00 3.51
3243 3247 6.001460 AGAGAATGAGATAGAACTAGGTCCG 58.999 44.000 3.53 0.00 0.00 4.79
3318 3322 5.158494 GGGTTCATGAACAAATAAACGACC 58.842 41.667 33.42 19.99 42.85 4.79
3327 3331 1.102978 AATAAACGACCAGGGCATGC 58.897 50.000 9.90 9.90 0.00 4.06
3437 3445 3.181443 TGAAGAAGGGGGAGTTCTTTCAC 60.181 47.826 0.00 0.00 42.95 3.18
3619 3627 3.681417 GGCCTCAAAATCATGCTGTTTTC 59.319 43.478 0.00 0.00 0.00 2.29
3664 3672 3.191371 CCCTCAGGAATTTTTCTTCCACG 59.809 47.826 0.00 0.00 46.02 4.94
3787 3795 5.778750 GCTCCTACAGTAATCCCCATACTAA 59.221 44.000 0.00 0.00 32.47 2.24
3788 3796 6.269307 GCTCCTACAGTAATCCCCATACTAAA 59.731 42.308 0.00 0.00 32.47 1.85
3789 3797 7.202066 GCTCCTACAGTAATCCCCATACTAAAA 60.202 40.741 0.00 0.00 32.47 1.52
3845 3853 5.646606 AGTACAACACAACACAATTCCAAC 58.353 37.500 0.00 0.00 0.00 3.77
3846 3854 4.527509 ACAACACAACACAATTCCAACA 57.472 36.364 0.00 0.00 0.00 3.33
3849 3857 5.936956 ACAACACAACACAATTCCAACAAAT 59.063 32.000 0.00 0.00 0.00 2.32
3850 3858 6.128336 ACAACACAACACAATTCCAACAAATG 60.128 34.615 0.00 0.00 0.00 2.32
3851 3859 5.728471 ACACAACACAATTCCAACAAATGA 58.272 33.333 0.00 0.00 0.00 2.57
3852 3860 6.347696 ACACAACACAATTCCAACAAATGAT 58.652 32.000 0.00 0.00 0.00 2.45
3853 3861 6.822676 ACACAACACAATTCCAACAAATGATT 59.177 30.769 0.00 0.00 0.00 2.57
3854 3862 7.336427 ACACAACACAATTCCAACAAATGATTT 59.664 29.630 0.00 0.00 0.00 2.17
3855 3863 7.640630 CACAACACAATTCCAACAAATGATTTG 59.359 33.333 15.82 15.82 45.95 2.32
3856 3864 7.551974 ACAACACAATTCCAACAAATGATTTGA 59.448 29.630 23.37 1.92 43.26 2.69
3857 3865 8.396390 CAACACAATTCCAACAAATGATTTGAA 58.604 29.630 23.37 8.35 43.26 2.69
3858 3866 8.680039 ACACAATTCCAACAAATGATTTGAAT 57.320 26.923 23.37 10.19 43.26 2.57
3859 3867 9.122779 ACACAATTCCAACAAATGATTTGAATT 57.877 25.926 23.37 14.92 43.26 2.17
3860 3868 9.953697 CACAATTCCAACAAATGATTTGAATTT 57.046 25.926 23.37 5.74 43.26 1.82
3864 3872 8.961294 TTCCAACAAATGATTTGAATTTCAGT 57.039 26.923 23.37 0.00 43.26 3.41
3865 3873 8.961294 TCCAACAAATGATTTGAATTTCAGTT 57.039 26.923 23.37 2.96 43.26 3.16
3866 3874 9.393512 TCCAACAAATGATTTGAATTTCAGTTT 57.606 25.926 23.37 2.28 43.26 2.66
3874 3882 8.795786 TGATTTGAATTTCAGTTTAGTTTCGG 57.204 30.769 0.00 0.00 0.00 4.30
3875 3883 7.381139 TGATTTGAATTTCAGTTTAGTTTCGGC 59.619 33.333 0.00 0.00 0.00 5.54
3876 3884 5.759506 TGAATTTCAGTTTAGTTTCGGCA 57.240 34.783 0.00 0.00 0.00 5.69
3877 3885 5.516090 TGAATTTCAGTTTAGTTTCGGCAC 58.484 37.500 0.00 0.00 0.00 5.01
3878 3886 5.066634 TGAATTTCAGTTTAGTTTCGGCACA 59.933 36.000 0.00 0.00 0.00 4.57
3879 3887 5.705609 ATTTCAGTTTAGTTTCGGCACAT 57.294 34.783 0.00 0.00 0.00 3.21
3880 3888 5.508200 TTTCAGTTTAGTTTCGGCACATT 57.492 34.783 0.00 0.00 0.00 2.71
3881 3889 4.742438 TCAGTTTAGTTTCGGCACATTC 57.258 40.909 0.00 0.00 0.00 2.67
3882 3890 4.130857 TCAGTTTAGTTTCGGCACATTCA 58.869 39.130 0.00 0.00 0.00 2.57
3883 3891 4.576873 TCAGTTTAGTTTCGGCACATTCAA 59.423 37.500 0.00 0.00 0.00 2.69
3884 3892 5.066634 TCAGTTTAGTTTCGGCACATTCAAA 59.933 36.000 0.00 0.00 0.00 2.69
3885 3893 5.173131 CAGTTTAGTTTCGGCACATTCAAAC 59.827 40.000 0.00 0.00 0.00 2.93
3886 3894 2.399396 AGTTTCGGCACATTCAAACG 57.601 45.000 0.00 0.00 34.54 3.60
3887 3895 0.775861 GTTTCGGCACATTCAAACGC 59.224 50.000 0.00 0.00 0.00 4.84
3888 3896 0.382158 TTTCGGCACATTCAAACGCA 59.618 45.000 0.00 0.00 0.00 5.24
3889 3897 0.317436 TTCGGCACATTCAAACGCAC 60.317 50.000 0.00 0.00 0.00 5.34
3890 3898 1.009108 CGGCACATTCAAACGCACA 60.009 52.632 0.00 0.00 0.00 4.57
3891 3899 0.998226 CGGCACATTCAAACGCACAG 60.998 55.000 0.00 0.00 0.00 3.66
3892 3900 0.664166 GGCACATTCAAACGCACAGG 60.664 55.000 0.00 0.00 0.00 4.00
3893 3901 0.310543 GCACATTCAAACGCACAGGA 59.689 50.000 0.00 0.00 0.00 3.86
3894 3902 1.268999 GCACATTCAAACGCACAGGAA 60.269 47.619 0.00 0.00 0.00 3.36
3895 3903 2.797792 GCACATTCAAACGCACAGGAAA 60.798 45.455 0.00 0.00 0.00 3.13
3896 3904 2.788786 CACATTCAAACGCACAGGAAAC 59.211 45.455 0.00 0.00 0.00 2.78
3897 3905 2.425312 ACATTCAAACGCACAGGAAACA 59.575 40.909 0.00 0.00 0.00 2.83
3898 3906 2.842208 TTCAAACGCACAGGAAACAG 57.158 45.000 0.00 0.00 0.00 3.16
3899 3907 0.380378 TCAAACGCACAGGAAACAGC 59.620 50.000 0.00 0.00 0.00 4.40
3900 3908 0.100325 CAAACGCACAGGAAACAGCA 59.900 50.000 0.00 0.00 0.00 4.41
3901 3909 0.381801 AAACGCACAGGAAACAGCAG 59.618 50.000 0.00 0.00 0.00 4.24
3902 3910 0.463654 AACGCACAGGAAACAGCAGA 60.464 50.000 0.00 0.00 0.00 4.26
3903 3911 0.250467 ACGCACAGGAAACAGCAGAT 60.250 50.000 0.00 0.00 0.00 2.90
3904 3912 0.877071 CGCACAGGAAACAGCAGATT 59.123 50.000 0.00 0.00 0.00 2.40
3905 3913 1.400629 CGCACAGGAAACAGCAGATTG 60.401 52.381 0.00 0.00 0.00 2.67
3906 3914 1.668047 GCACAGGAAACAGCAGATTGC 60.668 52.381 0.00 0.00 45.46 3.56
3907 3915 1.068055 CACAGGAAACAGCAGATTGCC 60.068 52.381 0.00 0.00 46.52 4.52
3908 3916 0.529378 CAGGAAACAGCAGATTGCCC 59.471 55.000 0.00 0.00 46.52 5.36
3909 3917 0.407139 AGGAAACAGCAGATTGCCCT 59.593 50.000 0.00 0.00 46.52 5.19
3910 3918 1.203100 AGGAAACAGCAGATTGCCCTT 60.203 47.619 0.00 0.00 46.52 3.95
3911 3919 1.620323 GGAAACAGCAGATTGCCCTTT 59.380 47.619 0.00 0.00 46.52 3.11
3912 3920 2.611224 GGAAACAGCAGATTGCCCTTTG 60.611 50.000 0.00 0.00 46.52 2.77
3913 3921 0.971386 AACAGCAGATTGCCCTTTGG 59.029 50.000 0.00 0.00 46.52 3.28
3923 3931 2.365502 CCCTTTGGCCCCAATCCC 60.366 66.667 0.00 0.00 35.70 3.85
3924 3932 2.449312 CCTTTGGCCCCAATCCCA 59.551 61.111 0.00 0.00 35.70 4.37
3925 3933 1.686800 CCTTTGGCCCCAATCCCAG 60.687 63.158 0.00 0.00 35.70 4.45
3926 3934 1.387737 CTTTGGCCCCAATCCCAGA 59.612 57.895 0.00 0.00 35.70 3.86
3927 3935 0.972471 CTTTGGCCCCAATCCCAGAC 60.972 60.000 0.00 0.00 35.70 3.51
3928 3936 2.454459 TTTGGCCCCAATCCCAGACC 62.454 60.000 0.00 0.00 35.70 3.85
3929 3937 3.346734 GGCCCCAATCCCAGACCA 61.347 66.667 0.00 0.00 0.00 4.02
3930 3938 2.276740 GCCCCAATCCCAGACCAG 59.723 66.667 0.00 0.00 0.00 4.00
3931 3939 2.276740 CCCCAATCCCAGACCAGC 59.723 66.667 0.00 0.00 0.00 4.85
3932 3940 2.615465 CCCCAATCCCAGACCAGCA 61.615 63.158 0.00 0.00 0.00 4.41
3933 3941 1.383799 CCCAATCCCAGACCAGCAA 59.616 57.895 0.00 0.00 0.00 3.91
3934 3942 0.251742 CCCAATCCCAGACCAGCAAA 60.252 55.000 0.00 0.00 0.00 3.68
3935 3943 1.631405 CCAATCCCAGACCAGCAAAA 58.369 50.000 0.00 0.00 0.00 2.44
3936 3944 1.547372 CCAATCCCAGACCAGCAAAAG 59.453 52.381 0.00 0.00 0.00 2.27
3937 3945 2.517959 CAATCCCAGACCAGCAAAAGA 58.482 47.619 0.00 0.00 0.00 2.52
3938 3946 2.206576 ATCCCAGACCAGCAAAAGAC 57.793 50.000 0.00 0.00 0.00 3.01
3939 3947 0.110486 TCCCAGACCAGCAAAAGACC 59.890 55.000 0.00 0.00 0.00 3.85
3940 3948 0.111253 CCCAGACCAGCAAAAGACCT 59.889 55.000 0.00 0.00 0.00 3.85
3941 3949 1.351017 CCCAGACCAGCAAAAGACCTA 59.649 52.381 0.00 0.00 0.00 3.08
3942 3950 2.025887 CCCAGACCAGCAAAAGACCTAT 60.026 50.000 0.00 0.00 0.00 2.57
3943 3951 3.012518 CCAGACCAGCAAAAGACCTATG 58.987 50.000 0.00 0.00 0.00 2.23
3944 3952 3.307691 CCAGACCAGCAAAAGACCTATGA 60.308 47.826 0.00 0.00 0.00 2.15
3945 3953 3.937706 CAGACCAGCAAAAGACCTATGAG 59.062 47.826 0.00 0.00 0.00 2.90
3946 3954 2.680339 GACCAGCAAAAGACCTATGAGC 59.320 50.000 0.00 0.00 0.00 4.26
3947 3955 2.307098 ACCAGCAAAAGACCTATGAGCT 59.693 45.455 0.00 0.00 0.00 4.09
3948 3956 3.519510 ACCAGCAAAAGACCTATGAGCTA 59.480 43.478 0.00 0.00 0.00 3.32
3949 3957 4.164988 ACCAGCAAAAGACCTATGAGCTAT 59.835 41.667 0.00 0.00 0.00 2.97
3950 3958 5.128919 CCAGCAAAAGACCTATGAGCTATT 58.871 41.667 0.00 0.00 0.00 1.73
3951 3959 5.591877 CCAGCAAAAGACCTATGAGCTATTT 59.408 40.000 0.00 0.00 0.00 1.40
3952 3960 6.238593 CCAGCAAAAGACCTATGAGCTATTTC 60.239 42.308 0.00 0.00 0.00 2.17
3953 3961 6.317140 CAGCAAAAGACCTATGAGCTATTTCA 59.683 38.462 0.00 0.00 0.00 2.69
3954 3962 6.317391 AGCAAAAGACCTATGAGCTATTTCAC 59.683 38.462 0.00 0.00 0.00 3.18
3955 3963 6.458888 GCAAAAGACCTATGAGCTATTTCACC 60.459 42.308 0.00 0.00 0.00 4.02
4058 4066 5.371629 CGTTTACTCGGATTCAAGAACAAC 58.628 41.667 0.00 0.00 0.00 3.32
4154 4162 0.322997 ATCCCGCTATCTCCTCTCGG 60.323 60.000 0.00 0.00 39.79 4.63
4268 4276 0.179073 GCGATGGAGCTTGCTAGGAA 60.179 55.000 0.00 0.00 0.00 3.36
4269 4277 1.743772 GCGATGGAGCTTGCTAGGAAA 60.744 52.381 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.398200 GCATCAGCTCTGTCTATCATGAGACA 62.398 46.154 14.93 14.93 44.51 3.41
12 13 1.339291 CGGCATCAGCTCTGTCTATCA 59.661 52.381 0.00 0.00 41.70 2.15
45 46 0.459489 AGAGTGCGATCCTTCTCTGC 59.541 55.000 7.20 0.00 36.17 4.26
56 57 0.172578 CGTCCAATGGTAGAGTGCGA 59.827 55.000 0.00 0.00 0.00 5.10
62 63 1.403647 CGCAAGTCGTCCAATGGTAGA 60.404 52.381 0.00 0.00 0.00 2.59
108 109 1.483415 GGTTAACCTCTACGGCCATGA 59.517 52.381 17.83 0.00 35.61 3.07
186 187 2.815589 GCTTCACTGGGACAAACCTCAT 60.816 50.000 0.00 0.00 38.70 2.90
279 280 3.375299 GGTGTGTCATTCCTTCTACATGC 59.625 47.826 0.00 0.00 0.00 4.06
373 374 2.165437 TGAAGCCAAATTTATCCACCGC 59.835 45.455 0.00 0.00 0.00 5.68
420 421 3.329814 TCACCCTAGATGGCGAGTAGATA 59.670 47.826 0.00 0.00 0.00 1.98
421 422 2.108425 TCACCCTAGATGGCGAGTAGAT 59.892 50.000 0.00 0.00 0.00 1.98
440 441 2.945440 GCAGGCATATCCACAAACCTCA 60.945 50.000 0.00 0.00 37.29 3.86
466 467 4.360563 TCAGAAGAAGTCGTTGACAAGTC 58.639 43.478 0.00 0.00 34.60 3.01
467 468 4.386867 TCAGAAGAAGTCGTTGACAAGT 57.613 40.909 0.00 0.00 34.60 3.16
468 469 5.321983 CTTCAGAAGAAGTCGTTGACAAG 57.678 43.478 3.82 0.00 44.97 3.16
482 483 3.667497 TGTGACCTGCTACTTCAGAAG 57.333 47.619 8.77 8.77 36.19 2.85
680 681 3.350377 CAACAATGCCCGGACGTT 58.650 55.556 0.73 0.00 0.00 3.99
805 806 4.908736 AGTGACAACAGAAACGACATTTG 58.091 39.130 0.00 0.00 0.00 2.32
829 830 0.804364 GCATGAGTGCCATTCAACGA 59.196 50.000 0.00 0.00 45.76 3.85
846 847 6.127054 ACAAGCATGTTATCTTAGTCTAGGCA 60.127 38.462 0.00 0.00 35.91 4.75
861 862 3.266772 TCCTATCTTCCCACAAGCATGTT 59.733 43.478 0.00 0.00 37.82 2.71
862 863 2.846206 TCCTATCTTCCCACAAGCATGT 59.154 45.455 0.00 0.00 41.61 3.21
863 864 3.118112 AGTCCTATCTTCCCACAAGCATG 60.118 47.826 0.00 0.00 0.00 4.06
864 865 3.118112 CAGTCCTATCTTCCCACAAGCAT 60.118 47.826 0.00 0.00 0.00 3.79
865 866 2.237143 CAGTCCTATCTTCCCACAAGCA 59.763 50.000 0.00 0.00 0.00 3.91
874 875 4.125703 CAAGTCATGCCAGTCCTATCTTC 58.874 47.826 0.00 0.00 0.00 2.87
1019 1020 1.819288 CAAGGAAGAGGAGCAGTACGA 59.181 52.381 0.00 0.00 0.00 3.43
1024 1025 1.077858 GGCCAAGGAAGAGGAGCAG 60.078 63.158 0.00 0.00 0.00 4.24
1057 1058 3.181463 TGGTCACCAGTACCAGTAACAAC 60.181 47.826 0.00 0.00 42.10 3.32
1227 1228 1.761784 AGAGTGCTGCTATTGGAGGAG 59.238 52.381 0.00 0.00 46.16 3.69
1228 1229 1.483827 CAGAGTGCTGCTATTGGAGGA 59.516 52.381 0.00 0.00 34.95 3.71
1229 1230 1.950828 CAGAGTGCTGCTATTGGAGG 58.049 55.000 0.00 0.00 34.95 4.30
1355 1356 2.203070 GGAGGCCCATGTACTGCG 60.203 66.667 0.00 0.00 0.00 5.18
1380 1381 1.804396 TTGCCATGCCGTTGTTCTGG 61.804 55.000 0.00 0.00 0.00 3.86
1544 1545 4.625972 ACAAGGGTCAAGTTGTTAAACG 57.374 40.909 2.11 0.00 41.45 3.60
1628 1629 2.833121 GGTTTAGCGGGGCCATGG 60.833 66.667 7.63 7.63 0.00 3.66
1664 1665 2.953648 TCGTGCTTGGTCGATATTAGGA 59.046 45.455 0.00 0.00 0.00 2.94
1665 1666 3.050619 GTCGTGCTTGGTCGATATTAGG 58.949 50.000 0.00 0.00 38.32 2.69
1718 1719 0.108472 TGCTGCTGACGAGAATCCAG 60.108 55.000 0.00 0.00 0.00 3.86
1728 1729 3.745803 GCCTTGCCTGCTGCTGAC 61.746 66.667 8.20 0.00 42.00 3.51
1854 1855 8.482128 AGAATTATCTCTAGAAACTTGGACAGG 58.518 37.037 0.00 0.00 0.00 4.00
1917 1918 2.798283 TCTTACGAGCAGAAAAACCACG 59.202 45.455 0.00 0.00 0.00 4.94
1935 1936 3.205784 GCATACCTCAGATGCCTTCTT 57.794 47.619 0.00 0.00 43.24 2.52
2148 2149 6.581388 TCTGTTATGAATTCCTTCATCCCT 57.419 37.500 2.27 0.00 46.83 4.20
2164 2165 5.105756 GGCCAATGCTAACAACTTCTGTTAT 60.106 40.000 0.00 0.00 46.88 1.89
2239 2240 7.726033 ATTCATACACTAGAAGGAGTTCACT 57.274 36.000 0.00 0.00 34.82 3.41
2427 2428 1.154016 ATCGTCGAGGAGCACGTTG 60.154 57.895 13.85 0.00 37.30 4.10
2586 2587 3.181524 ACACGCCGAAAGAAAATACATCG 60.182 43.478 0.00 0.00 0.00 3.84
2611 2612 1.001974 CCCACATGTGACCTCGAGAAA 59.998 52.381 27.46 0.00 0.00 2.52
2754 2755 2.165030 CACCAAACATGCCTCTTGATCC 59.835 50.000 0.00 0.00 0.00 3.36
2805 2806 3.134127 GGCCTTGCGTCCATGGAC 61.134 66.667 31.59 31.59 38.26 4.02
2903 2904 0.252479 CTGCATCAAGGCCAGAGTCT 59.748 55.000 5.01 0.00 0.00 3.24
2973 2974 4.880164 AGGAAAGTACTGACCCATAGCTA 58.120 43.478 12.98 0.00 0.00 3.32
2982 2983 4.767928 TCTCCTGAGAAGGAAAGTACTGAC 59.232 45.833 0.00 0.00 37.55 3.51
2986 2987 6.347859 TCTTTCTCCTGAGAAGGAAAGTAC 57.652 41.667 16.55 0.00 46.23 2.73
3120 3121 5.416639 AGATTCTTAATGCATTGCACTCACA 59.583 36.000 22.27 0.00 43.04 3.58
3121 3122 5.742453 CAGATTCTTAATGCATTGCACTCAC 59.258 40.000 22.27 7.92 43.04 3.51
3254 3258 0.883833 CAAGTGACAATGCAGACCCC 59.116 55.000 0.00 0.00 0.00 4.95
3327 3331 3.940209 ACAACATTGTGGGCACATAAG 57.060 42.857 3.97 0.00 41.52 1.73
3336 3340 8.761575 ATGCTTATTTTTCTACAACATTGTGG 57.238 30.769 7.53 4.67 42.31 4.17
3437 3445 8.159447 TGAGATATAATGGATGGAGAAACCTTG 58.841 37.037 0.00 0.00 39.86 3.61
3550 3558 8.243961 TGAAAATACAGGTGGATGAAGAAAAA 57.756 30.769 0.00 0.00 0.00 1.94
3592 3600 5.448654 ACAGCATGATTTTGAGGCCTAATA 58.551 37.500 4.42 0.00 39.69 0.98
3606 3614 2.238646 TCCCTACGGAAAACAGCATGAT 59.761 45.455 0.00 0.00 35.32 2.45
3789 3797 7.171848 TGCGTAGTTATGGCGATATATGTTTTT 59.828 33.333 0.00 0.00 0.00 1.94
3813 3821 6.491394 TGTGTTGTGTTGTACTTAAATCTGC 58.509 36.000 0.00 0.00 0.00 4.26
3849 3857 7.381139 GCCGAAACTAAACTGAAATTCAAATCA 59.619 33.333 0.00 0.00 0.00 2.57
3850 3858 7.381139 TGCCGAAACTAAACTGAAATTCAAATC 59.619 33.333 0.00 0.00 0.00 2.17
3851 3859 7.169140 GTGCCGAAACTAAACTGAAATTCAAAT 59.831 33.333 0.00 0.00 0.00 2.32
3852 3860 6.474102 GTGCCGAAACTAAACTGAAATTCAAA 59.526 34.615 0.00 0.00 0.00 2.69
3853 3861 5.974751 GTGCCGAAACTAAACTGAAATTCAA 59.025 36.000 0.00 0.00 0.00 2.69
3854 3862 5.066634 TGTGCCGAAACTAAACTGAAATTCA 59.933 36.000 0.00 0.00 0.00 2.57
3855 3863 5.516090 TGTGCCGAAACTAAACTGAAATTC 58.484 37.500 0.00 0.00 0.00 2.17
3856 3864 5.508200 TGTGCCGAAACTAAACTGAAATT 57.492 34.783 0.00 0.00 0.00 1.82
3857 3865 5.705609 ATGTGCCGAAACTAAACTGAAAT 57.294 34.783 0.00 0.00 0.00 2.17
3858 3866 5.066634 TGAATGTGCCGAAACTAAACTGAAA 59.933 36.000 0.00 0.00 0.00 2.69
3859 3867 4.576873 TGAATGTGCCGAAACTAAACTGAA 59.423 37.500 0.00 0.00 0.00 3.02
3860 3868 4.130857 TGAATGTGCCGAAACTAAACTGA 58.869 39.130 0.00 0.00 0.00 3.41
3861 3869 4.481930 TGAATGTGCCGAAACTAAACTG 57.518 40.909 0.00 0.00 0.00 3.16
3862 3870 5.278604 GTTTGAATGTGCCGAAACTAAACT 58.721 37.500 0.00 0.00 0.00 2.66
3863 3871 4.145756 CGTTTGAATGTGCCGAAACTAAAC 59.854 41.667 0.00 0.00 0.00 2.01
3864 3872 4.283678 CGTTTGAATGTGCCGAAACTAAA 58.716 39.130 0.00 0.00 0.00 1.85
3865 3873 3.850374 GCGTTTGAATGTGCCGAAACTAA 60.850 43.478 0.00 0.00 0.00 2.24
3866 3874 2.350007 GCGTTTGAATGTGCCGAAACTA 60.350 45.455 0.00 0.00 0.00 2.24
3867 3875 1.599419 GCGTTTGAATGTGCCGAAACT 60.599 47.619 0.00 0.00 0.00 2.66
3868 3876 0.775861 GCGTTTGAATGTGCCGAAAC 59.224 50.000 0.00 0.00 0.00 2.78
3869 3877 0.382158 TGCGTTTGAATGTGCCGAAA 59.618 45.000 0.00 0.00 0.00 3.46
3870 3878 0.317436 GTGCGTTTGAATGTGCCGAA 60.317 50.000 0.00 0.00 0.00 4.30
3871 3879 1.281353 GTGCGTTTGAATGTGCCGA 59.719 52.632 0.00 0.00 0.00 5.54
3872 3880 0.998226 CTGTGCGTTTGAATGTGCCG 60.998 55.000 0.00 0.00 0.00 5.69
3873 3881 0.664166 CCTGTGCGTTTGAATGTGCC 60.664 55.000 0.00 0.00 0.00 5.01
3874 3882 0.310543 TCCTGTGCGTTTGAATGTGC 59.689 50.000 0.00 0.00 0.00 4.57
3875 3883 2.772568 TTCCTGTGCGTTTGAATGTG 57.227 45.000 0.00 0.00 0.00 3.21
3876 3884 2.425312 TGTTTCCTGTGCGTTTGAATGT 59.575 40.909 0.00 0.00 0.00 2.71
3877 3885 3.044986 CTGTTTCCTGTGCGTTTGAATG 58.955 45.455 0.00 0.00 0.00 2.67
3878 3886 2.543653 GCTGTTTCCTGTGCGTTTGAAT 60.544 45.455 0.00 0.00 0.00 2.57
3879 3887 1.202245 GCTGTTTCCTGTGCGTTTGAA 60.202 47.619 0.00 0.00 0.00 2.69
3880 3888 0.380378 GCTGTTTCCTGTGCGTTTGA 59.620 50.000 0.00 0.00 0.00 2.69
3881 3889 0.100325 TGCTGTTTCCTGTGCGTTTG 59.900 50.000 0.00 0.00 0.00 2.93
3882 3890 0.381801 CTGCTGTTTCCTGTGCGTTT 59.618 50.000 0.00 0.00 0.00 3.60
3883 3891 0.463654 TCTGCTGTTTCCTGTGCGTT 60.464 50.000 0.00 0.00 0.00 4.84
3884 3892 0.250467 ATCTGCTGTTTCCTGTGCGT 60.250 50.000 0.00 0.00 0.00 5.24
3885 3893 0.877071 AATCTGCTGTTTCCTGTGCG 59.123 50.000 0.00 0.00 0.00 5.34
3886 3894 1.668047 GCAATCTGCTGTTTCCTGTGC 60.668 52.381 0.00 0.00 40.96 4.57
3887 3895 1.068055 GGCAATCTGCTGTTTCCTGTG 60.068 52.381 0.00 0.00 44.28 3.66
3888 3896 1.251251 GGCAATCTGCTGTTTCCTGT 58.749 50.000 0.00 0.00 44.28 4.00
3889 3897 0.529378 GGGCAATCTGCTGTTTCCTG 59.471 55.000 0.00 0.00 44.28 3.86
3890 3898 0.407139 AGGGCAATCTGCTGTTTCCT 59.593 50.000 0.00 0.00 44.28 3.36
3891 3899 1.260544 AAGGGCAATCTGCTGTTTCC 58.739 50.000 0.00 0.00 44.28 3.13
3892 3900 2.611224 CCAAAGGGCAATCTGCTGTTTC 60.611 50.000 0.00 0.00 44.28 2.78
3893 3901 1.345415 CCAAAGGGCAATCTGCTGTTT 59.655 47.619 0.00 0.00 44.28 2.83
3894 3902 0.971386 CCAAAGGGCAATCTGCTGTT 59.029 50.000 0.00 0.00 44.28 3.16
3895 3903 2.662309 CCAAAGGGCAATCTGCTGT 58.338 52.632 0.00 0.00 44.28 4.40
3906 3914 2.365502 GGGATTGGGGCCAAAGGG 60.366 66.667 4.39 0.00 39.55 3.95
3907 3915 1.686800 CTGGGATTGGGGCCAAAGG 60.687 63.158 4.39 0.00 39.55 3.11
3908 3916 0.972471 GTCTGGGATTGGGGCCAAAG 60.972 60.000 4.39 0.00 39.55 2.77
3909 3917 1.078347 GTCTGGGATTGGGGCCAAA 59.922 57.895 4.39 0.00 39.55 3.28
3910 3918 2.770130 GTCTGGGATTGGGGCCAA 59.230 61.111 4.39 0.00 40.47 4.52
3911 3919 3.346734 GGTCTGGGATTGGGGCCA 61.347 66.667 4.39 0.00 0.00 5.36
3912 3920 3.346734 TGGTCTGGGATTGGGGCC 61.347 66.667 0.00 0.00 0.00 5.80
3913 3921 2.276740 CTGGTCTGGGATTGGGGC 59.723 66.667 0.00 0.00 0.00 5.80
3914 3922 2.153898 TTGCTGGTCTGGGATTGGGG 62.154 60.000 0.00 0.00 0.00 4.96
3915 3923 0.251742 TTTGCTGGTCTGGGATTGGG 60.252 55.000 0.00 0.00 0.00 4.12
3916 3924 1.547372 CTTTTGCTGGTCTGGGATTGG 59.453 52.381 0.00 0.00 0.00 3.16
3917 3925 2.229784 GTCTTTTGCTGGTCTGGGATTG 59.770 50.000 0.00 0.00 0.00 2.67
3918 3926 2.519013 GTCTTTTGCTGGTCTGGGATT 58.481 47.619 0.00 0.00 0.00 3.01
3919 3927 1.272147 GGTCTTTTGCTGGTCTGGGAT 60.272 52.381 0.00 0.00 0.00 3.85
3920 3928 0.110486 GGTCTTTTGCTGGTCTGGGA 59.890 55.000 0.00 0.00 0.00 4.37
3921 3929 0.111253 AGGTCTTTTGCTGGTCTGGG 59.889 55.000 0.00 0.00 0.00 4.45
3922 3930 2.859165 TAGGTCTTTTGCTGGTCTGG 57.141 50.000 0.00 0.00 0.00 3.86
3923 3931 3.937706 CTCATAGGTCTTTTGCTGGTCTG 59.062 47.826 0.00 0.00 0.00 3.51
3924 3932 3.620966 GCTCATAGGTCTTTTGCTGGTCT 60.621 47.826 0.00 0.00 0.00 3.85
3925 3933 2.680339 GCTCATAGGTCTTTTGCTGGTC 59.320 50.000 0.00 0.00 0.00 4.02
3926 3934 2.307098 AGCTCATAGGTCTTTTGCTGGT 59.693 45.455 0.00 0.00 0.00 4.00
3927 3935 2.996631 AGCTCATAGGTCTTTTGCTGG 58.003 47.619 0.00 0.00 0.00 4.85
3928 3936 6.317140 TGAAATAGCTCATAGGTCTTTTGCTG 59.683 38.462 0.00 0.00 0.00 4.41
3929 3937 6.317391 GTGAAATAGCTCATAGGTCTTTTGCT 59.683 38.462 0.00 0.00 0.00 3.91
3930 3938 6.458888 GGTGAAATAGCTCATAGGTCTTTTGC 60.459 42.308 0.00 0.00 0.00 3.68
3931 3939 6.238211 CGGTGAAATAGCTCATAGGTCTTTTG 60.238 42.308 0.00 0.00 0.00 2.44
3932 3940 5.817816 CGGTGAAATAGCTCATAGGTCTTTT 59.182 40.000 0.00 0.00 0.00 2.27
3933 3941 5.128827 TCGGTGAAATAGCTCATAGGTCTTT 59.871 40.000 0.00 0.00 0.00 2.52
3934 3942 4.649674 TCGGTGAAATAGCTCATAGGTCTT 59.350 41.667 0.00 0.00 0.00 3.01
3935 3943 4.215908 TCGGTGAAATAGCTCATAGGTCT 58.784 43.478 0.00 0.00 0.00 3.85
3936 3944 4.585955 TCGGTGAAATAGCTCATAGGTC 57.414 45.455 0.00 0.00 0.00 3.85
3937 3945 4.021016 GGATCGGTGAAATAGCTCATAGGT 60.021 45.833 0.00 0.00 0.00 3.08
3938 3946 4.021104 TGGATCGGTGAAATAGCTCATAGG 60.021 45.833 0.00 0.00 0.00 2.57
3939 3947 5.139435 TGGATCGGTGAAATAGCTCATAG 57.861 43.478 0.00 0.00 0.00 2.23
3940 3948 5.304357 TCTTGGATCGGTGAAATAGCTCATA 59.696 40.000 0.00 0.00 0.00 2.15
3941 3949 4.101585 TCTTGGATCGGTGAAATAGCTCAT 59.898 41.667 0.00 0.00 0.00 2.90
3942 3950 3.450817 TCTTGGATCGGTGAAATAGCTCA 59.549 43.478 0.00 0.00 0.00 4.26
3943 3951 4.054671 CTCTTGGATCGGTGAAATAGCTC 58.945 47.826 0.00 0.00 0.00 4.09
3944 3952 3.742640 GCTCTTGGATCGGTGAAATAGCT 60.743 47.826 0.00 0.00 0.00 3.32
3945 3953 2.545946 GCTCTTGGATCGGTGAAATAGC 59.454 50.000 0.00 0.00 0.00 2.97
3946 3954 3.557595 GTGCTCTTGGATCGGTGAAATAG 59.442 47.826 0.00 0.00 0.00 1.73
3947 3955 3.531538 GTGCTCTTGGATCGGTGAAATA 58.468 45.455 0.00 0.00 0.00 1.40
3948 3956 2.359900 GTGCTCTTGGATCGGTGAAAT 58.640 47.619 0.00 0.00 0.00 2.17
3949 3957 1.610624 GGTGCTCTTGGATCGGTGAAA 60.611 52.381 0.00 0.00 0.00 2.69
3950 3958 0.036388 GGTGCTCTTGGATCGGTGAA 60.036 55.000 0.00 0.00 0.00 3.18
3951 3959 1.596934 GGTGCTCTTGGATCGGTGA 59.403 57.895 0.00 0.00 0.00 4.02
3952 3960 1.450312 GGGTGCTCTTGGATCGGTG 60.450 63.158 0.00 0.00 0.00 4.94
3953 3961 1.903877 CTGGGTGCTCTTGGATCGGT 61.904 60.000 0.00 0.00 0.00 4.69
3954 3962 1.153289 CTGGGTGCTCTTGGATCGG 60.153 63.158 0.00 0.00 0.00 4.18
3955 3963 1.153289 CCTGGGTGCTCTTGGATCG 60.153 63.158 0.00 0.00 0.00 3.69
4043 4051 2.744202 CCTCCAGTTGTTCTTGAATCCG 59.256 50.000 0.00 0.00 0.00 4.18
4058 4066 4.737855 TCCTCTCGTTAATTTCCTCCAG 57.262 45.455 0.00 0.00 0.00 3.86
4268 4276 0.887933 CCCAAACTAACCGCTGCATT 59.112 50.000 0.00 0.00 0.00 3.56
4269 4277 0.965363 CCCCAAACTAACCGCTGCAT 60.965 55.000 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.