Multiple sequence alignment - TraesCS3A01G201500

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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 TraesCS3A01G201500 chr3A 100.000 3954 0 0 1 3954 336597409 336601362 0.000000e+00 7302.0
1 TraesCS3A01G201500 chr3D 97.259 2992 69 5 1 2989 253519056 253522037 0.000000e+00 5059.0
2 TraesCS3A01G201500 chr3D 94.030 536 19 8 3388 3922 253522036 253522559 0.000000e+00 800.0
3 TraesCS3A01G201500 chr3D 100.000 91 0 0 3041 3131 604112394 604112304 6.800000e-38 169.0
4 TraesCS3A01G201500 chr3D 97.222 36 1 0 3919 3954 145194607 145194642 1.190000e-05 62.1
5 TraesCS3A01G201500 chr3B 96.312 2061 69 2 981 3041 309421487 309419434 0.000000e+00 3378.0
6 TraesCS3A01G201500 chr3B 95.181 996 24 6 1 986 309615932 309614951 0.000000e+00 1552.0
7 TraesCS3A01G201500 chr3B 95.068 365 15 2 3559 3922 309419054 309418692 4.430000e-159 571.0
8 TraesCS3A01G201500 chr3B 91.858 393 14 6 3131 3517 309419434 309419054 2.090000e-147 532.0
9 TraesCS3A01G201500 chr7D 100.000 91 0 0 3041 3131 635512068 635512158 6.800000e-38 169.0
10 TraesCS3A01G201500 chr4B 100.000 91 0 0 3041 3131 308680941 308681031 6.800000e-38 169.0
11 TraesCS3A01G201500 chr2B 100.000 91 0 0 3041 3131 474903175 474903085 6.800000e-38 169.0
12 TraesCS3A01G201500 chr2B 100.000 32 0 0 3923 3954 219737948 219737917 4.270000e-05 60.2
13 TraesCS3A01G201500 chr2B 94.872 39 0 1 3916 3954 465126599 465126635 4.270000e-05 60.2
14 TraesCS3A01G201500 chr1A 100.000 91 0 0 3041 3131 554461313 554461223 6.800000e-38 169.0
15 TraesCS3A01G201500 chr1A 100.000 91 0 0 3041 3131 554461860 554461770 6.800000e-38 169.0
16 TraesCS3A01G201500 chr5D 98.913 92 1 0 3041 3132 503290157 503290066 8.790000e-37 165.0
17 TraesCS3A01G201500 chr5D 100.000 31 0 0 3924 3954 565528547 565528517 1.530000e-04 58.4
18 TraesCS3A01G201500 chr6D 98.901 91 1 0 3041 3131 45508721 45508811 3.160000e-36 163.0
19 TraesCS3A01G201500 chr1D 98.901 91 1 0 3041 3131 254433831 254433741 3.160000e-36 163.0
20 TraesCS3A01G201500 chrUn 92.857 42 1 1 3913 3954 86999367 86999406 4.270000e-05 60.2
21 TraesCS3A01G201500 chr7B 92.857 42 1 1 3913 3954 420069090 420069129 4.270000e-05 60.2
22 TraesCS3A01G201500 chr7B 100.000 32 0 0 3923 3954 729316277 729316246 4.270000e-05 60.2
23 TraesCS3A01G201500 chr5B 92.857 42 1 1 3913 3954 666212302 666212341 4.270000e-05 60.2
24 TraesCS3A01G201500 chr4A 100.000 32 0 0 3923 3954 484546552 484546521 4.270000e-05 60.2


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 TraesCS3A01G201500 chr3A 336597409 336601362 3953 False 7302.000000 7302 100.000000 1 3954 1 chr3A.!!$F1 3953
1 TraesCS3A01G201500 chr3D 253519056 253522559 3503 False 2929.500000 5059 95.644500 1 3922 2 chr3D.!!$F2 3921
2 TraesCS3A01G201500 chr3B 309614951 309615932 981 True 1552.000000 1552 95.181000 1 986 1 chr3B.!!$R1 985
3 TraesCS3A01G201500 chr3B 309418692 309421487 2795 True 1493.666667 3378 94.412667 981 3922 3 chr3B.!!$R2 2941

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
879 889 0.889186 TCTTTTTCTCTGGTGGCGGC 60.889 55.0 0.0 0.0 0.0 6.53 F
2078 2093 1.288508 TGGAGATGGTGGGGAATGGG 61.289 60.0 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 2459 0.979709 CATCTGAGCTCCTCCCCACA 60.980 60.0 12.15 0.0 0.00 4.17 R
3055 3070 0.107831 TGGTCACTGCTAACCGCTTT 59.892 50.0 0.00 0.0 38.45 3.51 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
97 98 2.708216 TCTCCACACAGAAAGCAACA 57.292 45.000 0.00 0.00 0.00 3.33
316 317 3.011517 AGCTTCATGGCCTCCGGT 61.012 61.111 3.32 0.00 0.00 5.28
725 735 3.461773 CCTCATCCCGTGCCTCGT 61.462 66.667 0.00 0.00 37.94 4.18
857 867 3.435601 GCTCATCTCTCCCTCTCTCTCTT 60.436 52.174 0.00 0.00 0.00 2.85
861 871 4.503714 TCTCTCCCTCTCTCTCTTTCTC 57.496 50.000 0.00 0.00 0.00 2.87
865 875 5.650283 TCTCCCTCTCTCTCTTTCTCTTTT 58.350 41.667 0.00 0.00 0.00 2.27
869 879 6.210584 TCCCTCTCTCTCTTTCTCTTTTTCTC 59.789 42.308 0.00 0.00 0.00 2.87
870 880 6.211384 CCCTCTCTCTCTTTCTCTTTTTCTCT 59.789 42.308 0.00 0.00 0.00 3.10
871 881 7.092716 CCTCTCTCTCTTTCTCTTTTTCTCTG 58.907 42.308 0.00 0.00 0.00 3.35
872 882 6.991938 TCTCTCTCTTTCTCTTTTTCTCTGG 58.008 40.000 0.00 0.00 0.00 3.86
873 883 6.553100 TCTCTCTCTTTCTCTTTTTCTCTGGT 59.447 38.462 0.00 0.00 0.00 4.00
874 884 6.520272 TCTCTCTTTCTCTTTTTCTCTGGTG 58.480 40.000 0.00 0.00 0.00 4.17
875 885 5.615289 TCTCTTTCTCTTTTTCTCTGGTGG 58.385 41.667 0.00 0.00 0.00 4.61
876 886 4.137543 TCTTTCTCTTTTTCTCTGGTGGC 58.862 43.478 0.00 0.00 0.00 5.01
877 887 2.169832 TCTCTTTTTCTCTGGTGGCG 57.830 50.000 0.00 0.00 0.00 5.69
878 888 1.160137 CTCTTTTTCTCTGGTGGCGG 58.840 55.000 0.00 0.00 0.00 6.13
879 889 0.889186 TCTTTTTCTCTGGTGGCGGC 60.889 55.000 0.00 0.00 0.00 6.53
979 989 4.485163 GGCCAACATGTCATACAAAGAAC 58.515 43.478 0.00 0.00 0.00 3.01
1101 1116 2.177518 ACCCTGACCTCCCTCCTCA 61.178 63.158 0.00 0.00 0.00 3.86
1180 1195 2.046314 CGCGGAACCCACCAAGAT 60.046 61.111 0.00 0.00 0.00 2.40
1266 1281 2.032681 GCCACTCTCACCCGCTTT 59.967 61.111 0.00 0.00 0.00 3.51
1289 1304 2.656651 CTCCGCTTCCTCATCGCG 60.657 66.667 0.00 0.00 45.86 5.87
1499 1514 4.070552 GTCAAGGCGCTCCTCCGT 62.071 66.667 7.64 0.00 43.40 4.69
1847 1862 2.029844 GGACGCTCTGCACCTGTTC 61.030 63.158 0.00 0.00 0.00 3.18
2075 2090 1.779092 CTGATGGAGATGGTGGGGAAT 59.221 52.381 0.00 0.00 0.00 3.01
2078 2093 1.288508 TGGAGATGGTGGGGAATGGG 61.289 60.000 0.00 0.00 0.00 4.00
2085 2100 3.797353 TGGGGAATGGGCTCTCGC 61.797 66.667 0.00 0.00 0.00 5.03
2124 2139 5.718146 TCAAGAGTGTGATTGAGAGTCATC 58.282 41.667 0.00 0.00 31.93 2.92
2188 2203 5.109210 GCCTTTAAGGAAATATGGTGTTGC 58.891 41.667 16.18 0.00 37.67 4.17
2192 2207 7.581270 CCTTTAAGGAAATATGGTGTTGCCATT 60.581 37.037 4.75 0.00 46.88 3.16
2514 2529 0.616111 AGGTCTCCAGCCGAATGAGT 60.616 55.000 0.00 0.00 0.00 3.41
2678 2693 2.234661 CAGGAGCACCACAGAGTCATTA 59.765 50.000 2.07 0.00 38.94 1.90
2726 2741 1.338020 GGTTTTGTCCCAAGCAGTGAG 59.662 52.381 0.00 0.00 0.00 3.51
2784 2799 4.622740 GCATTGCTTAAGTTGCTAAACTGG 59.377 41.667 15.51 0.00 46.15 4.00
2923 2938 4.518211 AGAACATTTGTGGAAGAGCTGAAG 59.482 41.667 0.00 0.00 0.00 3.02
2994 3009 9.665719 TTAAGTGATGTGAGAATGCTGTTAATA 57.334 29.630 0.00 0.00 0.00 0.98
3024 3039 6.554334 TCCTCATAAAGACTTGGTTTTTCG 57.446 37.500 0.00 0.00 0.00 3.46
3026 3041 6.204108 TCCTCATAAAGACTTGGTTTTTCGAC 59.796 38.462 0.00 0.00 0.00 4.20
3031 3046 1.607148 GACTTGGTTTTTCGACCCAGG 59.393 52.381 0.00 0.00 36.90 4.45
3040 3055 3.426787 TTTCGACCCAGGCAAATTCTA 57.573 42.857 0.00 0.00 0.00 2.10
3041 3056 3.426787 TTCGACCCAGGCAAATTCTAA 57.573 42.857 0.00 0.00 0.00 2.10
3042 3057 3.426787 TCGACCCAGGCAAATTCTAAA 57.573 42.857 0.00 0.00 0.00 1.85
3043 3058 3.343617 TCGACCCAGGCAAATTCTAAAG 58.656 45.455 0.00 0.00 0.00 1.85
3044 3059 3.008594 TCGACCCAGGCAAATTCTAAAGA 59.991 43.478 0.00 0.00 0.00 2.52
3045 3060 3.947834 CGACCCAGGCAAATTCTAAAGAT 59.052 43.478 0.00 0.00 0.00 2.40
3046 3061 4.399303 CGACCCAGGCAAATTCTAAAGATT 59.601 41.667 0.00 0.00 0.00 2.40
3047 3062 5.105756 CGACCCAGGCAAATTCTAAAGATTT 60.106 40.000 0.00 0.00 0.00 2.17
3048 3063 6.041423 ACCCAGGCAAATTCTAAAGATTTG 57.959 37.500 5.45 5.45 38.07 2.32
3049 3064 5.046376 ACCCAGGCAAATTCTAAAGATTTGG 60.046 40.000 10.48 2.58 36.21 3.28
3050 3065 5.422145 CCAGGCAAATTCTAAAGATTTGGG 58.578 41.667 10.48 1.92 36.21 4.12
3051 3066 5.187576 CCAGGCAAATTCTAAAGATTTGGGA 59.812 40.000 10.48 0.00 36.21 4.37
3052 3067 6.101997 CAGGCAAATTCTAAAGATTTGGGAC 58.898 40.000 10.48 2.75 36.21 4.46
3053 3068 5.187772 AGGCAAATTCTAAAGATTTGGGACC 59.812 40.000 10.48 4.83 36.21 4.46
3054 3069 5.046663 GGCAAATTCTAAAGATTTGGGACCA 60.047 40.000 10.48 0.00 36.21 4.02
3055 3070 6.463360 GCAAATTCTAAAGATTTGGGACCAA 58.537 36.000 0.00 0.00 36.21 3.67
3062 3077 4.688770 TTTGGGACCAAAAGCGGT 57.311 50.000 13.79 0.00 42.16 5.68
3063 3078 2.903404 TTTGGGACCAAAAGCGGTT 58.097 47.368 13.79 0.00 42.16 4.44
3064 3079 2.068834 TTTGGGACCAAAAGCGGTTA 57.931 45.000 13.79 0.00 42.16 2.85
3065 3080 1.611519 TTGGGACCAAAAGCGGTTAG 58.388 50.000 0.00 0.00 40.22 2.34
3066 3081 2.425904 TTGGGACCAAAAGCGGTTAGC 61.426 52.381 0.00 0.00 40.22 3.09
3067 3082 4.986230 TTGGGACCAAAAGCGGTTAGCA 62.986 50.000 0.00 0.00 40.22 3.49
3078 3093 2.093306 CGGTTAGCAGTGACCATTGA 57.907 50.000 0.00 0.00 35.63 2.57
3079 3094 2.422597 CGGTTAGCAGTGACCATTGAA 58.577 47.619 0.00 0.00 35.63 2.69
3080 3095 3.009723 CGGTTAGCAGTGACCATTGAAT 58.990 45.455 0.00 0.00 35.63 2.57
3081 3096 4.188462 CGGTTAGCAGTGACCATTGAATA 58.812 43.478 0.00 0.00 35.63 1.75
3082 3097 4.634004 CGGTTAGCAGTGACCATTGAATAA 59.366 41.667 0.00 0.00 35.63 1.40
3083 3098 5.220662 CGGTTAGCAGTGACCATTGAATAAG 60.221 44.000 0.00 0.00 35.63 1.73
3084 3099 5.648092 GGTTAGCAGTGACCATTGAATAAGT 59.352 40.000 0.00 0.00 35.95 2.24
3085 3100 6.151144 GGTTAGCAGTGACCATTGAATAAGTT 59.849 38.462 0.00 0.00 35.95 2.66
3086 3101 7.309194 GGTTAGCAGTGACCATTGAATAAGTTT 60.309 37.037 0.00 0.00 35.95 2.66
3087 3102 6.259550 AGCAGTGACCATTGAATAAGTTTC 57.740 37.500 0.00 0.00 0.00 2.78
3088 3103 6.006449 AGCAGTGACCATTGAATAAGTTTCT 58.994 36.000 0.00 0.00 0.00 2.52
3089 3104 6.491403 AGCAGTGACCATTGAATAAGTTTCTT 59.509 34.615 0.00 0.00 0.00 2.52
3090 3105 6.803807 GCAGTGACCATTGAATAAGTTTCTTC 59.196 38.462 0.00 0.00 0.00 2.87
3091 3106 7.522073 GCAGTGACCATTGAATAAGTTTCTTCA 60.522 37.037 0.00 0.00 0.00 3.02
3092 3107 8.019669 CAGTGACCATTGAATAAGTTTCTTCAG 58.980 37.037 0.00 0.00 33.25 3.02
3093 3108 6.803807 GTGACCATTGAATAAGTTTCTTCAGC 59.196 38.462 2.13 0.00 33.25 4.26
3094 3109 6.716628 TGACCATTGAATAAGTTTCTTCAGCT 59.283 34.615 0.00 0.00 33.25 4.24
3095 3110 7.231317 TGACCATTGAATAAGTTTCTTCAGCTT 59.769 33.333 0.00 0.00 33.25 3.74
3096 3111 7.373493 ACCATTGAATAAGTTTCTTCAGCTTG 58.627 34.615 0.00 0.00 33.25 4.01
3097 3112 7.231317 ACCATTGAATAAGTTTCTTCAGCTTGA 59.769 33.333 0.00 0.00 33.25 3.02
3098 3113 7.754027 CCATTGAATAAGTTTCTTCAGCTTGAG 59.246 37.037 0.00 0.00 33.25 3.02
3099 3114 7.807977 TTGAATAAGTTTCTTCAGCTTGAGT 57.192 32.000 0.00 0.00 33.25 3.41
3100 3115 7.807977 TGAATAAGTTTCTTCAGCTTGAGTT 57.192 32.000 0.00 0.00 0.00 3.01
3101 3116 7.642669 TGAATAAGTTTCTTCAGCTTGAGTTG 58.357 34.615 0.00 0.00 0.00 3.16
3102 3117 4.907879 AAGTTTCTTCAGCTTGAGTTGG 57.092 40.909 0.00 0.00 0.00 3.77
3103 3118 3.217626 AGTTTCTTCAGCTTGAGTTGGG 58.782 45.455 0.00 0.00 0.00 4.12
3104 3119 2.952310 GTTTCTTCAGCTTGAGTTGGGT 59.048 45.455 0.00 0.00 0.00 4.51
3105 3120 3.297134 TTCTTCAGCTTGAGTTGGGTT 57.703 42.857 0.00 0.00 0.00 4.11
3106 3121 4.431416 TTCTTCAGCTTGAGTTGGGTTA 57.569 40.909 0.00 0.00 0.00 2.85
3107 3122 4.431416 TCTTCAGCTTGAGTTGGGTTAA 57.569 40.909 0.00 0.00 0.00 2.01
3108 3123 4.787551 TCTTCAGCTTGAGTTGGGTTAAA 58.212 39.130 0.00 0.00 0.00 1.52
3109 3124 5.197451 TCTTCAGCTTGAGTTGGGTTAAAA 58.803 37.500 0.00 0.00 0.00 1.52
3110 3125 5.299279 TCTTCAGCTTGAGTTGGGTTAAAAG 59.701 40.000 0.00 0.00 0.00 2.27
3111 3126 3.317993 TCAGCTTGAGTTGGGTTAAAAGC 59.682 43.478 0.00 0.00 40.18 3.51
3112 3127 3.068024 CAGCTTGAGTTGGGTTAAAAGCA 59.932 43.478 7.82 0.00 41.87 3.91
3113 3128 3.068165 AGCTTGAGTTGGGTTAAAAGCAC 59.932 43.478 7.82 0.00 41.87 4.40
3114 3129 3.628017 CTTGAGTTGGGTTAAAAGCACG 58.372 45.455 0.00 0.00 0.00 5.34
3115 3130 1.950909 TGAGTTGGGTTAAAAGCACGG 59.049 47.619 0.00 0.00 0.00 4.94
3116 3131 2.223745 GAGTTGGGTTAAAAGCACGGA 58.776 47.619 0.00 0.00 0.00 4.69
3117 3132 2.619646 GAGTTGGGTTAAAAGCACGGAA 59.380 45.455 0.00 0.00 0.00 4.30
3118 3133 2.621526 AGTTGGGTTAAAAGCACGGAAG 59.378 45.455 0.00 0.00 0.00 3.46
3119 3134 1.611519 TGGGTTAAAAGCACGGAAGG 58.388 50.000 0.00 0.00 0.00 3.46
3120 3135 1.133730 TGGGTTAAAAGCACGGAAGGT 60.134 47.619 0.00 0.00 0.00 3.50
3121 3136 2.106166 TGGGTTAAAAGCACGGAAGGTA 59.894 45.455 0.00 0.00 0.00 3.08
3122 3137 3.244981 TGGGTTAAAAGCACGGAAGGTAT 60.245 43.478 0.00 0.00 0.00 2.73
3123 3138 3.760151 GGGTTAAAAGCACGGAAGGTATT 59.240 43.478 0.00 0.00 0.00 1.89
3124 3139 4.219070 GGGTTAAAAGCACGGAAGGTATTT 59.781 41.667 0.00 0.00 0.00 1.40
3125 3140 5.158494 GGTTAAAAGCACGGAAGGTATTTG 58.842 41.667 0.00 0.00 0.00 2.32
3126 3141 3.297830 AAAAGCACGGAAGGTATTTGC 57.702 42.857 0.00 0.00 0.00 3.68
3127 3142 1.904287 AAGCACGGAAGGTATTTGCA 58.096 45.000 0.00 0.00 35.57 4.08
3128 3143 1.165270 AGCACGGAAGGTATTTGCAC 58.835 50.000 0.00 0.00 35.57 4.57
3129 3144 0.170339 GCACGGAAGGTATTTGCACC 59.830 55.000 0.00 0.00 39.02 5.01
3212 3227 1.225704 GCTGATGGCTTAGTGGGCT 59.774 57.895 0.00 0.00 38.06 5.19
3213 3228 0.469917 GCTGATGGCTTAGTGGGCTA 59.530 55.000 0.00 0.00 38.06 3.93
3220 3235 4.577988 TGGCTTAGTGGGCTATAACAAA 57.422 40.909 0.00 0.00 0.00 2.83
3260 3281 3.305131 GCTGAATGATGGCCATGTACATG 60.305 47.826 26.56 26.02 35.24 3.21
3270 3291 1.220529 CATGTACATGCCTCGCGATT 58.779 50.000 22.27 0.00 31.39 3.34
3283 3304 1.369091 CGCGATTCTGGGTTCCTTGG 61.369 60.000 0.00 0.00 0.00 3.61
3296 3317 4.021104 GGGTTCCTTGGATTTTTGGAGAAG 60.021 45.833 0.00 0.00 0.00 2.85
3308 3329 1.730501 TGGAGAAGAGATGCAAAGCG 58.269 50.000 0.00 0.00 0.00 4.68
3426 3447 3.509517 GCTGGAATGCCATCCTTCT 57.490 52.632 0.00 0.00 44.91 2.85
3427 3448 1.030457 GCTGGAATGCCATCCTTCTG 58.970 55.000 0.00 0.00 44.91 3.02
3428 3449 1.030457 CTGGAATGCCATCCTTCTGC 58.970 55.000 0.00 0.00 44.91 4.26
3429 3450 0.396139 TGGAATGCCATCCTTCTGCC 60.396 55.000 0.00 0.00 39.92 4.85
3430 3451 0.396139 GGAATGCCATCCTTCTGCCA 60.396 55.000 0.00 0.00 36.50 4.92
3431 3452 1.030457 GAATGCCATCCTTCTGCCAG 58.970 55.000 0.00 0.00 0.00 4.85
3432 3453 0.396695 AATGCCATCCTTCTGCCAGG 60.397 55.000 0.00 0.00 34.86 4.45
3433 3454 1.578215 ATGCCATCCTTCTGCCAGGT 61.578 55.000 0.00 0.00 35.15 4.00
3434 3455 0.913934 TGCCATCCTTCTGCCAGGTA 60.914 55.000 0.00 0.00 35.15 3.08
3435 3456 0.179034 GCCATCCTTCTGCCAGGTAG 60.179 60.000 0.00 0.00 35.15 3.18
3465 3486 0.595095 GCAAACTGCTCTTGTCCTGG 59.405 55.000 0.00 0.00 40.96 4.45
3466 3487 1.242076 CAAACTGCTCTTGTCCTGGG 58.758 55.000 0.00 0.00 0.00 4.45
3507 3528 7.891561 AGCATGGCTAACAAATTACTGTAAAA 58.108 30.769 4.11 0.00 36.99 1.52
3516 3537 5.010617 ACAAATTACTGTAAAACCCCTGCTG 59.989 40.000 4.11 0.00 0.00 4.41
3569 3590 1.712056 TAGCCCTAGATTAAGCGGCA 58.288 50.000 10.18 0.00 42.28 5.69
3579 3600 3.812053 AGATTAAGCGGCAGACATGATTC 59.188 43.478 0.00 0.00 0.00 2.52
3614 3635 4.870123 TTAAGTGTTGCATCCAATTGCT 57.130 36.364 0.00 0.00 43.18 3.91
3623 3644 5.911378 TGCATCCAATTGCTACAATTGTA 57.089 34.783 23.96 17.16 43.18 2.41
3624 3645 5.649557 TGCATCCAATTGCTACAATTGTAC 58.350 37.500 23.96 11.61 43.18 2.90
3755 3777 1.051008 TGAGATGGTGTGAGCACTGT 58.949 50.000 1.99 0.00 44.65 3.55
3925 3947 7.284074 TGGTACACATATAAATTGGTAGTGGG 58.716 38.462 0.00 0.00 0.00 4.61
3926 3948 6.713450 GGTACACATATAAATTGGTAGTGGGG 59.287 42.308 0.00 0.00 0.00 4.96
3927 3949 5.137551 ACACATATAAATTGGTAGTGGGGC 58.862 41.667 0.00 0.00 0.00 5.80
3928 3950 4.215399 CACATATAAATTGGTAGTGGGGCG 59.785 45.833 0.00 0.00 0.00 6.13
3929 3951 4.141344 ACATATAAATTGGTAGTGGGGCGT 60.141 41.667 0.00 0.00 0.00 5.68
3930 3952 5.072058 ACATATAAATTGGTAGTGGGGCGTA 59.928 40.000 0.00 0.00 0.00 4.42
3931 3953 2.883122 AAATTGGTAGTGGGGCGTAA 57.117 45.000 0.00 0.00 0.00 3.18
3932 3954 2.118313 AATTGGTAGTGGGGCGTAAC 57.882 50.000 0.00 0.00 0.00 2.50
3933 3955 0.253894 ATTGGTAGTGGGGCGTAACC 59.746 55.000 0.00 0.00 37.93 2.85
3942 3964 2.202756 GGCGTAACCCTCTCAGCG 60.203 66.667 0.00 0.00 0.00 5.18
3943 3965 2.707849 GGCGTAACCCTCTCAGCGA 61.708 63.158 0.00 0.00 0.00 4.93
3944 3966 1.516603 GCGTAACCCTCTCAGCGAC 60.517 63.158 0.00 0.00 0.00 5.19
3945 3967 1.226323 CGTAACCCTCTCAGCGACG 60.226 63.158 0.00 0.00 0.00 5.12
3946 3968 1.516603 GTAACCCTCTCAGCGACGC 60.517 63.158 13.03 13.03 0.00 5.19
3947 3969 3.047718 TAACCCTCTCAGCGACGCG 62.048 63.158 15.18 3.53 0.00 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 1.954362 GCGACAGACTGGATGAGGCT 61.954 60.000 7.51 0.00 43.08 4.58
316 317 2.354704 CCTCTGCAAGAACGGATTGGTA 60.355 50.000 0.00 0.00 46.34 3.25
810 820 2.292794 GATTCCGGCTAGGTCACGCA 62.293 60.000 0.00 0.00 41.99 5.24
857 867 2.494059 CGCCACCAGAGAAAAAGAGAA 58.506 47.619 0.00 0.00 0.00 2.87
861 871 1.581447 GCCGCCACCAGAGAAAAAG 59.419 57.895 0.00 0.00 0.00 2.27
979 989 1.511768 GAAACCCTCCGACTCCGAG 59.488 63.158 0.00 0.00 38.22 4.63
1048 1063 1.003839 GACACGGCCTTGGACATGA 60.004 57.895 14.57 0.00 0.00 3.07
1180 1195 4.816984 GGCCGGAGAGGTCGAGGA 62.817 72.222 5.05 0.00 43.70 3.71
1266 1281 2.683933 GAGGAAGCGGAGGGTGGA 60.684 66.667 0.00 0.00 0.00 4.02
1729 1744 1.198713 CTCCTCTAAGAAGCCCTGCA 58.801 55.000 0.00 0.00 0.00 4.41
1847 1862 2.253758 CCTGGGCGGCATAACATCG 61.254 63.158 12.47 0.00 0.00 3.84
2021 2036 3.001414 CTCCTTCACTCTGCACTCATTG 58.999 50.000 0.00 0.00 0.00 2.82
2057 2072 1.202976 CCATTCCCCACCATCTCCATC 60.203 57.143 0.00 0.00 0.00 3.51
2085 2100 2.167281 TCTTGAGAGCGAATCCTTCAGG 59.833 50.000 0.00 0.00 0.00 3.86
2124 2139 2.559668 TGAGCAGCTTCCCAATTTTGAG 59.440 45.455 0.00 0.00 0.00 3.02
2188 2203 3.328382 TGTAACTCTCCAACGGAATGG 57.672 47.619 0.00 0.00 42.12 3.16
2192 2207 3.071479 GCAATTGTAACTCTCCAACGGA 58.929 45.455 7.40 0.00 0.00 4.69
2234 2249 1.077212 AGCATGAGGGCGCATTTCT 60.077 52.632 10.83 0.00 39.27 2.52
2237 2252 3.524606 GCAGCATGAGGGCGCATT 61.525 61.111 10.83 0.00 39.69 3.56
2243 2258 4.517934 CCCCTGGCAGCATGAGGG 62.518 72.222 9.56 10.29 46.95 4.30
2259 2274 4.843728 TCTATCATCCACTGGAACAAACC 58.156 43.478 0.66 0.00 38.70 3.27
2444 2459 0.979709 CATCTGAGCTCCTCCCCACA 60.980 60.000 12.15 0.00 0.00 4.17
2514 2529 4.099266 ACAAACCAAAGCAGCACAAATAGA 59.901 37.500 0.00 0.00 0.00 1.98
2678 2693 3.508793 CCAACATCCTGTTCTGCAATTCT 59.491 43.478 0.00 0.00 38.77 2.40
2726 2741 5.235186 CCCATAAACAAGAGATCGACATGTC 59.765 44.000 16.21 16.21 0.00 3.06
2883 2898 2.679837 GTTCTCGTTCATCATGCATGGT 59.320 45.455 25.97 17.67 32.64 3.55
2923 2938 5.233689 GCTTTCTGCTGCATAATCCAATTTC 59.766 40.000 1.31 0.00 38.95 2.17
2982 2997 8.874744 ATGAGGAGCATTATATTAACAGCATT 57.125 30.769 0.00 0.00 31.73 3.56
2994 3009 6.904626 ACCAAGTCTTTATGAGGAGCATTAT 58.095 36.000 0.00 0.00 38.44 1.28
2999 3014 5.966742 AAAACCAAGTCTTTATGAGGAGC 57.033 39.130 0.00 0.00 0.00 4.70
3024 3039 5.921962 AATCTTTAGAATTTGCCTGGGTC 57.078 39.130 0.00 0.00 0.00 4.46
3026 3041 5.422145 CCAAATCTTTAGAATTTGCCTGGG 58.578 41.667 0.00 0.00 34.84 4.45
3031 3046 6.036577 TGGTCCCAAATCTTTAGAATTTGC 57.963 37.500 3.61 0.00 34.84 3.68
3040 3055 2.037121 CCGCTTTTGGTCCCAAATCTTT 59.963 45.455 12.04 0.00 44.14 2.52
3041 3056 1.618343 CCGCTTTTGGTCCCAAATCTT 59.382 47.619 12.04 0.00 44.14 2.40
3042 3057 1.256812 CCGCTTTTGGTCCCAAATCT 58.743 50.000 12.04 0.00 44.14 2.40
3043 3058 0.966179 ACCGCTTTTGGTCCCAAATC 59.034 50.000 12.04 6.85 44.14 2.17
3044 3059 1.419381 AACCGCTTTTGGTCCCAAAT 58.581 45.000 12.04 0.00 44.14 2.32
3045 3060 1.957877 CTAACCGCTTTTGGTCCCAAA 59.042 47.619 7.40 7.40 42.89 3.28
3046 3061 1.611519 CTAACCGCTTTTGGTCCCAA 58.388 50.000 0.00 0.00 42.89 4.12
3047 3062 0.891904 GCTAACCGCTTTTGGTCCCA 60.892 55.000 0.00 0.00 42.89 4.37
3048 3063 0.891904 TGCTAACCGCTTTTGGTCCC 60.892 55.000 0.00 0.00 42.89 4.46
3049 3064 0.521735 CTGCTAACCGCTTTTGGTCC 59.478 55.000 0.00 0.00 42.89 4.46
3050 3065 1.069227 CACTGCTAACCGCTTTTGGTC 60.069 52.381 0.00 0.00 42.89 4.02
3051 3066 0.951558 CACTGCTAACCGCTTTTGGT 59.048 50.000 0.00 0.00 46.67 3.67
3052 3067 1.069227 GTCACTGCTAACCGCTTTTGG 60.069 52.381 0.00 0.00 40.11 3.28
3053 3068 1.069227 GGTCACTGCTAACCGCTTTTG 60.069 52.381 0.00 0.00 40.11 2.44
3054 3069 1.235724 GGTCACTGCTAACCGCTTTT 58.764 50.000 0.00 0.00 40.11 2.27
3055 3070 0.107831 TGGTCACTGCTAACCGCTTT 59.892 50.000 0.00 0.00 38.45 3.51
3056 3071 0.324943 ATGGTCACTGCTAACCGCTT 59.675 50.000 0.00 0.00 38.45 4.68
3057 3072 0.324943 AATGGTCACTGCTAACCGCT 59.675 50.000 0.00 0.00 38.45 5.52
3058 3073 0.447801 CAATGGTCACTGCTAACCGC 59.552 55.000 0.00 0.00 38.45 5.68
3059 3074 2.093306 TCAATGGTCACTGCTAACCG 57.907 50.000 0.00 0.00 38.45 4.44
3060 3075 5.648092 ACTTATTCAATGGTCACTGCTAACC 59.352 40.000 0.00 0.00 36.03 2.85
3061 3076 6.743575 ACTTATTCAATGGTCACTGCTAAC 57.256 37.500 0.00 0.00 0.00 2.34
3062 3077 7.665559 AGAAACTTATTCAATGGTCACTGCTAA 59.334 33.333 0.00 0.00 0.00 3.09
3063 3078 7.168219 AGAAACTTATTCAATGGTCACTGCTA 58.832 34.615 0.00 0.00 0.00 3.49
3064 3079 6.006449 AGAAACTTATTCAATGGTCACTGCT 58.994 36.000 0.00 0.00 0.00 4.24
3065 3080 6.259550 AGAAACTTATTCAATGGTCACTGC 57.740 37.500 0.00 0.00 0.00 4.40
3066 3081 7.874940 TGAAGAAACTTATTCAATGGTCACTG 58.125 34.615 0.00 0.00 35.67 3.66
3067 3082 7.308830 GCTGAAGAAACTTATTCAATGGTCACT 60.309 37.037 1.58 0.00 37.87 3.41
3068 3083 6.803807 GCTGAAGAAACTTATTCAATGGTCAC 59.196 38.462 1.58 0.00 37.87 3.67
3069 3084 6.716628 AGCTGAAGAAACTTATTCAATGGTCA 59.283 34.615 1.58 0.00 37.87 4.02
3070 3085 7.150783 AGCTGAAGAAACTTATTCAATGGTC 57.849 36.000 1.58 0.00 37.87 4.02
3071 3086 7.231317 TCAAGCTGAAGAAACTTATTCAATGGT 59.769 33.333 1.58 0.00 37.87 3.55
3072 3087 7.596494 TCAAGCTGAAGAAACTTATTCAATGG 58.404 34.615 1.58 0.00 37.87 3.16
3073 3088 8.295288 ACTCAAGCTGAAGAAACTTATTCAATG 58.705 33.333 2.77 2.28 37.87 2.82
3074 3089 8.401490 ACTCAAGCTGAAGAAACTTATTCAAT 57.599 30.769 2.77 0.00 37.87 2.57
3075 3090 7.807977 ACTCAAGCTGAAGAAACTTATTCAA 57.192 32.000 2.77 0.00 37.87 2.69
3076 3091 7.255242 CCAACTCAAGCTGAAGAAACTTATTCA 60.255 37.037 2.77 0.08 36.19 2.57
3077 3092 7.080724 CCAACTCAAGCTGAAGAAACTTATTC 58.919 38.462 2.77 0.00 0.00 1.75
3078 3093 6.015940 CCCAACTCAAGCTGAAGAAACTTATT 60.016 38.462 2.77 0.00 0.00 1.40
3079 3094 5.474876 CCCAACTCAAGCTGAAGAAACTTAT 59.525 40.000 2.77 0.00 0.00 1.73
3080 3095 4.821805 CCCAACTCAAGCTGAAGAAACTTA 59.178 41.667 2.77 0.00 0.00 2.24
3081 3096 3.633986 CCCAACTCAAGCTGAAGAAACTT 59.366 43.478 2.77 0.00 0.00 2.66
3082 3097 3.217626 CCCAACTCAAGCTGAAGAAACT 58.782 45.455 2.77 0.00 0.00 2.66
3083 3098 2.952310 ACCCAACTCAAGCTGAAGAAAC 59.048 45.455 2.77 0.00 0.00 2.78
3084 3099 3.297134 ACCCAACTCAAGCTGAAGAAA 57.703 42.857 2.77 0.00 0.00 2.52
3085 3100 3.297134 AACCCAACTCAAGCTGAAGAA 57.703 42.857 2.77 0.00 0.00 2.52
3086 3101 4.431416 TTAACCCAACTCAAGCTGAAGA 57.569 40.909 2.77 0.00 0.00 2.87
3087 3102 5.514274 TTTTAACCCAACTCAAGCTGAAG 57.486 39.130 0.00 0.00 0.00 3.02
3088 3103 4.202111 GCTTTTAACCCAACTCAAGCTGAA 60.202 41.667 0.00 0.00 34.94 3.02
3089 3104 3.317993 GCTTTTAACCCAACTCAAGCTGA 59.682 43.478 0.00 0.00 34.94 4.26
3090 3105 3.068024 TGCTTTTAACCCAACTCAAGCTG 59.932 43.478 5.99 0.00 37.97 4.24
3091 3106 3.068165 GTGCTTTTAACCCAACTCAAGCT 59.932 43.478 5.99 0.00 37.97 3.74
3092 3107 3.381045 GTGCTTTTAACCCAACTCAAGC 58.619 45.455 0.00 0.00 37.69 4.01
3093 3108 3.550030 CCGTGCTTTTAACCCAACTCAAG 60.550 47.826 0.00 0.00 0.00 3.02
3094 3109 2.359531 CCGTGCTTTTAACCCAACTCAA 59.640 45.455 0.00 0.00 0.00 3.02
3095 3110 1.950909 CCGTGCTTTTAACCCAACTCA 59.049 47.619 0.00 0.00 0.00 3.41
3096 3111 2.223745 TCCGTGCTTTTAACCCAACTC 58.776 47.619 0.00 0.00 0.00 3.01
3097 3112 2.351706 TCCGTGCTTTTAACCCAACT 57.648 45.000 0.00 0.00 0.00 3.16
3098 3113 2.287970 CCTTCCGTGCTTTTAACCCAAC 60.288 50.000 0.00 0.00 0.00 3.77
3099 3114 1.957877 CCTTCCGTGCTTTTAACCCAA 59.042 47.619 0.00 0.00 0.00 4.12
3100 3115 1.133730 ACCTTCCGTGCTTTTAACCCA 60.134 47.619 0.00 0.00 0.00 4.51
3101 3116 1.612676 ACCTTCCGTGCTTTTAACCC 58.387 50.000 0.00 0.00 0.00 4.11
3102 3117 5.158494 CAAATACCTTCCGTGCTTTTAACC 58.842 41.667 0.00 0.00 0.00 2.85
3103 3118 4.619760 GCAAATACCTTCCGTGCTTTTAAC 59.380 41.667 0.00 0.00 32.43 2.01
3104 3119 4.278669 TGCAAATACCTTCCGTGCTTTTAA 59.721 37.500 0.00 0.00 36.18 1.52
3105 3120 3.821600 TGCAAATACCTTCCGTGCTTTTA 59.178 39.130 0.00 0.00 36.18 1.52
3106 3121 2.625790 TGCAAATACCTTCCGTGCTTTT 59.374 40.909 0.00 0.00 36.18 2.27
3107 3122 2.030274 GTGCAAATACCTTCCGTGCTTT 60.030 45.455 0.00 0.00 36.18 3.51
3108 3123 1.539827 GTGCAAATACCTTCCGTGCTT 59.460 47.619 0.00 0.00 36.18 3.91
3109 3124 1.165270 GTGCAAATACCTTCCGTGCT 58.835 50.000 0.00 0.00 36.18 4.40
3110 3125 0.170339 GGTGCAAATACCTTCCGTGC 59.830 55.000 0.00 0.00 37.74 5.34
3111 3126 1.468520 CTGGTGCAAATACCTTCCGTG 59.531 52.381 0.00 0.00 41.43 4.94
3112 3127 1.073284 ACTGGTGCAAATACCTTCCGT 59.927 47.619 0.00 0.00 41.43 4.69
3113 3128 1.737793 GACTGGTGCAAATACCTTCCG 59.262 52.381 0.00 0.00 41.43 4.30
3114 3129 2.749621 CAGACTGGTGCAAATACCTTCC 59.250 50.000 0.00 0.00 41.43 3.46
3115 3130 3.189287 CACAGACTGGTGCAAATACCTTC 59.811 47.826 7.51 0.00 41.43 3.46
3116 3131 3.149196 CACAGACTGGTGCAAATACCTT 58.851 45.455 7.51 0.00 41.43 3.50
3117 3132 2.106511 ACACAGACTGGTGCAAATACCT 59.893 45.455 7.51 0.00 42.55 3.08
3118 3133 2.226437 CACACAGACTGGTGCAAATACC 59.774 50.000 7.51 0.00 42.55 2.73
3119 3134 3.138304 TCACACAGACTGGTGCAAATAC 58.862 45.455 15.38 0.00 42.55 1.89
3120 3135 3.483808 TCACACAGACTGGTGCAAATA 57.516 42.857 15.38 0.87 42.55 1.40
3121 3136 2.346766 TCACACAGACTGGTGCAAAT 57.653 45.000 15.38 0.00 42.55 2.32
3122 3137 1.948834 CATCACACAGACTGGTGCAAA 59.051 47.619 15.38 3.89 42.55 3.68
3123 3138 1.596603 CATCACACAGACTGGTGCAA 58.403 50.000 15.38 4.43 42.55 4.08
3124 3139 0.886043 GCATCACACAGACTGGTGCA 60.886 55.000 15.38 8.13 42.55 4.57
3125 3140 0.886043 TGCATCACACAGACTGGTGC 60.886 55.000 15.38 12.75 42.55 5.01
3126 3141 1.265095 GTTGCATCACACAGACTGGTG 59.735 52.381 7.51 11.80 44.35 4.17
3127 3142 1.141657 AGTTGCATCACACAGACTGGT 59.858 47.619 7.51 0.00 0.00 4.00
3128 3143 1.888215 AGTTGCATCACACAGACTGG 58.112 50.000 7.51 0.00 0.00 4.00
3129 3144 2.615447 ACAAGTTGCATCACACAGACTG 59.385 45.455 1.81 0.00 0.00 3.51
3212 3227 1.287217 TGGGGCCTCGGTTTGTTATA 58.713 50.000 0.84 0.00 0.00 0.98
3213 3228 0.629058 ATGGGGCCTCGGTTTGTTAT 59.371 50.000 0.84 0.00 0.00 1.89
3220 3235 2.610859 AAGTCATGGGGCCTCGGT 60.611 61.111 0.84 0.00 0.00 4.69
3260 3281 2.125106 AACCCAGAATCGCGAGGC 60.125 61.111 16.66 9.07 0.00 4.70
3270 3291 3.116939 TCCAAAAATCCAAGGAACCCAGA 60.117 43.478 0.00 0.00 0.00 3.86
3283 3304 5.575995 GCTTTGCATCTCTTCTCCAAAAATC 59.424 40.000 0.00 0.00 0.00 2.17
3308 3329 4.749099 CAGCATTAGTCCTCATGAACTAGC 59.251 45.833 7.22 8.36 0.00 3.42
3420 3441 0.835971 TGCACTACCTGGCAGAAGGA 60.836 55.000 17.94 0.00 40.02 3.36
3421 3442 0.254178 ATGCACTACCTGGCAGAAGG 59.746 55.000 17.94 2.24 44.24 3.46
3422 3443 1.339438 ACATGCACTACCTGGCAGAAG 60.339 52.381 17.94 15.12 44.24 2.85
3424 3445 0.692476 AACATGCACTACCTGGCAGA 59.308 50.000 17.94 0.00 44.24 4.26
3425 3446 1.200716 CAAACATGCACTACCTGGCAG 59.799 52.381 7.75 7.75 44.24 4.85
3426 3447 1.246649 CAAACATGCACTACCTGGCA 58.753 50.000 0.00 0.00 45.23 4.92
3427 3448 0.527565 CCAAACATGCACTACCTGGC 59.472 55.000 0.00 0.00 0.00 4.85
3428 3449 0.527565 GCCAAACATGCACTACCTGG 59.472 55.000 0.00 0.00 0.00 4.45
3429 3450 1.246649 TGCCAAACATGCACTACCTG 58.753 50.000 0.00 0.00 32.85 4.00
3430 3451 1.993956 TTGCCAAACATGCACTACCT 58.006 45.000 0.00 0.00 38.72 3.08
3431 3452 2.035832 AGTTTGCCAAACATGCACTACC 59.964 45.455 21.45 0.00 43.79 3.18
3432 3453 3.052036 CAGTTTGCCAAACATGCACTAC 58.948 45.455 21.45 2.59 43.79 2.73
3433 3454 2.545532 GCAGTTTGCCAAACATGCACTA 60.546 45.455 25.85 0.00 43.79 2.74
3434 3455 1.807377 GCAGTTTGCCAAACATGCACT 60.807 47.619 25.85 5.83 43.79 4.40
3435 3456 0.582960 GCAGTTTGCCAAACATGCAC 59.417 50.000 25.85 9.67 43.79 4.57
3491 3512 5.600898 AGCAGGGGTTTTACAGTAATTTGTT 59.399 36.000 0.00 0.00 32.56 2.83
3507 3528 3.392616 CTCTAATTCCATACAGCAGGGGT 59.607 47.826 0.00 0.00 0.00 4.95
3516 3537 9.883142 AGCAATATTAGCTCTCTAATTCCATAC 57.117 33.333 0.00 0.00 41.45 2.39
3548 3569 2.037251 TGCCGCTTAATCTAGGGCTAAG 59.963 50.000 5.66 4.43 44.07 2.18
3614 3635 6.708502 AGTGCACTGTGTAATGTACAATTGTA 59.291 34.615 20.97 14.35 40.93 2.41
3755 3777 6.209192 AGGAAGATTACATCAACATTTGTGCA 59.791 34.615 0.00 0.00 0.00 4.57
3907 3929 4.394729 ACGCCCCACTACCAATTTATATG 58.605 43.478 0.00 0.00 0.00 1.78
3925 3947 2.202756 CGCTGAGAGGGTTACGCC 60.203 66.667 0.00 0.00 0.00 5.68
3926 3948 1.516603 GTCGCTGAGAGGGTTACGC 60.517 63.158 0.00 0.00 0.00 4.42
3927 3949 1.226323 CGTCGCTGAGAGGGTTACG 60.226 63.158 0.00 0.00 0.00 3.18
3928 3950 1.516603 GCGTCGCTGAGAGGGTTAC 60.517 63.158 10.68 0.00 35.42 2.50
3929 3951 2.882876 GCGTCGCTGAGAGGGTTA 59.117 61.111 10.68 0.00 35.42 2.85
3930 3952 4.421479 CGCGTCGCTGAGAGGGTT 62.421 66.667 16.36 0.00 35.42 4.11


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

AutoCloner maintained by Alex Coulton.