Multiple sequence alignment - TraesCS6D01G196100

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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 TraesCS6D01G196100 chr6D 100.000 4086 0 0 1 4086 272110690 272106605 0.000000e+00 7546.0
1 TraesCS6D01G196100 chr6B 95.237 3653 96 32 1 3620 433273915 433270308 0.000000e+00 5710.0
2 TraesCS6D01G196100 chr6A 94.681 2369 68 19 587 2924 388211473 388209132 0.000000e+00 3624.0
3 TraesCS6D01G196100 chr6A 93.531 742 39 6 2927 3664 388208873 388208137 0.000000e+00 1096.0
4 TraesCS6D01G196100 chr6A 95.691 557 17 1 1 550 388212007 388211451 0.000000e+00 889.0
5 TraesCS6D01G196100 chr6A 100.000 31 0 0 3400 3430 91906104 91906134 1.590000e-04 58.4
6 TraesCS6D01G196100 chr7B 97.010 1739 25 13 1 1727 438422426 438420703 0.000000e+00 2898.0
7 TraesCS6D01G196100 chr7B 93.166 1156 29 19 1718 2840 438399764 438398626 0.000000e+00 1652.0
8 TraesCS6D01G196100 chr7B 89.455 825 41 13 2832 3653 438396804 438396023 0.000000e+00 1000.0
9 TraesCS6D01G196100 chr2A 79.379 354 49 20 2387 2727 679993204 679992862 1.140000e-55 228.0
10 TraesCS6D01G196100 chr2A 85.124 121 16 2 1925 2043 679993950 679993830 5.550000e-24 122.0
11 TraesCS6D01G196100 chr2A 73.502 317 67 14 3777 4085 214244583 214244890 2.010000e-18 104.0
12 TraesCS6D01G196100 chr3B 80.364 275 39 12 3811 4084 766380266 766380526 1.160000e-45 195.0
13 TraesCS6D01G196100 chr2D 92.391 92 7 0 1952 2043 537459936 537459845 9.220000e-27 132.0
14 TraesCS6D01G196100 chr2B 86.179 123 13 4 1925 2043 640104695 640104573 3.310000e-26 130.0
15 TraesCS6D01G196100 chr3A 88.421 95 9 2 3987 4080 552610419 552610326 3.340000e-21 113.0
16 TraesCS6D01G196100 chr3A 89.873 79 7 1 4006 4084 711074010 711073933 2.600000e-17 100.0
17 TraesCS6D01G196100 chr4A 87.368 95 10 2 3987 4080 467156760 467156853 1.550000e-19 108.0
18 TraesCS6D01G196100 chr5A 87.778 90 9 2 3992 4080 688262962 688262874 2.010000e-18 104.0
19 TraesCS6D01G196100 chr4D 85.000 100 12 3 3987 4084 10763116 10763018 9.350000e-17 99.0
20 TraesCS6D01G196100 chr4B 85.567 97 11 3 3985 4080 643624635 643624541 9.350000e-17 99.0
21 TraesCS6D01G196100 chr1B 83.505 97 12 4 3990 4084 653789229 653789135 2.020000e-13 87.9


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 TraesCS6D01G196100 chr6D 272106605 272110690 4085 True 7546.000000 7546 100.000000 1 4086 1 chr6D.!!$R1 4085
1 TraesCS6D01G196100 chr6B 433270308 433273915 3607 True 5710.000000 5710 95.237000 1 3620 1 chr6B.!!$R1 3619
2 TraesCS6D01G196100 chr6A 388208137 388212007 3870 True 1869.666667 3624 94.634333 1 3664 3 chr6A.!!$R1 3663
3 TraesCS6D01G196100 chr7B 438420703 438422426 1723 True 2898.000000 2898 97.010000 1 1727 1 chr7B.!!$R1 1726
4 TraesCS6D01G196100 chr7B 438396023 438399764 3741 True 1326.000000 1652 91.310500 1718 3653 2 chr7B.!!$R2 1935


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
378 386 2.705658 TCGGGATTTACATCTGGCAGAT 59.294 45.455 24.01 24.01 34.74 2.90 F
1450 1460 2.222976 CGCATGTCTCAGCAATCTGTTC 60.223 50.000 0.00 0.00 41.10 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1450 1460 1.227999 ACAGAAATGGTGGTGACGCG 61.228 55.0 3.53 3.53 43.50 6.01 R
3433 5584 0.618968 ATTCTTGGTCGAGCCTCCCT 60.619 55.0 12.85 0.00 38.35 4.20 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
378 386 2.705658 TCGGGATTTACATCTGGCAGAT 59.294 45.455 24.01 24.01 34.74 2.90
1450 1460 2.222976 CGCATGTCTCAGCAATCTGTTC 60.223 50.000 0.00 0.00 41.10 3.18
1531 1546 0.598065 GCAATTGCTTCCACGGACTT 59.402 50.000 23.21 0.00 38.21 3.01
1532 1547 1.810151 GCAATTGCTTCCACGGACTTA 59.190 47.619 23.21 0.00 38.21 2.24
1533 1548 2.414161 GCAATTGCTTCCACGGACTTAC 60.414 50.000 23.21 0.00 38.21 2.34
1534 1549 3.074412 CAATTGCTTCCACGGACTTACT 58.926 45.455 0.00 0.00 0.00 2.24
1535 1550 4.250464 CAATTGCTTCCACGGACTTACTA 58.750 43.478 0.00 0.00 0.00 1.82
1536 1551 3.308438 TTGCTTCCACGGACTTACTAC 57.692 47.619 0.00 0.00 0.00 2.73
2058 2073 4.062293 TCAAGGTTAGTTTGATGACCGTG 58.938 43.478 0.00 0.00 41.18 4.94
2060 2075 3.660865 AGGTTAGTTTGATGACCGTGTC 58.339 45.455 0.00 0.00 37.26 3.67
2077 2094 5.178067 ACCGTGTCCGTTTAGTAAATCTTTG 59.822 40.000 0.00 0.00 0.00 2.77
2142 2159 4.569943 TCCAGACATCTGAAAAGTGCTAC 58.430 43.478 10.55 0.00 46.59 3.58
2187 2223 1.765314 AGTTTGTCCTGCACTGTCTCT 59.235 47.619 0.00 0.00 0.00 3.10
2288 2324 6.205464 GGCGGAATATTCTTTGATGATCTCAA 59.795 38.462 14.95 0.00 42.15 3.02
2334 2370 2.186076 GACTTCGCGACAGGTATCAAG 58.814 52.381 9.15 2.05 0.00 3.02
2356 2397 5.073428 AGAAACTCTGAATTTGGGTCCTTC 58.927 41.667 0.00 0.00 0.00 3.46
2720 2775 7.441458 GGTGGGAGTATGATCATGTAAGTTAAC 59.559 40.741 18.72 5.71 0.00 2.01
2779 2837 3.663025 ACATTTTGATCCCCGCAAAAAG 58.337 40.909 0.00 0.00 45.14 2.27
2846 4734 5.108254 GGCGCTGCAATATTTAAAATCTTCG 60.108 40.000 7.64 0.00 0.00 3.79
2913 4801 8.020819 TGGAAAGATTCATTTGACACGTTAATC 58.979 33.333 0.00 0.00 0.00 1.75
2998 5143 6.042143 CAGTGGCATTTTGTCAAGTTTACTT 58.958 36.000 0.00 0.00 31.67 2.24
3011 5156 7.066043 TGTCAAGTTTACTTACGACCATTTGTT 59.934 33.333 9.35 0.00 34.28 2.83
3150 5295 7.860872 CCGCTAACTTTATTTTGAAGTGTCTTT 59.139 33.333 0.00 0.00 37.41 2.52
3226 5371 3.299503 AGCTTGGAAATCTGTGTTTGGT 58.700 40.909 0.00 0.00 0.00 3.67
3249 5394 9.745880 TGGTTGTTTGCTTAATTTTCGTATAAA 57.254 25.926 0.00 0.00 0.00 1.40
3282 5431 6.399639 TGGTCTTGTTCCTTCCAATAAAAC 57.600 37.500 0.00 0.00 0.00 2.43
3305 5454 3.428725 CCTCCGTTCAAGTGAGATCTCTG 60.429 52.174 22.95 13.38 0.00 3.35
3309 5458 3.613671 CGTTCAAGTGAGATCTCTGCTGT 60.614 47.826 22.95 9.47 0.00 4.40
3339 5488 6.762187 ACATAGCAGATCATGACAAAGAAGAG 59.238 38.462 0.00 0.00 0.00 2.85
3340 5489 5.163281 AGCAGATCATGACAAAGAAGAGT 57.837 39.130 0.00 0.00 0.00 3.24
3341 5490 5.558818 AGCAGATCATGACAAAGAAGAGTT 58.441 37.500 0.00 0.00 0.00 3.01
3342 5491 6.705302 AGCAGATCATGACAAAGAAGAGTTA 58.295 36.000 0.00 0.00 0.00 2.24
3346 5497 9.985318 CAGATCATGACAAAGAAGAGTTATTTC 57.015 33.333 0.00 0.00 0.00 2.17
3361 5512 9.467796 AAGAGTTATTTCATCTAAAAAGAGGGG 57.532 33.333 0.00 0.00 0.00 4.79
3364 5515 9.244292 AGTTATTTCATCTAAAAAGAGGGGAAC 57.756 33.333 0.00 0.00 0.00 3.62
3381 5532 4.758251 CGTCCACCGGCATCTGCA 62.758 66.667 0.00 0.00 44.36 4.41
3433 5584 8.729805 ATTGCAAAGTTTTAAGATCCAAACAA 57.270 26.923 1.71 4.45 35.66 2.83
3451 5602 0.836400 AAGGGAGGCTCGACCAAGAA 60.836 55.000 8.69 0.00 43.14 2.52
3493 5644 0.669077 GGCGATGTCCTACTCGATGT 59.331 55.000 0.00 0.00 37.05 3.06
3498 5649 3.181500 CGATGTCCTACTCGATGTTGACA 60.181 47.826 15.38 15.38 40.74 3.58
3532 5683 1.806542 ACGGAGATGACATGTTGCAAC 59.193 47.619 22.83 22.83 0.00 4.17
3568 5719 4.019174 CCATGAAGAAGCAACCACCTATT 58.981 43.478 0.00 0.00 0.00 1.73
3635 5786 6.750148 AGATCTTCAGACTCGTACAAACTTT 58.250 36.000 0.00 0.00 0.00 2.66
3664 5815 7.869429 GGATCATTCACATATTAAAGGGCTTTG 59.131 37.037 0.00 0.00 34.23 2.77
3665 5816 7.111247 TCATTCACATATTAAAGGGCTTTGG 57.889 36.000 0.00 0.00 34.23 3.28
3666 5817 5.930837 TTCACATATTAAAGGGCTTTGGG 57.069 39.130 0.00 0.00 34.23 4.12
3667 5818 4.285863 TCACATATTAAAGGGCTTTGGGG 58.714 43.478 0.00 0.00 34.23 4.96
3668 5819 4.017037 TCACATATTAAAGGGCTTTGGGGA 60.017 41.667 0.00 0.00 34.23 4.81
3669 5820 4.714308 CACATATTAAAGGGCTTTGGGGAA 59.286 41.667 0.00 0.00 34.23 3.97
3670 5821 5.188751 CACATATTAAAGGGCTTTGGGGAAA 59.811 40.000 0.00 0.00 34.23 3.13
3671 5822 5.188948 ACATATTAAAGGGCTTTGGGGAAAC 59.811 40.000 0.00 0.00 34.23 2.78
3672 5823 2.777459 TAAAGGGCTTTGGGGAAACA 57.223 45.000 0.00 0.00 34.23 2.83
3673 5824 1.886422 AAAGGGCTTTGGGGAAACAA 58.114 45.000 0.00 0.00 0.00 2.83
3674 5825 1.886422 AAGGGCTTTGGGGAAACAAA 58.114 45.000 0.00 0.00 37.96 2.83
3675 5826 2.116869 AGGGCTTTGGGGAAACAAAT 57.883 45.000 0.00 0.00 39.39 2.32
3676 5827 1.699083 AGGGCTTTGGGGAAACAAATG 59.301 47.619 0.00 0.00 39.39 2.32
3677 5828 1.271325 GGGCTTTGGGGAAACAAATGG 60.271 52.381 0.00 0.00 39.39 3.16
3678 5829 1.696884 GGCTTTGGGGAAACAAATGGA 59.303 47.619 0.00 0.00 39.39 3.41
3679 5830 2.305635 GGCTTTGGGGAAACAAATGGAT 59.694 45.455 0.00 0.00 39.39 3.41
3680 5831 3.244875 GGCTTTGGGGAAACAAATGGATT 60.245 43.478 0.00 0.00 39.39 3.01
3681 5832 4.397420 GCTTTGGGGAAACAAATGGATTT 58.603 39.130 0.00 0.00 39.39 2.17
3682 5833 4.826733 GCTTTGGGGAAACAAATGGATTTT 59.173 37.500 0.00 0.00 39.39 1.82
3684 5835 5.636903 TTGGGGAAACAAATGGATTTTGA 57.363 34.783 5.17 0.00 46.36 2.69
3685 5836 5.636903 TGGGGAAACAAATGGATTTTGAA 57.363 34.783 5.17 0.00 46.36 2.69
3686 5837 5.372373 TGGGGAAACAAATGGATTTTGAAC 58.628 37.500 5.17 0.00 46.36 3.18
3687 5838 4.450757 GGGGAAACAAATGGATTTTGAACG 59.549 41.667 5.17 0.00 46.36 3.95
3688 5839 4.084066 GGGAAACAAATGGATTTTGAACGC 60.084 41.667 5.17 1.87 46.36 4.84
3689 5840 4.509600 GGAAACAAATGGATTTTGAACGCA 59.490 37.500 5.17 0.00 46.36 5.24
3690 5841 5.333263 GGAAACAAATGGATTTTGAACGCAG 60.333 40.000 5.17 0.00 46.36 5.18
3691 5842 3.059166 ACAAATGGATTTTGAACGCAGC 58.941 40.909 5.17 0.00 46.36 5.25
3692 5843 3.243839 ACAAATGGATTTTGAACGCAGCT 60.244 39.130 5.17 0.00 46.36 4.24
3693 5844 2.927553 ATGGATTTTGAACGCAGCTC 57.072 45.000 0.00 0.00 0.00 4.09
3694 5845 0.881118 TGGATTTTGAACGCAGCTCC 59.119 50.000 0.00 0.00 0.00 4.70
3695 5846 1.168714 GGATTTTGAACGCAGCTCCT 58.831 50.000 0.00 0.00 0.00 3.69
3696 5847 1.135575 GGATTTTGAACGCAGCTCCTG 60.136 52.381 0.00 0.00 34.12 3.86
3705 5856 4.834453 CAGCTCCTGCGCTCCTGG 62.834 72.222 9.73 5.95 45.42 4.45
3740 5891 4.473520 CGCCCCTGTCGCCAGAAT 62.474 66.667 0.00 0.00 41.50 2.40
3741 5892 2.825836 GCCCCTGTCGCCAGAATG 60.826 66.667 0.00 0.00 41.50 2.67
3742 5893 2.825836 CCCCTGTCGCCAGAATGC 60.826 66.667 0.00 0.00 41.50 3.56
3743 5894 2.825836 CCCTGTCGCCAGAATGCC 60.826 66.667 0.00 0.00 41.50 4.40
3744 5895 2.825836 CCTGTCGCCAGAATGCCC 60.826 66.667 0.00 0.00 41.50 5.36
3745 5896 2.046023 CTGTCGCCAGAATGCCCA 60.046 61.111 0.00 0.00 41.50 5.36
3746 5897 2.359850 TGTCGCCAGAATGCCCAC 60.360 61.111 0.00 0.00 31.97 4.61
3747 5898 3.134127 GTCGCCAGAATGCCCACC 61.134 66.667 0.00 0.00 31.97 4.61
3748 5899 4.424711 TCGCCAGAATGCCCACCC 62.425 66.667 0.00 0.00 31.97 4.61
3751 5902 4.738998 CCAGAATGCCCACCCGCA 62.739 66.667 0.00 0.00 44.35 5.69
3752 5903 3.136123 CAGAATGCCCACCCGCAG 61.136 66.667 0.00 0.00 43.26 5.18
3823 5974 4.935495 CAGGCCACGGTGCTGTGT 62.935 66.667 5.01 0.00 38.20 3.72
3824 5975 4.189580 AGGCCACGGTGCTGTGTT 62.190 61.111 5.01 0.00 38.20 3.32
3825 5976 3.964875 GGCCACGGTGCTGTGTTG 61.965 66.667 1.68 0.00 38.20 3.33
3826 5977 3.964875 GCCACGGTGCTGTGTTGG 61.965 66.667 1.68 0.00 38.20 3.77
3827 5978 3.286751 CCACGGTGCTGTGTTGGG 61.287 66.667 1.68 0.00 38.20 4.12
3828 5979 3.964875 CACGGTGCTGTGTTGGGC 61.965 66.667 0.00 0.00 35.12 5.36
3831 5982 4.947147 GGTGCTGTGTTGGGCCGA 62.947 66.667 0.00 0.00 0.00 5.54
3832 5983 2.672996 GTGCTGTGTTGGGCCGAT 60.673 61.111 0.00 0.00 0.00 4.18
3833 5984 2.672651 TGCTGTGTTGGGCCGATG 60.673 61.111 0.00 0.00 0.00 3.84
3834 5985 2.672996 GCTGTGTTGGGCCGATGT 60.673 61.111 0.00 0.00 0.00 3.06
3835 5986 2.690778 GCTGTGTTGGGCCGATGTC 61.691 63.158 0.00 0.00 0.00 3.06
3836 5987 2.358125 TGTGTTGGGCCGATGTCG 60.358 61.111 0.00 0.00 39.44 4.35
3837 5988 3.799755 GTGTTGGGCCGATGTCGC 61.800 66.667 0.00 0.00 38.18 5.19
3846 5997 3.209812 CGATGTCGCGGAGGAGGA 61.210 66.667 6.13 0.00 0.00 3.71
3847 5998 2.413765 GATGTCGCGGAGGAGGAC 59.586 66.667 6.13 0.00 0.00 3.85
3848 5999 3.471244 GATGTCGCGGAGGAGGACG 62.471 68.421 6.13 0.00 33.45 4.79
3849 6000 3.989838 ATGTCGCGGAGGAGGACGA 62.990 63.158 6.13 0.00 33.45 4.20
3850 6001 4.176851 GTCGCGGAGGAGGACGAC 62.177 72.222 6.13 0.00 46.64 4.34
3853 6004 4.477975 GCGGAGGAGGACGACGTG 62.478 72.222 4.58 0.00 0.00 4.49
3854 6005 3.812019 CGGAGGAGGACGACGTGG 61.812 72.222 4.58 0.00 0.00 4.94
3855 6006 4.131088 GGAGGAGGACGACGTGGC 62.131 72.222 4.58 0.00 0.00 5.01
3856 6007 4.131088 GAGGAGGACGACGTGGCC 62.131 72.222 4.58 0.36 0.00 5.36
3874 6025 4.767255 GCTGGCTGTCCCCTCGTG 62.767 72.222 0.00 0.00 0.00 4.35
3875 6026 4.767255 CTGGCTGTCCCCTCGTGC 62.767 72.222 0.00 0.00 0.00 5.34
3901 6052 4.394712 CCCTCGGCTCGCAAGGTT 62.395 66.667 8.25 0.00 38.47 3.50
3902 6053 3.121030 CCTCGGCTCGCAAGGTTG 61.121 66.667 2.42 0.00 38.47 3.77
3903 6054 2.357517 CTCGGCTCGCAAGGTTGT 60.358 61.111 0.00 0.00 38.47 3.32
3904 6055 2.664851 TCGGCTCGCAAGGTTGTG 60.665 61.111 0.00 0.00 39.93 3.33
3905 6056 2.664851 CGGCTCGCAAGGTTGTGA 60.665 61.111 5.86 5.86 44.63 3.58
3906 6057 2.946762 GGCTCGCAAGGTTGTGAC 59.053 61.111 1.79 0.81 42.25 3.67
3907 6058 2.617274 GGCTCGCAAGGTTGTGACC 61.617 63.158 1.79 5.72 46.92 4.02
3915 6066 2.280797 GGTTGTGACCAGCGCAGA 60.281 61.111 11.47 0.00 45.77 4.26
3916 6067 2.320587 GGTTGTGACCAGCGCAGAG 61.321 63.158 11.47 0.00 45.77 3.35
3917 6068 1.300931 GTTGTGACCAGCGCAGAGA 60.301 57.895 11.47 0.00 38.43 3.10
3918 6069 1.005748 TTGTGACCAGCGCAGAGAG 60.006 57.895 11.47 0.00 38.43 3.20
3919 6070 2.813042 GTGACCAGCGCAGAGAGC 60.813 66.667 11.47 0.00 40.87 4.09
3939 6090 3.414700 GCTGTCGCCTCGTTGTGG 61.415 66.667 0.00 0.00 0.00 4.17
3940 6091 3.414700 CTGTCGCCTCGTTGTGGC 61.415 66.667 0.00 0.00 46.42 5.01
3946 6097 3.052082 CCTCGTTGTGGCAGCCTG 61.052 66.667 14.15 0.00 0.00 4.85
3947 6098 3.052082 CTCGTTGTGGCAGCCTGG 61.052 66.667 14.15 0.00 0.00 4.45
3948 6099 4.641645 TCGTTGTGGCAGCCTGGG 62.642 66.667 14.15 0.00 0.00 4.45
3955 6106 4.792804 GGCAGCCTGGGCACTCTC 62.793 72.222 14.39 0.00 44.88 3.20
3956 6107 3.715097 GCAGCCTGGGCACTCTCT 61.715 66.667 14.39 0.00 44.88 3.10
3957 6108 3.076092 CAGCCTGGGCACTCTCTT 58.924 61.111 14.39 0.00 44.88 2.85
3958 6109 1.376942 CAGCCTGGGCACTCTCTTG 60.377 63.158 14.39 0.00 44.88 3.02
3959 6110 2.749441 GCCTGGGCACTCTCTTGC 60.749 66.667 6.75 0.00 42.18 4.01
3960 6111 2.435586 CCTGGGCACTCTCTTGCG 60.436 66.667 0.00 0.00 44.00 4.85
3961 6112 2.435586 CTGGGCACTCTCTTGCGG 60.436 66.667 0.00 0.00 44.00 5.69
3962 6113 3.241530 TGGGCACTCTCTTGCGGT 61.242 61.111 0.00 0.00 44.00 5.68
3963 6114 2.435059 GGGCACTCTCTTGCGGTC 60.435 66.667 0.00 0.00 44.00 4.79
3964 6115 2.811317 GGCACTCTCTTGCGGTCG 60.811 66.667 0.00 0.00 44.00 4.79
3965 6116 3.482783 GCACTCTCTTGCGGTCGC 61.483 66.667 8.54 8.54 42.35 5.19
3966 6117 3.175240 CACTCTCTTGCGGTCGCG 61.175 66.667 10.79 0.00 45.51 5.87
4025 6176 3.503099 GGGCCACCTTGGGTTCTA 58.497 61.111 4.39 0.00 38.19 2.10
4026 6177 1.303282 GGGCCACCTTGGGTTCTAG 59.697 63.158 4.39 0.00 38.19 2.43
4027 6178 1.303282 GGCCACCTTGGGTTCTAGG 59.697 63.158 0.00 0.00 38.19 3.02
4028 6179 1.205460 GGCCACCTTGGGTTCTAGGA 61.205 60.000 0.00 0.00 38.19 2.94
4029 6180 0.035343 GCCACCTTGGGTTCTAGGAC 60.035 60.000 0.00 0.00 38.19 3.85
4030 6181 0.618981 CCACCTTGGGTTCTAGGACC 59.381 60.000 12.35 12.35 38.88 4.46
4031 6182 0.249398 CACCTTGGGTTCTAGGACCG 59.751 60.000 14.38 2.68 40.75 4.79
4032 6183 1.221021 CCTTGGGTTCTAGGACCGC 59.779 63.158 14.38 7.83 40.75 5.68
4033 6184 1.265454 CCTTGGGTTCTAGGACCGCT 61.265 60.000 14.38 0.00 40.75 5.52
4034 6185 0.175989 CTTGGGTTCTAGGACCGCTC 59.824 60.000 14.38 0.94 40.75 5.03
4035 6186 1.601419 TTGGGTTCTAGGACCGCTCG 61.601 60.000 14.38 0.00 40.75 5.03
4036 6187 2.104530 GGTTCTAGGACCGCTCGC 59.895 66.667 3.86 0.00 0.00 5.03
4037 6188 2.104530 GTTCTAGGACCGCTCGCC 59.895 66.667 0.00 0.00 0.00 5.54
4038 6189 3.515286 TTCTAGGACCGCTCGCCG 61.515 66.667 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
378 386 1.338973 GCCTTACGATGGTACCGATCA 59.661 52.381 18.49 0.00 0.00 2.92
582 590 2.496871 TGGTGCCATGAACCATGATTTC 59.503 45.455 14.28 0.00 43.81 2.17
1244 1254 2.049433 CGGCCTTCTCGAACACGT 60.049 61.111 0.00 0.00 0.00 4.49
1450 1460 1.227999 ACAGAAATGGTGGTGACGCG 61.228 55.000 3.53 3.53 43.50 6.01
1531 1546 7.064134 CGCCAAAACAAGAATCATGTAGTAGTA 59.936 37.037 0.00 0.00 0.00 1.82
1532 1547 6.128282 CGCCAAAACAAGAATCATGTAGTAGT 60.128 38.462 0.00 0.00 0.00 2.73
1533 1548 6.128282 ACGCCAAAACAAGAATCATGTAGTAG 60.128 38.462 0.00 0.00 0.00 2.57
1534 1549 5.703592 ACGCCAAAACAAGAATCATGTAGTA 59.296 36.000 0.00 0.00 0.00 1.82
1535 1550 4.518970 ACGCCAAAACAAGAATCATGTAGT 59.481 37.500 0.00 0.00 0.00 2.73
1536 1551 5.046910 ACGCCAAAACAAGAATCATGTAG 57.953 39.130 0.00 0.00 0.00 2.74
1691 1706 9.559732 TCTCTGAATTTGACTTGAATTCTGTTA 57.440 29.630 7.05 0.23 41.70 2.41
1692 1707 8.455903 TCTCTGAATTTGACTTGAATTCTGTT 57.544 30.769 7.05 0.00 41.70 3.16
1693 1708 8.632906 ATCTCTGAATTTGACTTGAATTCTGT 57.367 30.769 7.05 5.73 41.70 3.41
1806 1821 9.628746 TGTCATACAGAATGAAAATGTTTGATG 57.371 29.630 0.00 0.00 46.17 3.07
1942 1957 7.087639 TGTTTTTGAACCTGAAAGTGTACAAG 58.912 34.615 0.00 0.00 0.00 3.16
2058 2073 5.005740 ACCCCAAAGATTTACTAAACGGAC 58.994 41.667 0.00 0.00 0.00 4.79
2060 2075 5.005094 TCACCCCAAAGATTTACTAAACGG 58.995 41.667 0.00 0.00 0.00 4.44
2077 2094 5.099042 ACATTGTACAGACTAATCACCCC 57.901 43.478 0.00 0.00 0.00 4.95
2142 2159 4.212847 CACATTGCGGGATATTCAGAAGAG 59.787 45.833 0.00 0.00 0.00 2.85
2202 2238 9.722184 AGACAAGTAATCATCTCCATGAATATG 57.278 33.333 0.00 0.00 42.53 1.78
2288 2324 6.719301 AGAAGAGTTTCTTGATCATGGTCAT 58.281 36.000 10.04 0.00 40.79 3.06
2334 2370 5.073428 AGAAGGACCCAAATTCAGAGTTTC 58.927 41.667 0.00 0.00 0.00 2.78
2356 2397 6.705381 CCTTAGCATTTCAGAAGATGGTAGAG 59.295 42.308 12.75 12.54 37.49 2.43
2383 2424 2.911926 GCAGGGAAGGAAGGCAGGT 61.912 63.158 0.00 0.00 0.00 4.00
2720 2775 9.973450 AGAGTTATATAACAGTAACAGAGCATG 57.027 33.333 24.05 0.00 38.62 4.06
2755 2810 6.378564 TCTTTTTGCGGGGATCAAAATGTATA 59.621 34.615 0.00 0.00 41.35 1.47
2815 2873 7.518731 TTTAAATATTGCAGCGCCTTTAAAG 57.481 32.000 2.29 8.32 0.00 1.85
2816 2874 7.891183 TTTTAAATATTGCAGCGCCTTTAAA 57.109 28.000 2.29 7.04 0.00 1.52
2817 2875 7.978975 AGATTTTAAATATTGCAGCGCCTTTAA 59.021 29.630 2.29 1.19 0.00 1.52
2818 2876 7.488322 AGATTTTAAATATTGCAGCGCCTTTA 58.512 30.769 2.29 0.00 0.00 1.85
2819 2877 6.340522 AGATTTTAAATATTGCAGCGCCTTT 58.659 32.000 2.29 0.00 0.00 3.11
2820 2878 5.906073 AGATTTTAAATATTGCAGCGCCTT 58.094 33.333 2.29 0.00 0.00 4.35
2821 2879 5.520376 AGATTTTAAATATTGCAGCGCCT 57.480 34.783 2.29 0.00 0.00 5.52
2998 5143 4.498345 GGTTTCTGCAAACAAATGGTCGTA 60.498 41.667 3.80 0.00 43.41 3.43
3150 5295 5.233902 GCAAATGCACAAAATCTACACACAA 59.766 36.000 0.00 0.00 41.59 3.33
3282 5431 1.827969 AGATCTCACTTGAACGGAGGG 59.172 52.381 0.00 0.00 0.00 4.30
3305 5454 2.421073 TGATCTGCTATGTTGCAACAGC 59.579 45.455 33.44 30.39 43.04 4.40
3309 5458 4.263435 TGTCATGATCTGCTATGTTGCAA 58.737 39.130 0.00 0.00 42.83 4.08
3339 5488 8.182227 CGTTCCCCTCTTTTTAGATGAAATAAC 58.818 37.037 0.00 0.00 0.00 1.89
3340 5489 7.886446 ACGTTCCCCTCTTTTTAGATGAAATAA 59.114 33.333 0.00 0.00 0.00 1.40
3341 5490 7.399634 ACGTTCCCCTCTTTTTAGATGAAATA 58.600 34.615 0.00 0.00 0.00 1.40
3342 5491 6.246163 ACGTTCCCCTCTTTTTAGATGAAAT 58.754 36.000 0.00 0.00 0.00 2.17
3346 5497 3.939592 GGACGTTCCCCTCTTTTTAGATG 59.060 47.826 0.00 0.00 0.00 2.90
3361 5512 2.100631 CAGATGCCGGTGGACGTTC 61.101 63.158 1.90 0.00 42.24 3.95
3364 5515 4.758251 TGCAGATGCCGGTGGACG 62.758 66.667 1.90 0.00 41.18 4.79
3433 5584 0.618968 ATTCTTGGTCGAGCCTCCCT 60.619 55.000 12.85 0.00 38.35 4.20
3451 5602 4.476628 ACTATTCGTACCACGGGAAAAT 57.523 40.909 0.00 0.00 42.81 1.82
3493 5644 2.223144 CGTGATTCGAAGCCTTTGTCAA 59.777 45.455 11.45 0.00 42.86 3.18
3498 5649 1.275291 TCTCCGTGATTCGAAGCCTTT 59.725 47.619 11.45 0.00 42.86 3.11
3520 5671 3.536158 ACATACACGTTGCAACATGTC 57.464 42.857 32.03 4.14 36.62 3.06
3523 5674 3.006940 CCCTACATACACGTTGCAACAT 58.993 45.455 28.01 11.97 0.00 2.71
3532 5683 3.383505 TCTTCATGGACCCTACATACACG 59.616 47.826 0.00 0.00 0.00 4.49
3535 5686 4.141711 TGCTTCTTCATGGACCCTACATAC 60.142 45.833 0.00 0.00 0.00 2.39
3536 5687 4.037222 TGCTTCTTCATGGACCCTACATA 58.963 43.478 0.00 0.00 0.00 2.29
3538 5689 2.265367 TGCTTCTTCATGGACCCTACA 58.735 47.619 0.00 0.00 0.00 2.74
3568 5719 1.142667 TGTGGTCAGAAGCCATTGTGA 59.857 47.619 0.00 0.00 38.40 3.58
3621 5772 6.877611 ATGATCCAAAAAGTTTGTACGAGT 57.122 33.333 0.00 0.00 0.00 4.18
3635 5786 7.564660 AGCCCTTTAATATGTGAATGATCCAAA 59.435 33.333 0.00 0.00 0.00 3.28
3664 5815 4.450757 CGTTCAAAATCCATTTGTTTCCCC 59.549 41.667 1.35 0.00 46.89 4.81
3665 5816 4.084066 GCGTTCAAAATCCATTTGTTTCCC 60.084 41.667 1.35 0.00 46.89 3.97
3666 5817 4.509600 TGCGTTCAAAATCCATTTGTTTCC 59.490 37.500 1.35 0.00 46.89 3.13
3667 5818 5.649602 TGCGTTCAAAATCCATTTGTTTC 57.350 34.783 1.35 0.00 46.89 2.78
3668 5819 4.024977 GCTGCGTTCAAAATCCATTTGTTT 60.025 37.500 1.35 0.00 46.89 2.83
3669 5820 3.494251 GCTGCGTTCAAAATCCATTTGTT 59.506 39.130 1.35 0.00 46.89 2.83
3670 5821 3.059166 GCTGCGTTCAAAATCCATTTGT 58.941 40.909 1.35 0.00 46.89 2.83
3672 5823 3.578688 GAGCTGCGTTCAAAATCCATTT 58.421 40.909 0.00 0.00 0.00 2.32
3673 5824 2.094545 GGAGCTGCGTTCAAAATCCATT 60.095 45.455 0.00 0.00 0.00 3.16
3674 5825 1.474077 GGAGCTGCGTTCAAAATCCAT 59.526 47.619 0.00 0.00 0.00 3.41
3675 5826 0.881118 GGAGCTGCGTTCAAAATCCA 59.119 50.000 0.00 0.00 0.00 3.41
3676 5827 1.135575 CAGGAGCTGCGTTCAAAATCC 60.136 52.381 0.00 0.00 0.00 3.01
3677 5828 2.253392 CAGGAGCTGCGTTCAAAATC 57.747 50.000 0.00 0.00 0.00 2.17
3731 5882 4.424711 GGGTGGGCATTCTGGCGA 62.425 66.667 0.00 0.00 44.78 5.54
3734 5885 4.738998 TGCGGGTGGGCATTCTGG 62.739 66.667 0.00 0.00 38.17 3.86
3735 5886 3.136123 CTGCGGGTGGGCATTCTG 61.136 66.667 0.00 0.00 42.99 3.02
3806 5957 4.935495 ACACAGCACCGTGGCCTG 62.935 66.667 3.32 2.81 41.38 4.85
3807 5958 4.189580 AACACAGCACCGTGGCCT 62.190 61.111 3.32 0.00 41.38 5.19
3808 5959 3.964875 CAACACAGCACCGTGGCC 61.965 66.667 0.00 0.00 41.38 5.36
3809 5960 3.964875 CCAACACAGCACCGTGGC 61.965 66.667 0.00 0.00 41.38 5.01
3810 5961 3.286751 CCCAACACAGCACCGTGG 61.287 66.667 0.00 0.00 41.38 4.94
3811 5962 3.964875 GCCCAACACAGCACCGTG 61.965 66.667 0.00 0.00 42.81 4.94
3814 5965 4.947147 TCGGCCCAACACAGCACC 62.947 66.667 0.00 0.00 0.00 5.01
3815 5966 2.672996 ATCGGCCCAACACAGCAC 60.673 61.111 0.00 0.00 0.00 4.40
3816 5967 2.672651 CATCGGCCCAACACAGCA 60.673 61.111 0.00 0.00 0.00 4.41
3817 5968 2.672996 ACATCGGCCCAACACAGC 60.673 61.111 0.00 0.00 0.00 4.40
3818 5969 2.390599 CGACATCGGCCCAACACAG 61.391 63.158 0.00 0.00 35.37 3.66
3819 5970 2.358125 CGACATCGGCCCAACACA 60.358 61.111 0.00 0.00 35.37 3.72
3820 5971 3.799755 GCGACATCGGCCCAACAC 61.800 66.667 0.00 0.00 40.23 3.32
3829 5980 3.209812 TCCTCCTCCGCGACATCG 61.210 66.667 8.23 0.00 43.27 3.84
3830 5981 2.413765 GTCCTCCTCCGCGACATC 59.586 66.667 8.23 0.00 0.00 3.06
3831 5982 3.518998 CGTCCTCCTCCGCGACAT 61.519 66.667 8.23 0.00 0.00 3.06
3832 5983 4.710167 TCGTCCTCCTCCGCGACA 62.710 66.667 8.23 0.00 0.00 4.35
3833 5984 4.176851 GTCGTCCTCCTCCGCGAC 62.177 72.222 8.23 0.00 44.93 5.19
3836 5987 4.477975 CACGTCGTCCTCCTCCGC 62.478 72.222 0.00 0.00 0.00 5.54
3837 5988 3.812019 CCACGTCGTCCTCCTCCG 61.812 72.222 0.00 0.00 0.00 4.63
3838 5989 4.131088 GCCACGTCGTCCTCCTCC 62.131 72.222 0.00 0.00 0.00 4.30
3839 5990 4.131088 GGCCACGTCGTCCTCCTC 62.131 72.222 0.00 0.00 0.00 3.71
3857 6008 4.767255 CACGAGGGGACAGCCAGC 62.767 72.222 0.00 0.00 35.15 4.85
3858 6009 4.767255 GCACGAGGGGACAGCCAG 62.767 72.222 0.00 0.00 35.15 4.85
3886 6037 2.357517 ACAACCTTGCGAGCCGAG 60.358 61.111 0.00 0.00 0.00 4.63
3887 6038 2.664851 CACAACCTTGCGAGCCGA 60.665 61.111 0.00 0.00 0.00 5.54
3888 6039 2.664851 TCACAACCTTGCGAGCCG 60.665 61.111 0.00 0.00 0.00 5.52
3889 6040 2.617274 GGTCACAACCTTGCGAGCC 61.617 63.158 0.00 0.00 42.80 4.70
3890 6041 1.845809 CTGGTCACAACCTTGCGAGC 61.846 60.000 0.00 0.00 46.60 5.03
3891 6042 1.845809 GCTGGTCACAACCTTGCGAG 61.846 60.000 0.00 0.00 46.60 5.03
3892 6043 1.891919 GCTGGTCACAACCTTGCGA 60.892 57.895 0.00 0.00 46.60 5.10
3893 6044 2.639286 GCTGGTCACAACCTTGCG 59.361 61.111 0.00 0.00 46.60 4.85
3894 6045 2.639286 CGCTGGTCACAACCTTGC 59.361 61.111 0.00 0.51 46.60 4.01
3895 6046 2.121564 CTGCGCTGGTCACAACCTTG 62.122 60.000 9.73 0.00 46.60 3.61
3896 6047 1.893808 CTGCGCTGGTCACAACCTT 60.894 57.895 9.73 0.00 46.60 3.50
3897 6048 2.281070 CTGCGCTGGTCACAACCT 60.281 61.111 9.73 0.00 46.60 3.50
3898 6049 2.280797 TCTGCGCTGGTCACAACC 60.281 61.111 14.70 0.00 46.66 3.77
3899 6050 1.287730 CTCTCTGCGCTGGTCACAAC 61.288 60.000 14.70 0.00 0.00 3.32
3900 6051 1.005748 CTCTCTGCGCTGGTCACAA 60.006 57.895 14.70 0.00 0.00 3.33
3901 6052 2.653115 CTCTCTGCGCTGGTCACA 59.347 61.111 14.70 0.00 0.00 3.58
3902 6053 2.813042 GCTCTCTGCGCTGGTCAC 60.813 66.667 14.70 0.00 0.00 3.67
3922 6073 3.414700 CCACAACGAGGCGACAGC 61.415 66.667 0.00 0.00 44.18 4.40
3923 6074 3.414700 GCCACAACGAGGCGACAG 61.415 66.667 0.00 0.00 43.15 3.51
3929 6080 3.052082 CAGGCTGCCACAACGAGG 61.052 66.667 22.65 0.00 0.00 4.63
3930 6081 3.052082 CCAGGCTGCCACAACGAG 61.052 66.667 22.65 1.23 0.00 4.18
3931 6082 4.641645 CCCAGGCTGCCACAACGA 62.642 66.667 22.65 0.00 0.00 3.85
3938 6089 4.792804 GAGAGTGCCCAGGCTGCC 62.793 72.222 11.65 11.65 42.51 4.85
3939 6090 3.265272 AAGAGAGTGCCCAGGCTGC 62.265 63.158 9.56 0.00 42.51 5.25
3940 6091 1.376942 CAAGAGAGTGCCCAGGCTG 60.377 63.158 7.75 7.75 42.51 4.85
3941 6092 3.076092 CAAGAGAGTGCCCAGGCT 58.924 61.111 10.58 0.00 42.51 4.58
3942 6093 2.749441 GCAAGAGAGTGCCCAGGC 60.749 66.667 0.38 0.38 38.66 4.85
3943 6094 2.435586 CGCAAGAGAGTGCCCAGG 60.436 66.667 0.00 0.00 41.73 4.45
3944 6095 2.435586 CCGCAAGAGAGTGCCCAG 60.436 66.667 0.00 0.00 41.73 4.45
3945 6096 3.240134 GACCGCAAGAGAGTGCCCA 62.240 63.158 0.00 0.00 41.73 5.36
3946 6097 2.435059 GACCGCAAGAGAGTGCCC 60.435 66.667 0.00 0.00 41.73 5.36
3947 6098 2.811317 CGACCGCAAGAGAGTGCC 60.811 66.667 0.00 0.00 41.73 5.01
3948 6099 3.482783 GCGACCGCAAGAGAGTGC 61.483 66.667 9.73 0.00 41.49 4.40
3949 6100 3.175240 CGCGACCGCAAGAGAGTG 61.175 66.667 14.91 0.00 42.06 3.51
4007 6158 1.151677 TAGAACCCAAGGTGGCCCT 60.152 57.895 0.00 0.00 45.63 5.19
4008 6159 1.303282 CTAGAACCCAAGGTGGCCC 59.697 63.158 0.00 0.00 35.34 5.80
4009 6160 1.205460 TCCTAGAACCCAAGGTGGCC 61.205 60.000 0.00 0.00 35.34 5.36
4010 6161 0.035343 GTCCTAGAACCCAAGGTGGC 60.035 60.000 0.00 0.00 35.34 5.01
4011 6162 0.618981 GGTCCTAGAACCCAAGGTGG 59.381 60.000 0.00 0.00 35.34 4.61
4012 6163 0.249398 CGGTCCTAGAACCCAAGGTG 59.751 60.000 0.00 0.00 35.34 4.00
4013 6164 1.551019 GCGGTCCTAGAACCCAAGGT 61.551 60.000 0.00 0.00 37.65 3.50
4014 6165 1.221021 GCGGTCCTAGAACCCAAGG 59.779 63.158 0.00 0.00 35.79 3.61
4015 6166 0.175989 GAGCGGTCCTAGAACCCAAG 59.824 60.000 2.39 0.00 35.79 3.61
4016 6167 1.601419 CGAGCGGTCCTAGAACCCAA 61.601 60.000 9.39 0.00 35.79 4.12
4017 6168 2.050350 CGAGCGGTCCTAGAACCCA 61.050 63.158 9.39 0.00 35.79 4.51
4018 6169 2.806237 CGAGCGGTCCTAGAACCC 59.194 66.667 9.39 0.00 35.79 4.11
4019 6170 2.104530 GCGAGCGGTCCTAGAACC 59.895 66.667 9.39 0.00 35.86 3.62
4020 6171 2.104530 GGCGAGCGGTCCTAGAAC 59.895 66.667 9.39 0.00 0.00 3.01
4021 6172 3.515286 CGGCGAGCGGTCCTAGAA 61.515 66.667 9.39 0.00 0.00 2.10



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

AutoCloner maintained by Alex Coulton.