Multiple sequence alignment - TraesCS3A01G377000

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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 TraesCS3A01G377000 chr3A 100.000 3220 0 0 1 3220 626017672 626014453 0.000000e+00 5947
1 TraesCS3A01G377000 chr3B 92.029 2873 118 42 25 2870 646004226 646001438 0.000000e+00 3934
2 TraesCS3A01G377000 chr3D 93.968 2404 66 29 14 2378 483178451 483176088 0.000000e+00 3563
3 TraesCS3A01G377000 chr3D 89.293 495 36 5 2376 2870 483175992 483175515 3.550000e-169 604
4 TraesCS3A01G377000 chr1D 84.194 310 36 10 1145 1446 370342120 370342424 4.060000e-74 289
5 TraesCS3A01G377000 chr1B 95.556 180 8 0 1145 1324 493857836 493858015 4.060000e-74 289
6 TraesCS3A01G377000 chr1A 84.194 310 36 10 1145 1446 469309801 469310105 4.060000e-74 289
7 TraesCS3A01G377000 chr2D 89.610 154 14 2 1160 1312 32763270 32763422 9.110000e-46 195
8 TraesCS3A01G377000 chr2A 89.610 154 14 2 1160 1312 35976015 35976167 9.110000e-46 195
9 TraesCS3A01G377000 chr6D 88.199 161 19 0 1152 1312 358326165 358326005 3.280000e-45 193
10 TraesCS3A01G377000 chr6A 88.199 161 19 0 1152 1312 500083784 500083624 3.280000e-45 193


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 TraesCS3A01G377000 chr3A 626014453 626017672 3219 True 5947.0 5947 100.0000 1 3220 1 chr3A.!!$R1 3219
1 TraesCS3A01G377000 chr3B 646001438 646004226 2788 True 3934.0 3934 92.0290 25 2870 1 chr3B.!!$R1 2845
2 TraesCS3A01G377000 chr3D 483175515 483178451 2936 True 2083.5 3563 91.6305 14 2870 2 chr3D.!!$R1 2856

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
601 626 0.17668 AGCAGCGTCCTTTGATCGAT 59.823 50.0 0.0 0.0 0.0 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2407 2560 0.308993 GCAAGCAATATCTCACCGGC 59.691 55.0 0.0 0.0 0.0 6.13 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
20 21 2.560172 AAGCTAGACGACGACGACGC 62.560 60.000 18.98 11.87 43.96 5.19
63 66 1.815421 GCACACGTCCCCAGCATAG 60.815 63.158 0.00 0.00 0.00 2.23
64 67 1.596934 CACACGTCCCCAGCATAGT 59.403 57.895 0.00 0.00 0.00 2.12
65 68 0.821517 CACACGTCCCCAGCATAGTA 59.178 55.000 0.00 0.00 0.00 1.82
66 69 1.112113 ACACGTCCCCAGCATAGTAG 58.888 55.000 0.00 0.00 0.00 2.57
504 526 1.802715 CCACGCCGTAGTAACCACG 60.803 63.158 0.00 0.00 39.10 4.94
507 529 1.870901 CGCCGTAGTAACCACGAGC 60.871 63.158 0.00 0.36 41.91 5.03
536 561 5.007724 AGACTGAAACAAGAAATTCACGGTC 59.992 40.000 0.00 0.00 33.95 4.79
537 562 4.881850 ACTGAAACAAGAAATTCACGGTCT 59.118 37.500 0.00 0.00 32.46 3.85
549 574 2.244695 TCACGGTCTGGAGTACAACAT 58.755 47.619 0.00 0.00 0.00 2.71
578 603 0.386838 AAACAGTGAAAGCCTGCAGC 59.613 50.000 8.66 3.91 44.25 5.25
599 624 1.712081 CAGCAGCGTCCTTTGATCG 59.288 57.895 0.00 0.00 0.00 3.69
600 625 0.737367 CAGCAGCGTCCTTTGATCGA 60.737 55.000 0.00 0.00 0.00 3.59
601 626 0.176680 AGCAGCGTCCTTTGATCGAT 59.823 50.000 0.00 0.00 0.00 3.59
602 627 0.579156 GCAGCGTCCTTTGATCGATC 59.421 55.000 18.72 18.72 0.00 3.69
636 661 2.150809 GATGCGTCCATCATCGTGCG 62.151 60.000 0.00 0.00 45.75 5.34
637 662 2.582226 GCGTCCATCATCGTGCGA 60.582 61.111 0.00 0.00 0.00 5.10
645 670 2.221749 CCATCATCGTGCGATAACAAGG 59.778 50.000 6.77 2.40 32.93 3.61
648 673 0.178068 ATCGTGCGATAACAAGGCCT 59.822 50.000 0.00 0.00 32.36 5.19
946 972 0.179097 GTCACCATCTCTTCTCCGGC 60.179 60.000 0.00 0.00 0.00 6.13
988 1014 2.032860 AATCCCTCTCACATCGCCCG 62.033 60.000 0.00 0.00 0.00 6.13
1017 1046 3.221222 GGCTGGCCGTAGTCTGAT 58.779 61.111 0.00 0.00 0.00 2.90
1018 1047 1.068250 GGCTGGCCGTAGTCTGATC 59.932 63.158 0.00 0.00 0.00 2.92
1548 1577 3.207547 GAACAACCAGCAACCGGCC 62.208 63.158 0.00 0.00 46.50 6.13
1899 1928 1.443872 GTCGTGGTGCTCGATCGTT 60.444 57.895 15.94 0.00 39.45 3.85
2050 2079 5.730296 AGCTCTCTACATGCCGTAATTAT 57.270 39.130 0.00 0.00 0.00 1.28
2139 2176 9.726438 TTTACTTTCTTTCAATTTGGTTTGGAA 57.274 25.926 0.00 0.00 0.00 3.53
2203 2243 1.067821 GAGAGGAGTGAGGCGGTAATG 59.932 57.143 0.00 0.00 0.00 1.90
2256 2296 7.255520 GGTCGGTATACTTGTGAGATAGATGTT 60.256 40.741 2.25 0.00 0.00 2.71
2257 2297 7.591795 GTCGGTATACTTGTGAGATAGATGTTG 59.408 40.741 2.25 0.00 0.00 3.33
2258 2298 7.501225 TCGGTATACTTGTGAGATAGATGTTGA 59.499 37.037 2.25 0.00 0.00 3.18
2259 2299 8.135529 CGGTATACTTGTGAGATAGATGTTGAA 58.864 37.037 2.25 0.00 0.00 2.69
2346 2398 4.658435 TGCAAGCTCCCCTATAGAACATTA 59.342 41.667 0.00 0.00 0.00 1.90
2360 2412 7.693969 ATAGAACATTATATTGAAGCTGCCC 57.306 36.000 0.00 0.00 0.00 5.36
2407 2560 5.900339 ACAATTCTACATATAACCGCACG 57.100 39.130 0.00 0.00 0.00 5.34
2473 2626 4.513692 TCCCATCTTACCGCAAATTATTCG 59.486 41.667 0.00 0.00 0.00 3.34
2483 2636 4.260620 CCGCAAATTATTCGGTGTAGAAGG 60.261 45.833 5.18 0.00 38.47 3.46
2502 2655 1.404391 GGAATGACCATGCAAGCTCTG 59.596 52.381 0.00 0.00 38.79 3.35
2516 2669 4.813697 GCAAGCTCTGGAACTAATTAGAGG 59.186 45.833 19.38 4.49 37.67 3.69
2673 2826 0.105194 TGTGTCCCTTGTCTCCCTCA 60.105 55.000 0.00 0.00 0.00 3.86
2687 2840 0.107017 CCCTCATGCTCGGTGGAAAT 60.107 55.000 0.00 0.00 0.00 2.17
2701 2854 3.057806 GGTGGAAATGGTTAGTCAAACGG 60.058 47.826 0.00 0.00 39.13 4.44
2725 2878 3.560068 AGCTAGCGGTCCAATTAAATTCG 59.440 43.478 9.55 0.00 0.00 3.34
2727 2880 2.021457 AGCGGTCCAATTAAATTCGGG 58.979 47.619 0.00 0.00 0.00 5.14
2728 2881 1.535226 GCGGTCCAATTAAATTCGGGC 60.535 52.381 0.00 0.00 0.00 6.13
2733 2886 4.204799 GTCCAATTAAATTCGGGCTAGGT 58.795 43.478 0.00 0.00 0.00 3.08
2742 2895 2.689034 GGGCTAGGTGGAGTGGCT 60.689 66.667 0.00 0.00 0.00 4.75
2743 2896 2.586792 GGCTAGGTGGAGTGGCTG 59.413 66.667 0.00 0.00 0.00 4.85
2744 2897 2.124942 GCTAGGTGGAGTGGCTGC 60.125 66.667 0.00 0.00 0.00 5.25
2764 2917 1.143183 GCCATTCAGCCATTGCCTG 59.857 57.895 0.00 0.00 38.69 4.85
2903 3056 6.790232 AACACAAGAATTTCTTTTGGAGGA 57.210 33.333 22.66 0.00 38.21 3.71
2904 3057 6.983906 ACACAAGAATTTCTTTTGGAGGAT 57.016 33.333 22.66 5.33 38.21 3.24
2905 3058 6.986250 ACACAAGAATTTCTTTTGGAGGATC 58.014 36.000 22.66 0.00 38.21 3.36
2906 3059 6.015095 ACACAAGAATTTCTTTTGGAGGATCC 60.015 38.462 22.66 2.48 45.87 3.36
2907 3060 6.210185 CACAAGAATTTCTTTTGGAGGATCCT 59.790 38.462 16.13 16.13 45.86 3.24
2908 3061 6.784473 ACAAGAATTTCTTTTGGAGGATCCTT 59.216 34.615 17.42 0.00 45.86 3.36
2909 3062 7.290948 ACAAGAATTTCTTTTGGAGGATCCTTT 59.709 33.333 17.42 1.21 45.86 3.11
2910 3063 8.152898 CAAGAATTTCTTTTGGAGGATCCTTTT 58.847 33.333 17.42 0.00 45.86 2.27
2911 3064 8.717717 AAGAATTTCTTTTGGAGGATCCTTTTT 58.282 29.630 17.42 0.00 45.57 1.94
2923 3076 7.101652 GAGGATCCTTTTTGGGTTAAATCTC 57.898 40.000 17.42 0.00 36.20 2.75
2924 3077 5.958380 AGGATCCTTTTTGGGTTAAATCTCC 59.042 40.000 9.02 0.00 36.20 3.71
2925 3078 5.958380 GGATCCTTTTTGGGTTAAATCTCCT 59.042 40.000 3.84 0.00 36.20 3.69
2926 3079 6.096987 GGATCCTTTTTGGGTTAAATCTCCTC 59.903 42.308 3.84 0.00 36.20 3.71
2927 3080 6.214177 TCCTTTTTGGGTTAAATCTCCTCT 57.786 37.500 0.00 0.00 36.20 3.69
2928 3081 6.246163 TCCTTTTTGGGTTAAATCTCCTCTC 58.754 40.000 0.00 0.00 36.20 3.20
2929 3082 6.045577 TCCTTTTTGGGTTAAATCTCCTCTCT 59.954 38.462 0.00 0.00 36.20 3.10
2930 3083 6.375736 CCTTTTTGGGTTAAATCTCCTCTCTC 59.624 42.308 0.00 0.00 0.00 3.20
2931 3084 6.704056 TTTTGGGTTAAATCTCCTCTCTCT 57.296 37.500 0.00 0.00 0.00 3.10
2932 3085 5.941555 TTGGGTTAAATCTCCTCTCTCTC 57.058 43.478 0.00 0.00 0.00 3.20
2933 3086 5.213868 TGGGTTAAATCTCCTCTCTCTCT 57.786 43.478 0.00 0.00 0.00 3.10
2934 3087 5.205056 TGGGTTAAATCTCCTCTCTCTCTC 58.795 45.833 0.00 0.00 0.00 3.20
2935 3088 5.043732 TGGGTTAAATCTCCTCTCTCTCTCT 60.044 44.000 0.00 0.00 0.00 3.10
2936 3089 5.535030 GGGTTAAATCTCCTCTCTCTCTCTC 59.465 48.000 0.00 0.00 0.00 3.20
2937 3090 6.365520 GGTTAAATCTCCTCTCTCTCTCTCT 58.634 44.000 0.00 0.00 0.00 3.10
2938 3091 6.486993 GGTTAAATCTCCTCTCTCTCTCTCTC 59.513 46.154 0.00 0.00 0.00 3.20
2939 3092 4.713792 AATCTCCTCTCTCTCTCTCTCC 57.286 50.000 0.00 0.00 0.00 3.71
2940 3093 2.408565 TCTCCTCTCTCTCTCTCTCCC 58.591 57.143 0.00 0.00 0.00 4.30
2941 3094 2.022035 TCTCCTCTCTCTCTCTCTCCCT 60.022 54.545 0.00 0.00 0.00 4.20
2942 3095 2.370189 CTCCTCTCTCTCTCTCTCCCTC 59.630 59.091 0.00 0.00 0.00 4.30
2943 3096 2.022035 TCCTCTCTCTCTCTCTCCCTCT 60.022 54.545 0.00 0.00 0.00 3.69
2944 3097 2.370189 CCTCTCTCTCTCTCTCCCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
2945 3098 3.312890 CTCTCTCTCTCTCTCCCTCTCT 58.687 54.545 0.00 0.00 0.00 3.10
2946 3099 3.309296 TCTCTCTCTCTCTCCCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
2947 3100 3.051803 TCTCTCTCTCTCTCCCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
2948 3101 3.309296 TCTCTCTCTCTCCCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
2949 3102 3.051803 TCTCTCTCTCTCCCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
2950 3103 3.309296 TCTCTCTCTCCCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
2951 3104 3.051803 TCTCTCTCTCCCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
2952 3105 4.170053 TCTCTCTCTCCCTCTCTCTCTCTA 59.830 50.000 0.00 0.00 0.00 2.43
2953 3106 4.890988 TCTCTCTCCCTCTCTCTCTCTAA 58.109 47.826 0.00 0.00 0.00 2.10
2954 3107 4.901849 TCTCTCTCCCTCTCTCTCTCTAAG 59.098 50.000 0.00 0.00 0.00 2.18
2955 3108 4.890988 TCTCTCCCTCTCTCTCTCTAAGA 58.109 47.826 0.00 0.00 0.00 2.10
2956 3109 5.285401 TCTCTCCCTCTCTCTCTCTAAGAA 58.715 45.833 0.00 0.00 32.23 2.52
2957 3110 5.729229 TCTCTCCCTCTCTCTCTCTAAGAAA 59.271 44.000 0.00 0.00 32.23 2.52
2958 3111 6.216662 TCTCTCCCTCTCTCTCTCTAAGAAAA 59.783 42.308 0.00 0.00 32.23 2.29
2959 3112 6.423182 TCTCCCTCTCTCTCTCTAAGAAAAG 58.577 44.000 0.00 0.00 32.23 2.27
2960 3113 5.515106 TCCCTCTCTCTCTCTAAGAAAAGG 58.485 45.833 0.00 0.00 32.23 3.11
2961 3114 4.099419 CCCTCTCTCTCTCTAAGAAAAGGC 59.901 50.000 0.00 0.00 32.23 4.35
2962 3115 4.956075 CCTCTCTCTCTCTAAGAAAAGGCT 59.044 45.833 0.00 0.00 32.23 4.58
2963 3116 5.422012 CCTCTCTCTCTCTAAGAAAAGGCTT 59.578 44.000 0.00 0.00 32.23 4.35
2964 3117 6.070824 CCTCTCTCTCTCTAAGAAAAGGCTTT 60.071 42.308 6.68 6.68 32.23 3.51
2965 3118 6.930731 TCTCTCTCTCTAAGAAAAGGCTTTC 58.069 40.000 13.76 7.09 41.19 2.62
2966 3119 6.495181 TCTCTCTCTCTAAGAAAAGGCTTTCA 59.505 38.462 13.76 0.00 42.99 2.69
2967 3120 6.459923 TCTCTCTCTAAGAAAAGGCTTTCAC 58.540 40.000 13.76 10.57 42.99 3.18
2968 3121 5.552178 TCTCTCTAAGAAAAGGCTTTCACC 58.448 41.667 13.76 5.96 42.99 4.02
2969 3122 4.652822 TCTCTAAGAAAAGGCTTTCACCC 58.347 43.478 13.76 3.50 42.99 4.61
2970 3123 4.351111 TCTCTAAGAAAAGGCTTTCACCCT 59.649 41.667 13.76 5.73 42.99 4.34
2971 3124 4.398319 TCTAAGAAAAGGCTTTCACCCTG 58.602 43.478 13.76 3.11 42.99 4.45
2972 3125 1.332195 AGAAAAGGCTTTCACCCTGC 58.668 50.000 13.76 0.00 42.99 4.85
2973 3126 1.133356 AGAAAAGGCTTTCACCCTGCT 60.133 47.619 13.76 0.00 42.99 4.24
2974 3127 1.688735 GAAAAGGCTTTCACCCTGCTT 59.311 47.619 13.76 0.00 40.67 3.91
2975 3128 1.793414 AAAGGCTTTCACCCTGCTTT 58.207 45.000 6.68 0.00 31.73 3.51
2976 3129 1.793414 AAGGCTTTCACCCTGCTTTT 58.207 45.000 0.00 0.00 31.73 2.27
2977 3130 2.675658 AGGCTTTCACCCTGCTTTTA 57.324 45.000 0.00 0.00 0.00 1.52
2978 3131 3.175438 AGGCTTTCACCCTGCTTTTAT 57.825 42.857 0.00 0.00 0.00 1.40
2979 3132 4.316025 AGGCTTTCACCCTGCTTTTATA 57.684 40.909 0.00 0.00 0.00 0.98
2980 3133 4.273318 AGGCTTTCACCCTGCTTTTATAG 58.727 43.478 0.00 0.00 0.00 1.31
2981 3134 4.018415 AGGCTTTCACCCTGCTTTTATAGA 60.018 41.667 0.00 0.00 0.00 1.98
2982 3135 4.889995 GGCTTTCACCCTGCTTTTATAGAT 59.110 41.667 0.00 0.00 0.00 1.98
2983 3136 6.062095 GGCTTTCACCCTGCTTTTATAGATA 58.938 40.000 0.00 0.00 0.00 1.98
2984 3137 6.546034 GGCTTTCACCCTGCTTTTATAGATAA 59.454 38.462 0.00 0.00 0.00 1.75
2985 3138 7.068226 GGCTTTCACCCTGCTTTTATAGATAAA 59.932 37.037 0.00 0.00 0.00 1.40
2986 3139 8.466798 GCTTTCACCCTGCTTTTATAGATAAAA 58.533 33.333 7.13 7.13 39.24 1.52
2987 3140 9.788960 CTTTCACCCTGCTTTTATAGATAAAAC 57.211 33.333 3.79 3.21 37.33 2.43
2988 3141 8.871629 TTCACCCTGCTTTTATAGATAAAACA 57.128 30.769 3.79 6.60 37.33 2.83
2989 3142 8.871629 TCACCCTGCTTTTATAGATAAAACAA 57.128 30.769 3.79 0.00 37.33 2.83
2990 3143 9.303116 TCACCCTGCTTTTATAGATAAAACAAA 57.697 29.630 3.79 0.00 37.33 2.83
2991 3144 9.921637 CACCCTGCTTTTATAGATAAAACAAAA 57.078 29.630 3.79 0.00 37.33 2.44
3008 3161 1.541379 AAAAACCCGAGTACATGGCC 58.459 50.000 0.00 0.00 0.00 5.36
3009 3162 0.675522 AAAACCCGAGTACATGGCCG 60.676 55.000 0.00 0.00 0.00 6.13
3010 3163 1.546589 AAACCCGAGTACATGGCCGA 61.547 55.000 0.00 0.00 0.00 5.54
3011 3164 1.546589 AACCCGAGTACATGGCCGAA 61.547 55.000 0.00 0.00 0.00 4.30
3012 3165 1.520787 CCCGAGTACATGGCCGAAC 60.521 63.158 0.00 0.00 0.00 3.95
3013 3166 1.876714 CCGAGTACATGGCCGAACG 60.877 63.158 0.00 0.00 0.00 3.95
3014 3167 1.138036 CGAGTACATGGCCGAACGA 59.862 57.895 0.00 0.00 0.00 3.85
3015 3168 0.248907 CGAGTACATGGCCGAACGAT 60.249 55.000 0.00 0.00 0.00 3.73
3016 3169 1.209128 GAGTACATGGCCGAACGATG 58.791 55.000 0.00 0.00 40.14 3.84
3017 3170 0.810031 AGTACATGGCCGAACGATGC 60.810 55.000 0.00 0.00 37.98 3.91
3018 3171 1.087202 GTACATGGCCGAACGATGCA 61.087 55.000 0.00 0.00 37.98 3.96
3019 3172 0.809636 TACATGGCCGAACGATGCAG 60.810 55.000 0.00 0.00 37.98 4.41
3020 3173 1.815003 CATGGCCGAACGATGCAGA 60.815 57.895 0.00 0.00 0.00 4.26
3021 3174 1.522355 ATGGCCGAACGATGCAGAG 60.522 57.895 0.00 0.00 0.00 3.35
3022 3175 2.125512 GGCCGAACGATGCAGAGT 60.126 61.111 0.00 0.00 0.00 3.24
3023 3176 2.456119 GGCCGAACGATGCAGAGTG 61.456 63.158 0.00 0.00 0.00 3.51
3024 3177 1.446099 GCCGAACGATGCAGAGTGA 60.446 57.895 0.00 0.00 0.00 3.41
3025 3178 0.807667 GCCGAACGATGCAGAGTGAT 60.808 55.000 0.00 0.00 0.00 3.06
3026 3179 0.926155 CCGAACGATGCAGAGTGATG 59.074 55.000 0.00 0.00 0.00 3.07
3027 3180 1.469767 CCGAACGATGCAGAGTGATGA 60.470 52.381 0.00 0.00 0.00 2.92
3028 3181 1.851053 CGAACGATGCAGAGTGATGAG 59.149 52.381 0.00 0.00 0.00 2.90
3029 3182 2.200067 GAACGATGCAGAGTGATGAGG 58.800 52.381 0.00 0.00 0.00 3.86
3030 3183 1.478631 ACGATGCAGAGTGATGAGGA 58.521 50.000 0.00 0.00 0.00 3.71
3031 3184 1.408340 ACGATGCAGAGTGATGAGGAG 59.592 52.381 0.00 0.00 0.00 3.69
3032 3185 1.269673 CGATGCAGAGTGATGAGGAGG 60.270 57.143 0.00 0.00 0.00 4.30
3033 3186 0.469070 ATGCAGAGTGATGAGGAGGC 59.531 55.000 0.00 0.00 0.00 4.70
3034 3187 1.145819 GCAGAGTGATGAGGAGGCC 59.854 63.158 0.00 0.00 0.00 5.19
3035 3188 1.828768 CAGAGTGATGAGGAGGCCC 59.171 63.158 0.00 0.00 0.00 5.80
3037 3190 0.690411 AGAGTGATGAGGAGGCCCTG 60.690 60.000 0.00 0.00 44.53 4.45
3038 3191 0.980231 GAGTGATGAGGAGGCCCTGT 60.980 60.000 0.00 0.00 44.53 4.00
3039 3192 0.548682 AGTGATGAGGAGGCCCTGTT 60.549 55.000 0.00 0.00 44.53 3.16
3040 3193 1.204146 GTGATGAGGAGGCCCTGTTA 58.796 55.000 0.00 0.00 44.53 2.41
3041 3194 1.134371 GTGATGAGGAGGCCCTGTTAC 60.134 57.143 0.00 0.00 44.53 2.50
3042 3195 1.204146 GATGAGGAGGCCCTGTTACA 58.796 55.000 0.00 0.00 44.53 2.41
3043 3196 1.559682 GATGAGGAGGCCCTGTTACAA 59.440 52.381 0.00 0.00 44.53 2.41
3044 3197 1.440618 TGAGGAGGCCCTGTTACAAA 58.559 50.000 0.00 0.00 44.53 2.83
3045 3198 1.351017 TGAGGAGGCCCTGTTACAAAG 59.649 52.381 0.00 0.00 44.53 2.77
3046 3199 0.038310 AGGAGGCCCTGTTACAAAGC 59.962 55.000 0.00 0.00 42.42 3.51
3047 3200 0.251165 GGAGGCCCTGTTACAAAGCA 60.251 55.000 0.00 0.00 0.00 3.91
3048 3201 1.168714 GAGGCCCTGTTACAAAGCAG 58.831 55.000 0.00 0.00 0.00 4.24
3049 3202 0.771127 AGGCCCTGTTACAAAGCAGA 59.229 50.000 0.00 0.00 34.87 4.26
3050 3203 1.355720 AGGCCCTGTTACAAAGCAGAT 59.644 47.619 0.00 0.00 34.87 2.90
3051 3204 1.745653 GGCCCTGTTACAAAGCAGATC 59.254 52.381 8.24 0.00 34.87 2.75
3052 3205 2.619074 GGCCCTGTTACAAAGCAGATCT 60.619 50.000 8.24 0.00 34.87 2.75
3053 3206 3.084786 GCCCTGTTACAAAGCAGATCTT 58.915 45.455 0.00 0.00 34.87 2.40
3054 3207 3.119708 GCCCTGTTACAAAGCAGATCTTG 60.120 47.826 0.00 0.00 34.67 3.02
3055 3208 3.441572 CCCTGTTACAAAGCAGATCTTGG 59.558 47.826 0.00 0.00 34.67 3.61
3056 3209 3.441572 CCTGTTACAAAGCAGATCTTGGG 59.558 47.826 0.00 0.00 34.67 4.12
3057 3210 4.326826 CTGTTACAAAGCAGATCTTGGGA 58.673 43.478 0.00 0.00 34.67 4.37
3058 3211 4.922206 TGTTACAAAGCAGATCTTGGGAT 58.078 39.130 0.00 0.00 34.67 3.85
3059 3212 5.324409 TGTTACAAAGCAGATCTTGGGATT 58.676 37.500 0.00 0.00 34.67 3.01
3060 3213 6.480763 TGTTACAAAGCAGATCTTGGGATTA 58.519 36.000 0.00 0.00 34.67 1.75
3061 3214 6.945435 TGTTACAAAGCAGATCTTGGGATTAA 59.055 34.615 0.00 0.00 34.67 1.40
3062 3215 5.904362 ACAAAGCAGATCTTGGGATTAAC 57.096 39.130 0.00 0.00 34.67 2.01
3063 3216 4.396166 ACAAAGCAGATCTTGGGATTAACG 59.604 41.667 0.00 0.00 34.67 3.18
3064 3217 4.487714 AAGCAGATCTTGGGATTAACGA 57.512 40.909 0.00 0.00 32.79 3.85
3065 3218 3.798202 AGCAGATCTTGGGATTAACGAC 58.202 45.455 0.00 0.00 31.46 4.34
3066 3219 3.452627 AGCAGATCTTGGGATTAACGACT 59.547 43.478 0.00 0.00 31.46 4.18
3067 3220 4.649674 AGCAGATCTTGGGATTAACGACTA 59.350 41.667 0.00 0.00 31.46 2.59
3068 3221 4.745620 GCAGATCTTGGGATTAACGACTAC 59.254 45.833 0.00 0.00 31.46 2.73
3069 3222 4.976731 CAGATCTTGGGATTAACGACTACG 59.023 45.833 0.00 0.00 37.66 3.51
3070 3223 4.643784 AGATCTTGGGATTAACGACTACGT 59.356 41.667 0.00 0.00 42.55 3.57
3071 3224 5.126707 AGATCTTGGGATTAACGACTACGTT 59.873 40.000 12.26 12.26 46.47 3.99
3072 3225 5.231568 GATCTTGGGATTAACGACTACGTTG 59.768 44.000 16.30 0.00 45.49 4.10
3073 3226 7.657561 GATCTTGGGATTAACGACTACGTTGG 61.658 46.154 16.30 0.00 45.49 3.77
3079 3232 4.364817 CGACTACGTTGGGCCAAA 57.635 55.556 22.82 4.50 34.56 3.28
3080 3233 2.849081 CGACTACGTTGGGCCAAAT 58.151 52.632 22.82 14.94 34.56 2.32
3081 3234 2.012937 CGACTACGTTGGGCCAAATA 57.987 50.000 22.82 15.29 34.56 1.40
3082 3235 2.557317 CGACTACGTTGGGCCAAATAT 58.443 47.619 22.82 11.86 34.56 1.28
3083 3236 2.542595 CGACTACGTTGGGCCAAATATC 59.457 50.000 22.82 13.04 34.56 1.63
3084 3237 3.740141 CGACTACGTTGGGCCAAATATCT 60.740 47.826 22.82 3.43 34.56 1.98
3085 3238 4.500205 CGACTACGTTGGGCCAAATATCTA 60.500 45.833 22.82 5.12 34.56 1.98
3086 3239 4.700700 ACTACGTTGGGCCAAATATCTAC 58.299 43.478 22.82 6.34 0.00 2.59
3087 3240 2.927028 ACGTTGGGCCAAATATCTACC 58.073 47.619 22.82 4.76 0.00 3.18
3088 3241 2.240160 ACGTTGGGCCAAATATCTACCA 59.760 45.455 22.82 0.00 0.00 3.25
3089 3242 2.616842 CGTTGGGCCAAATATCTACCAC 59.383 50.000 22.82 3.85 0.00 4.16
3090 3243 3.684413 CGTTGGGCCAAATATCTACCACT 60.684 47.826 22.82 0.00 0.00 4.00
3091 3244 4.443739 CGTTGGGCCAAATATCTACCACTA 60.444 45.833 22.82 0.00 0.00 2.74
3092 3245 5.442391 GTTGGGCCAAATATCTACCACTAA 58.558 41.667 22.82 0.00 0.00 2.24
3093 3246 5.922960 TGGGCCAAATATCTACCACTAAT 57.077 39.130 2.13 0.00 0.00 1.73
3094 3247 6.274322 TGGGCCAAATATCTACCACTAATT 57.726 37.500 2.13 0.00 0.00 1.40
3095 3248 7.395525 TGGGCCAAATATCTACCACTAATTA 57.604 36.000 2.13 0.00 0.00 1.40
3096 3249 7.817440 TGGGCCAAATATCTACCACTAATTAA 58.183 34.615 2.13 0.00 0.00 1.40
3097 3250 7.942341 TGGGCCAAATATCTACCACTAATTAAG 59.058 37.037 2.13 0.00 0.00 1.85
3098 3251 8.161425 GGGCCAAATATCTACCACTAATTAAGA 58.839 37.037 4.39 0.00 0.00 2.10
3099 3252 9.569122 GGCCAAATATCTACCACTAATTAAGAA 57.431 33.333 0.00 0.00 0.00 2.52
3108 3261 8.404000 TCTACCACTAATTAAGAAACTAGCTCG 58.596 37.037 0.00 0.00 0.00 5.03
3109 3262 6.338937 ACCACTAATTAAGAAACTAGCTCGG 58.661 40.000 0.00 0.00 0.00 4.63
3110 3263 6.154021 ACCACTAATTAAGAAACTAGCTCGGA 59.846 38.462 0.00 0.00 0.00 4.55
3111 3264 7.039882 CCACTAATTAAGAAACTAGCTCGGAA 58.960 38.462 0.00 0.00 0.00 4.30
3112 3265 7.548075 CCACTAATTAAGAAACTAGCTCGGAAA 59.452 37.037 0.00 0.00 0.00 3.13
3113 3266 8.932791 CACTAATTAAGAAACTAGCTCGGAAAA 58.067 33.333 0.00 0.00 0.00 2.29
3114 3267 9.498176 ACTAATTAAGAAACTAGCTCGGAAAAA 57.502 29.630 0.00 0.00 0.00 1.94
3115 3268 9.974750 CTAATTAAGAAACTAGCTCGGAAAAAG 57.025 33.333 0.00 0.00 0.00 2.27
3116 3269 7.981102 ATTAAGAAACTAGCTCGGAAAAAGT 57.019 32.000 0.00 0.00 0.00 2.66
3117 3270 7.797038 TTAAGAAACTAGCTCGGAAAAAGTT 57.203 32.000 0.00 0.00 31.94 2.66
3118 3271 5.674933 AGAAACTAGCTCGGAAAAAGTTG 57.325 39.130 0.00 0.00 31.09 3.16
3119 3272 5.365619 AGAAACTAGCTCGGAAAAAGTTGA 58.634 37.500 0.00 0.00 31.09 3.18
3120 3273 5.467063 AGAAACTAGCTCGGAAAAAGTTGAG 59.533 40.000 0.00 0.00 31.09 3.02
3121 3274 3.665190 ACTAGCTCGGAAAAAGTTGAGG 58.335 45.455 0.00 0.00 0.00 3.86
3122 3275 2.640316 AGCTCGGAAAAAGTTGAGGT 57.360 45.000 0.00 0.00 34.59 3.85
3123 3276 2.495084 AGCTCGGAAAAAGTTGAGGTC 58.505 47.619 0.00 0.00 34.32 3.85
3124 3277 2.104963 AGCTCGGAAAAAGTTGAGGTCT 59.895 45.455 0.00 0.00 34.32 3.85
3125 3278 2.480802 GCTCGGAAAAAGTTGAGGTCTC 59.519 50.000 0.00 0.00 0.00 3.36
3126 3279 3.067833 CTCGGAAAAAGTTGAGGTCTCC 58.932 50.000 0.00 0.00 0.00 3.71
3127 3280 2.436542 TCGGAAAAAGTTGAGGTCTCCA 59.563 45.455 0.00 0.00 0.00 3.86
3128 3281 3.072476 TCGGAAAAAGTTGAGGTCTCCAT 59.928 43.478 0.00 0.00 0.00 3.41
3129 3282 3.821033 CGGAAAAAGTTGAGGTCTCCATT 59.179 43.478 0.00 0.00 0.00 3.16
3130 3283 4.278419 CGGAAAAAGTTGAGGTCTCCATTT 59.722 41.667 0.00 0.00 0.00 2.32
3131 3284 5.532557 GGAAAAAGTTGAGGTCTCCATTTG 58.467 41.667 0.00 0.00 0.00 2.32
3132 3285 5.069119 GGAAAAAGTTGAGGTCTCCATTTGT 59.931 40.000 0.00 0.00 0.00 2.83
3133 3286 6.406961 GGAAAAAGTTGAGGTCTCCATTTGTT 60.407 38.462 0.00 0.00 0.00 2.83
3134 3287 7.201875 GGAAAAAGTTGAGGTCTCCATTTGTTA 60.202 37.037 0.00 0.00 0.00 2.41
3135 3288 7.839680 AAAAGTTGAGGTCTCCATTTGTTAT 57.160 32.000 0.00 0.00 0.00 1.89
3136 3289 8.934023 AAAAGTTGAGGTCTCCATTTGTTATA 57.066 30.769 0.00 0.00 0.00 0.98
3137 3290 9.533831 AAAAGTTGAGGTCTCCATTTGTTATAT 57.466 29.630 0.00 0.00 0.00 0.86
3138 3291 9.533831 AAAGTTGAGGTCTCCATTTGTTATATT 57.466 29.630 0.00 0.00 0.00 1.28
3139 3292 8.511604 AGTTGAGGTCTCCATTTGTTATATTG 57.488 34.615 0.00 0.00 0.00 1.90
3140 3293 8.109634 AGTTGAGGTCTCCATTTGTTATATTGT 58.890 33.333 0.00 0.00 0.00 2.71
3141 3294 8.739972 GTTGAGGTCTCCATTTGTTATATTGTT 58.260 33.333 0.00 0.00 0.00 2.83
3142 3295 9.967451 TTGAGGTCTCCATTTGTTATATTGTTA 57.033 29.630 0.00 0.00 0.00 2.41
3207 3360 1.466167 CAGAGTTGTCTGGCCAAATCG 59.534 52.381 7.01 0.00 45.85 3.34
3208 3361 0.169009 GAGTTGTCTGGCCAAATCGC 59.831 55.000 7.01 0.00 30.89 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.583568 CGTCGTCGTCGTCTAGCTTC 60.584 60.000 3.67 0.00 38.33 3.86
1 2 1.419143 CGTCGTCGTCGTCTAGCTT 59.581 57.895 3.67 0.00 38.33 3.74
2 3 3.079417 CGTCGTCGTCGTCTAGCT 58.921 61.111 3.67 0.00 38.33 3.32
3 4 2.644095 GCGTCGTCGTCGTCTAGC 60.644 66.667 13.09 0.68 39.49 3.42
4 5 2.021106 GGCGTCGTCGTCGTCTAG 59.979 66.667 13.09 0.00 39.49 2.43
237 250 2.609350 TCGCCCATACGACTTTGTTAC 58.391 47.619 0.00 0.00 37.09 2.50
308 321 4.939368 CGGCCACGTGAAACCCCA 62.939 66.667 19.30 0.00 34.81 4.96
504 526 4.258702 TCTTGTTTCAGTCTAGTGGCTC 57.741 45.455 0.00 0.00 0.00 4.70
507 529 7.355778 GTGAATTTCTTGTTTCAGTCTAGTGG 58.644 38.462 0.00 0.00 32.79 4.00
536 561 9.180678 GTTTCATGTAAAAATGTTGTACTCCAG 57.819 33.333 0.00 0.00 0.00 3.86
537 562 8.687242 TGTTTCATGTAAAAATGTTGTACTCCA 58.313 29.630 0.00 0.00 0.00 3.86
549 574 6.756074 CAGGCTTTCACTGTTTCATGTAAAAA 59.244 34.615 0.00 0.00 0.00 1.94
578 603 1.303799 ATCAAAGGACGCTGCTGCTG 61.304 55.000 14.03 9.56 36.97 4.41
579 604 1.002868 ATCAAAGGACGCTGCTGCT 60.003 52.632 14.03 0.67 36.97 4.24
580 605 1.427020 GATCAAAGGACGCTGCTGC 59.573 57.895 5.34 5.34 0.00 5.25
581 606 0.737367 TCGATCAAAGGACGCTGCTG 60.737 55.000 0.00 0.00 0.00 4.41
582 607 0.176680 ATCGATCAAAGGACGCTGCT 59.823 50.000 0.00 0.00 0.00 4.24
583 608 0.579156 GATCGATCAAAGGACGCTGC 59.421 55.000 20.52 0.00 0.00 5.25
584 609 0.848942 CGATCGATCAAAGGACGCTG 59.151 55.000 24.40 0.96 0.00 5.18
585 610 0.456221 ACGATCGATCAAAGGACGCT 59.544 50.000 24.34 0.00 0.00 5.07
586 611 1.005975 CAACGATCGATCAAAGGACGC 60.006 52.381 24.34 0.00 0.00 5.19
594 619 2.029380 ACCACTGTTCAACGATCGATCA 60.029 45.455 24.34 11.37 0.00 2.92
599 624 3.667960 GCATCAACCACTGTTCAACGATC 60.668 47.826 0.00 0.00 30.42 3.69
600 625 2.226437 GCATCAACCACTGTTCAACGAT 59.774 45.455 0.00 0.00 30.42 3.73
601 626 1.601903 GCATCAACCACTGTTCAACGA 59.398 47.619 0.00 0.00 30.42 3.85
602 627 1.660052 CGCATCAACCACTGTTCAACG 60.660 52.381 0.00 0.00 30.42 4.10
631 656 1.019278 ACAGGCCTTGTTATCGCACG 61.019 55.000 0.00 0.00 36.31 5.34
636 661 4.120589 GCTACAGTACAGGCCTTGTTATC 58.879 47.826 12.91 5.34 41.29 1.75
637 662 3.118371 GGCTACAGTACAGGCCTTGTTAT 60.118 47.826 12.91 0.67 41.29 1.89
645 670 3.522553 CTTTAGTGGCTACAGTACAGGC 58.477 50.000 2.02 0.00 38.97 4.85
648 673 2.235402 GCCCTTTAGTGGCTACAGTACA 59.765 50.000 2.02 0.00 45.70 2.90
732 757 7.308951 CGAGCTTTGATTTAGGGTTAAAGGAAA 60.309 37.037 0.00 0.00 32.58 3.13
776 801 2.821366 GGGCCGAGATGCAGTGTG 60.821 66.667 0.00 0.00 0.00 3.82
946 972 2.284798 CTGATCGGAGGACACGGTGG 62.285 65.000 13.48 0.00 0.00 4.61
988 1014 4.632974 CCAGCCGGGGAGCTATGC 62.633 72.222 2.18 0.00 42.61 3.14
1003 1029 0.952280 GATCGATCAGACTACGGCCA 59.048 55.000 20.52 0.00 0.00 5.36
1015 1044 1.786004 CTTCTTCTGCAGCGATCGATC 59.214 52.381 21.57 15.68 0.00 3.69
1016 1045 1.537776 CCTTCTTCTGCAGCGATCGAT 60.538 52.381 21.57 10.64 0.00 3.59
1017 1046 0.179127 CCTTCTTCTGCAGCGATCGA 60.179 55.000 21.57 0.00 0.00 3.59
1018 1047 0.179127 TCCTTCTTCTGCAGCGATCG 60.179 55.000 11.69 11.69 0.00 3.69
1266 1295 2.116772 ACGTTCCGGAGAGACCCA 59.883 61.111 3.34 0.00 34.64 4.51
1269 1298 2.126031 GGCACGTTCCGGAGAGAC 60.126 66.667 3.34 0.00 0.00 3.36
1899 1928 1.215382 CCATGTCGACAAGCTCGGA 59.785 57.895 24.13 0.00 43.16 4.55
2116 2153 7.619965 TCTTCCAAACCAAATTGAAAGAAAGT 58.380 30.769 0.00 0.00 31.84 2.66
2346 2398 3.317455 TTGGATGGGCAGCTTCAATAT 57.683 42.857 0.00 0.00 0.00 1.28
2392 2545 0.318869 CCGGCGTGCGGTTATATGTA 60.319 55.000 6.01 0.00 0.00 2.29
2407 2560 0.308993 GCAAGCAATATCTCACCGGC 59.691 55.000 0.00 0.00 0.00 6.13
2417 2570 6.881065 AGTAGAATCAAGTCTTGCAAGCAATA 59.119 34.615 21.99 0.99 35.20 1.90
2473 2626 2.945668 GCATGGTCATTCCTTCTACACC 59.054 50.000 0.00 0.00 37.07 4.16
2476 2629 3.065925 GCTTGCATGGTCATTCCTTCTAC 59.934 47.826 1.34 0.00 37.07 2.59
2483 2636 1.404391 CCAGAGCTTGCATGGTCATTC 59.596 52.381 27.30 7.21 36.97 2.67
2502 2655 4.058817 CGCCATGTCCTCTAATTAGTTCC 58.941 47.826 12.19 0.86 0.00 3.62
2516 2669 4.092091 GCAAGCTAGATAATACGCCATGTC 59.908 45.833 0.00 0.00 0.00 3.06
2573 2726 5.046591 CACACAGGTACTCCCTCTGATTAAA 60.047 44.000 3.46 0.00 43.86 1.52
2579 2732 0.898320 CCACACAGGTACTCCCTCTG 59.102 60.000 0.00 0.00 43.86 3.35
2593 2746 2.295909 TGCTCCACAAATTAAGCCACAC 59.704 45.455 0.00 0.00 33.79 3.82
2638 2791 3.424829 GGACACATGCACTGTTGAATACG 60.425 47.826 0.00 0.00 35.29 3.06
2639 2792 3.119849 GGGACACATGCACTGTTGAATAC 60.120 47.826 0.00 0.00 35.29 1.89
2640 2793 3.081061 GGGACACATGCACTGTTGAATA 58.919 45.455 0.00 0.00 35.29 1.75
2641 2794 1.888512 GGGACACATGCACTGTTGAAT 59.111 47.619 0.00 0.00 35.29 2.57
2673 2826 2.026262 ACTAACCATTTCCACCGAGCAT 60.026 45.455 0.00 0.00 0.00 3.79
2687 2840 2.922740 AGCTTCCGTTTGACTAACCA 57.077 45.000 0.00 0.00 32.92 3.67
2701 2854 5.500645 AATTTAATTGGACCGCTAGCTTC 57.499 39.130 13.93 8.85 0.00 3.86
2725 2878 2.689034 AGCCACTCCACCTAGCCC 60.689 66.667 0.00 0.00 0.00 5.19
2727 2880 2.124942 GCAGCCACTCCACCTAGC 60.125 66.667 0.00 0.00 0.00 3.42
2728 2881 1.220206 CAGCAGCCACTCCACCTAG 59.780 63.158 0.00 0.00 0.00 3.02
2764 2917 7.319646 ACGATCAATCTCCTAGCTCATAATTC 58.680 38.462 0.00 0.00 0.00 2.17
2877 3030 8.923270 TCCTCCAAAAGAAATTCTTGTGTTTAT 58.077 29.630 20.78 0.00 39.51 1.40
2878 3031 8.299990 TCCTCCAAAAGAAATTCTTGTGTTTA 57.700 30.769 20.78 8.32 39.51 2.01
2879 3032 7.181569 TCCTCCAAAAGAAATTCTTGTGTTT 57.818 32.000 20.78 5.12 39.51 2.83
2880 3033 6.790232 TCCTCCAAAAGAAATTCTTGTGTT 57.210 33.333 20.78 5.44 39.51 3.32
2881 3034 6.015095 GGATCCTCCAAAAGAAATTCTTGTGT 60.015 38.462 20.78 5.61 39.51 3.72
2882 3035 6.210185 AGGATCCTCCAAAAGAAATTCTTGTG 59.790 38.462 16.89 16.89 40.56 3.33
2883 3036 6.318112 AGGATCCTCCAAAAGAAATTCTTGT 58.682 36.000 9.02 0.00 39.61 3.16
2884 3037 6.847421 AGGATCCTCCAAAAGAAATTCTTG 57.153 37.500 9.02 0.00 39.61 3.02
2885 3038 7.862274 AAAGGATCCTCCAAAAGAAATTCTT 57.138 32.000 16.52 1.80 39.61 2.52
2886 3039 7.862274 AAAAGGATCCTCCAAAAGAAATTCT 57.138 32.000 16.52 0.00 39.61 2.40
2887 3040 7.388776 CCAAAAAGGATCCTCCAAAAGAAATTC 59.611 37.037 16.52 0.00 39.61 2.17
2888 3041 7.226441 CCAAAAAGGATCCTCCAAAAGAAATT 58.774 34.615 16.52 0.00 39.61 1.82
2889 3042 6.239973 CCCAAAAAGGATCCTCCAAAAGAAAT 60.240 38.462 16.52 0.00 39.61 2.17
2890 3043 5.071653 CCCAAAAAGGATCCTCCAAAAGAAA 59.928 40.000 16.52 0.00 39.61 2.52
2891 3044 4.592778 CCCAAAAAGGATCCTCCAAAAGAA 59.407 41.667 16.52 0.00 39.61 2.52
2892 3045 4.159557 CCCAAAAAGGATCCTCCAAAAGA 58.840 43.478 16.52 0.00 39.61 2.52
2893 3046 3.903714 ACCCAAAAAGGATCCTCCAAAAG 59.096 43.478 16.52 5.98 39.61 2.27
2894 3047 3.935172 ACCCAAAAAGGATCCTCCAAAA 58.065 40.909 16.52 0.00 39.61 2.44
2895 3048 3.628832 ACCCAAAAAGGATCCTCCAAA 57.371 42.857 16.52 0.00 39.61 3.28
2896 3049 3.628832 AACCCAAAAAGGATCCTCCAA 57.371 42.857 16.52 0.00 39.61 3.53
2897 3050 4.750833 TTAACCCAAAAAGGATCCTCCA 57.249 40.909 16.52 0.00 39.61 3.86
2898 3051 5.958380 AGATTTAACCCAAAAAGGATCCTCC 59.042 40.000 16.52 0.00 41.22 4.30
2899 3052 6.096987 GGAGATTTAACCCAAAAAGGATCCTC 59.903 42.308 16.52 0.00 41.22 3.71
2900 3053 5.958380 GGAGATTTAACCCAAAAAGGATCCT 59.042 40.000 9.02 9.02 41.22 3.24
2901 3054 5.958380 AGGAGATTTAACCCAAAAAGGATCC 59.042 40.000 2.48 2.48 41.22 3.36
2902 3055 6.892456 AGAGGAGATTTAACCCAAAAAGGATC 59.108 38.462 0.00 0.00 41.22 3.36
2903 3056 6.805150 AGAGGAGATTTAACCCAAAAAGGAT 58.195 36.000 0.00 0.00 41.22 3.24
2904 3057 6.045577 AGAGAGGAGATTTAACCCAAAAAGGA 59.954 38.462 0.00 0.00 41.22 3.36
2905 3058 6.249192 AGAGAGGAGATTTAACCCAAAAAGG 58.751 40.000 0.00 0.00 37.03 3.11
2906 3059 7.171653 AGAGAGAGGAGATTTAACCCAAAAAG 58.828 38.462 0.00 0.00 0.00 2.27
2907 3060 7.017651 AGAGAGAGAGGAGATTTAACCCAAAAA 59.982 37.037 0.00 0.00 0.00 1.94
2908 3061 6.502158 AGAGAGAGAGGAGATTTAACCCAAAA 59.498 38.462 0.00 0.00 0.00 2.44
2909 3062 6.026186 AGAGAGAGAGGAGATTTAACCCAAA 58.974 40.000 0.00 0.00 0.00 3.28
2910 3063 5.594777 AGAGAGAGAGGAGATTTAACCCAA 58.405 41.667 0.00 0.00 0.00 4.12
2911 3064 5.043732 AGAGAGAGAGAGGAGATTTAACCCA 60.044 44.000 0.00 0.00 0.00 4.51
2912 3065 5.454966 AGAGAGAGAGAGGAGATTTAACCC 58.545 45.833 0.00 0.00 0.00 4.11
2913 3066 6.365520 AGAGAGAGAGAGAGGAGATTTAACC 58.634 44.000 0.00 0.00 0.00 2.85
2914 3067 6.486993 GGAGAGAGAGAGAGAGGAGATTTAAC 59.513 46.154 0.00 0.00 0.00 2.01
2915 3068 6.410388 GGGAGAGAGAGAGAGAGGAGATTTAA 60.410 46.154 0.00 0.00 0.00 1.52
2916 3069 5.073144 GGGAGAGAGAGAGAGAGGAGATTTA 59.927 48.000 0.00 0.00 0.00 1.40
2917 3070 4.141158 GGGAGAGAGAGAGAGAGGAGATTT 60.141 50.000 0.00 0.00 0.00 2.17
2918 3071 3.395941 GGGAGAGAGAGAGAGAGGAGATT 59.604 52.174 0.00 0.00 0.00 2.40
2919 3072 2.982488 GGGAGAGAGAGAGAGAGGAGAT 59.018 54.545 0.00 0.00 0.00 2.75
2920 3073 2.022035 AGGGAGAGAGAGAGAGAGGAGA 60.022 54.545 0.00 0.00 0.00 3.71
2921 3074 2.370189 GAGGGAGAGAGAGAGAGAGGAG 59.630 59.091 0.00 0.00 0.00 3.69
2922 3075 2.022035 AGAGGGAGAGAGAGAGAGAGGA 60.022 54.545 0.00 0.00 0.00 3.71
2923 3076 2.370189 GAGAGGGAGAGAGAGAGAGAGG 59.630 59.091 0.00 0.00 0.00 3.69
2924 3077 3.312890 AGAGAGGGAGAGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
2925 3078 3.051803 AGAGAGAGGGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
2926 3079 3.312890 AGAGAGAGGGAGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
2927 3080 3.051803 AGAGAGAGAGGGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
2928 3081 3.312890 AGAGAGAGAGGGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
2929 3082 3.051803 AGAGAGAGAGAGGGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
2930 3083 3.312890 AGAGAGAGAGAGGGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
2931 3084 3.421394 AGAGAGAGAGAGGGAGAGAGA 57.579 52.381 0.00 0.00 0.00 3.10
2932 3085 4.901849 TCTTAGAGAGAGAGAGGGAGAGAG 59.098 50.000 0.00 0.00 0.00 3.20
2933 3086 4.890988 TCTTAGAGAGAGAGAGGGAGAGA 58.109 47.826 0.00 0.00 0.00 3.10
2934 3087 5.630415 TTCTTAGAGAGAGAGAGGGAGAG 57.370 47.826 0.00 0.00 35.37 3.20
2935 3088 6.395780 TTTTCTTAGAGAGAGAGAGGGAGA 57.604 41.667 0.00 0.00 35.37 3.71
2936 3089 5.594317 CCTTTTCTTAGAGAGAGAGAGGGAG 59.406 48.000 0.00 0.00 35.37 4.30
2937 3090 5.515106 CCTTTTCTTAGAGAGAGAGAGGGA 58.485 45.833 0.00 0.00 35.37 4.20
2938 3091 4.099419 GCCTTTTCTTAGAGAGAGAGAGGG 59.901 50.000 0.00 0.00 35.37 4.30
2939 3092 4.956075 AGCCTTTTCTTAGAGAGAGAGAGG 59.044 45.833 0.00 0.00 35.37 3.69
2940 3093 6.530019 AAGCCTTTTCTTAGAGAGAGAGAG 57.470 41.667 0.00 0.00 35.37 3.20
2941 3094 6.495181 TGAAAGCCTTTTCTTAGAGAGAGAGA 59.505 38.462 0.00 0.00 42.56 3.10
2942 3095 6.589907 GTGAAAGCCTTTTCTTAGAGAGAGAG 59.410 42.308 0.00 0.00 42.56 3.20
2943 3096 6.459923 GTGAAAGCCTTTTCTTAGAGAGAGA 58.540 40.000 0.00 0.00 42.56 3.10
2944 3097 5.641636 GGTGAAAGCCTTTTCTTAGAGAGAG 59.358 44.000 0.00 0.00 42.56 3.20
2945 3098 5.552178 GGTGAAAGCCTTTTCTTAGAGAGA 58.448 41.667 0.00 0.00 42.56 3.10
2946 3099 5.871465 GGTGAAAGCCTTTTCTTAGAGAG 57.129 43.478 0.00 0.00 42.56 3.20
2959 3112 7.068226 TTTATCTATAAAAGCAGGGTGAAAGCC 59.932 37.037 0.00 0.00 41.03 4.35
2960 3113 7.568199 TTATCTATAAAAGCAGGGTGAAAGC 57.432 36.000 0.00 0.00 0.00 3.51
2961 3114 9.788960 GTTTTATCTATAAAAGCAGGGTGAAAG 57.211 33.333 7.89 0.00 41.38 2.62
2962 3115 9.303116 TGTTTTATCTATAAAAGCAGGGTGAAA 57.697 29.630 7.89 0.00 41.38 2.69
2963 3116 8.871629 TGTTTTATCTATAAAAGCAGGGTGAA 57.128 30.769 7.89 0.00 41.38 3.18
2964 3117 8.871629 TTGTTTTATCTATAAAAGCAGGGTGA 57.128 30.769 7.89 0.00 41.38 4.02
2965 3118 9.921637 TTTTGTTTTATCTATAAAAGCAGGGTG 57.078 29.630 7.89 0.00 41.38 4.61
2989 3142 1.541379 GGCCATGTACTCGGGTTTTT 58.459 50.000 0.00 0.00 0.00 1.94
2990 3143 0.675522 CGGCCATGTACTCGGGTTTT 60.676 55.000 2.24 0.00 0.00 2.43
2991 3144 1.078708 CGGCCATGTACTCGGGTTT 60.079 57.895 2.24 0.00 0.00 3.27
2992 3145 1.546589 TTCGGCCATGTACTCGGGTT 61.547 55.000 2.24 0.00 0.00 4.11
2993 3146 1.985662 TTCGGCCATGTACTCGGGT 60.986 57.895 2.24 0.00 0.00 5.28
2994 3147 1.520787 GTTCGGCCATGTACTCGGG 60.521 63.158 2.24 0.00 0.00 5.14
2995 3148 1.876714 CGTTCGGCCATGTACTCGG 60.877 63.158 2.24 0.00 0.00 4.63
2996 3149 0.248907 ATCGTTCGGCCATGTACTCG 60.249 55.000 2.24 0.00 0.00 4.18
2997 3150 1.209128 CATCGTTCGGCCATGTACTC 58.791 55.000 2.24 0.00 0.00 2.59
2998 3151 0.810031 GCATCGTTCGGCCATGTACT 60.810 55.000 2.24 0.00 0.00 2.73
2999 3152 1.087202 TGCATCGTTCGGCCATGTAC 61.087 55.000 2.24 0.00 0.00 2.90
3000 3153 0.809636 CTGCATCGTTCGGCCATGTA 60.810 55.000 2.24 0.00 0.00 2.29
3001 3154 2.046411 TGCATCGTTCGGCCATGT 60.046 55.556 2.24 0.00 0.00 3.21
3002 3155 1.769098 CTCTGCATCGTTCGGCCATG 61.769 60.000 2.24 0.00 0.00 3.66
3003 3156 1.522355 CTCTGCATCGTTCGGCCAT 60.522 57.895 2.24 0.00 0.00 4.40
3004 3157 2.125552 CTCTGCATCGTTCGGCCA 60.126 61.111 2.24 0.00 0.00 5.36
3005 3158 2.125512 ACTCTGCATCGTTCGGCC 60.126 61.111 0.00 0.00 0.00 6.13
3006 3159 0.807667 ATCACTCTGCATCGTTCGGC 60.808 55.000 0.00 0.00 0.00 5.54
3007 3160 0.926155 CATCACTCTGCATCGTTCGG 59.074 55.000 0.00 0.00 0.00 4.30
3008 3161 1.851053 CTCATCACTCTGCATCGTTCG 59.149 52.381 0.00 0.00 0.00 3.95
3009 3162 2.159184 TCCTCATCACTCTGCATCGTTC 60.159 50.000 0.00 0.00 0.00 3.95
3010 3163 1.827344 TCCTCATCACTCTGCATCGTT 59.173 47.619 0.00 0.00 0.00 3.85
3011 3164 1.408340 CTCCTCATCACTCTGCATCGT 59.592 52.381 0.00 0.00 0.00 3.73
3012 3165 1.269673 CCTCCTCATCACTCTGCATCG 60.270 57.143 0.00 0.00 0.00 3.84
3013 3166 1.540797 GCCTCCTCATCACTCTGCATC 60.541 57.143 0.00 0.00 0.00 3.91
3014 3167 0.469070 GCCTCCTCATCACTCTGCAT 59.531 55.000 0.00 0.00 0.00 3.96
3015 3168 1.620739 GGCCTCCTCATCACTCTGCA 61.621 60.000 0.00 0.00 0.00 4.41
3016 3169 1.145819 GGCCTCCTCATCACTCTGC 59.854 63.158 0.00 0.00 0.00 4.26
3017 3170 0.690411 AGGGCCTCCTCATCACTCTG 60.690 60.000 0.00 0.00 39.80 3.35
3018 3171 0.690411 CAGGGCCTCCTCATCACTCT 60.690 60.000 0.95 0.00 42.67 3.24
3019 3172 0.980231 ACAGGGCCTCCTCATCACTC 60.980 60.000 0.95 0.00 42.67 3.51
3020 3173 0.548682 AACAGGGCCTCCTCATCACT 60.549 55.000 0.95 0.00 42.67 3.41
3021 3174 1.134371 GTAACAGGGCCTCCTCATCAC 60.134 57.143 0.95 0.00 42.67 3.06
3022 3175 1.204146 GTAACAGGGCCTCCTCATCA 58.796 55.000 0.95 0.00 42.67 3.07
3023 3176 1.204146 TGTAACAGGGCCTCCTCATC 58.796 55.000 0.95 0.00 42.67 2.92
3024 3177 1.668826 TTGTAACAGGGCCTCCTCAT 58.331 50.000 0.95 0.00 42.67 2.90
3025 3178 1.351017 CTTTGTAACAGGGCCTCCTCA 59.649 52.381 0.95 0.00 42.67 3.86
3026 3179 1.950954 GCTTTGTAACAGGGCCTCCTC 60.951 57.143 0.95 0.00 42.67 3.71
3027 3180 0.038310 GCTTTGTAACAGGGCCTCCT 59.962 55.000 0.95 0.00 46.26 3.69
3028 3181 0.251165 TGCTTTGTAACAGGGCCTCC 60.251 55.000 0.95 0.00 0.00 4.30
3029 3182 1.168714 CTGCTTTGTAACAGGGCCTC 58.831 55.000 0.95 0.00 0.00 4.70
3030 3183 0.771127 TCTGCTTTGTAACAGGGCCT 59.229 50.000 0.00 0.00 34.57 5.19
3031 3184 1.745653 GATCTGCTTTGTAACAGGGCC 59.254 52.381 0.00 0.00 34.57 5.80
3032 3185 2.716217 AGATCTGCTTTGTAACAGGGC 58.284 47.619 0.00 0.00 34.57 5.19
3033 3186 3.441572 CCAAGATCTGCTTTGTAACAGGG 59.558 47.826 0.00 0.00 33.60 4.45
3034 3187 3.441572 CCCAAGATCTGCTTTGTAACAGG 59.558 47.826 0.00 0.00 33.60 4.00
3035 3188 4.326826 TCCCAAGATCTGCTTTGTAACAG 58.673 43.478 0.00 0.00 33.60 3.16
3036 3189 4.365514 TCCCAAGATCTGCTTTGTAACA 57.634 40.909 0.00 0.00 33.60 2.41
3037 3190 5.904362 AATCCCAAGATCTGCTTTGTAAC 57.096 39.130 0.00 0.00 33.60 2.50
3038 3191 6.093495 CGTTAATCCCAAGATCTGCTTTGTAA 59.907 38.462 0.00 0.00 33.60 2.41
3039 3192 5.584649 CGTTAATCCCAAGATCTGCTTTGTA 59.415 40.000 0.00 0.00 33.60 2.41
3040 3193 4.396166 CGTTAATCCCAAGATCTGCTTTGT 59.604 41.667 0.00 0.00 33.60 2.83
3041 3194 4.635765 TCGTTAATCCCAAGATCTGCTTTG 59.364 41.667 0.00 0.00 33.60 2.77
3042 3195 4.636206 GTCGTTAATCCCAAGATCTGCTTT 59.364 41.667 0.00 0.00 33.60 3.51
3043 3196 4.080863 AGTCGTTAATCCCAAGATCTGCTT 60.081 41.667 0.00 0.00 37.29 3.91
3044 3197 3.452627 AGTCGTTAATCCCAAGATCTGCT 59.547 43.478 0.00 0.00 0.00 4.24
3045 3198 3.798202 AGTCGTTAATCCCAAGATCTGC 58.202 45.455 0.00 0.00 0.00 4.26
3046 3199 4.976731 CGTAGTCGTTAATCCCAAGATCTG 59.023 45.833 0.00 0.00 0.00 2.90
3047 3200 5.184340 CGTAGTCGTTAATCCCAAGATCT 57.816 43.478 0.00 0.00 0.00 2.75
3062 3215 2.012937 TATTTGGCCCAACGTAGTCG 57.987 50.000 0.00 0.00 45.00 4.18
3063 3216 3.805207 AGATATTTGGCCCAACGTAGTC 58.195 45.455 0.00 0.00 45.00 2.59
3065 3218 4.062991 GGTAGATATTTGGCCCAACGTAG 58.937 47.826 0.00 0.00 0.00 3.51
3066 3219 3.455177 TGGTAGATATTTGGCCCAACGTA 59.545 43.478 0.00 0.00 0.00 3.57
3067 3220 2.240160 TGGTAGATATTTGGCCCAACGT 59.760 45.455 0.00 0.00 0.00 3.99
3068 3221 2.616842 GTGGTAGATATTTGGCCCAACG 59.383 50.000 0.00 0.00 0.00 4.10
3069 3222 3.898482 AGTGGTAGATATTTGGCCCAAC 58.102 45.455 0.00 0.00 0.00 3.77
3070 3223 5.718801 TTAGTGGTAGATATTTGGCCCAA 57.281 39.130 0.00 0.00 0.00 4.12
3071 3224 5.922960 ATTAGTGGTAGATATTTGGCCCA 57.077 39.130 0.00 0.00 0.00 5.36
3072 3225 8.161425 TCTTAATTAGTGGTAGATATTTGGCCC 58.839 37.037 0.00 0.00 0.00 5.80
3073 3226 9.569122 TTCTTAATTAGTGGTAGATATTTGGCC 57.431 33.333 0.00 0.00 0.00 5.36
3082 3235 8.404000 CGAGCTAGTTTCTTAATTAGTGGTAGA 58.596 37.037 0.00 0.00 0.00 2.59
3083 3236 7.648510 CCGAGCTAGTTTCTTAATTAGTGGTAG 59.351 40.741 0.00 0.00 0.00 3.18
3084 3237 7.340232 TCCGAGCTAGTTTCTTAATTAGTGGTA 59.660 37.037 0.00 0.00 0.00 3.25
3085 3238 6.154021 TCCGAGCTAGTTTCTTAATTAGTGGT 59.846 38.462 0.00 0.00 0.00 4.16
3086 3239 6.570692 TCCGAGCTAGTTTCTTAATTAGTGG 58.429 40.000 0.00 0.00 0.00 4.00
3087 3240 8.475331 TTTCCGAGCTAGTTTCTTAATTAGTG 57.525 34.615 0.00 0.00 0.00 2.74
3088 3241 9.498176 TTTTTCCGAGCTAGTTTCTTAATTAGT 57.502 29.630 0.00 0.00 0.00 2.24
3089 3242 9.974750 CTTTTTCCGAGCTAGTTTCTTAATTAG 57.025 33.333 0.00 0.00 0.00 1.73
3090 3243 9.498176 ACTTTTTCCGAGCTAGTTTCTTAATTA 57.502 29.630 0.00 0.00 0.00 1.40
3091 3244 8.392372 ACTTTTTCCGAGCTAGTTTCTTAATT 57.608 30.769 0.00 0.00 0.00 1.40
3092 3245 7.981102 ACTTTTTCCGAGCTAGTTTCTTAAT 57.019 32.000 0.00 0.00 0.00 1.40
3093 3246 7.496591 TCAACTTTTTCCGAGCTAGTTTCTTAA 59.503 33.333 0.00 0.00 0.00 1.85
3094 3247 6.987992 TCAACTTTTTCCGAGCTAGTTTCTTA 59.012 34.615 0.00 0.00 0.00 2.10
3095 3248 5.820947 TCAACTTTTTCCGAGCTAGTTTCTT 59.179 36.000 0.00 0.00 0.00 2.52
3096 3249 5.365619 TCAACTTTTTCCGAGCTAGTTTCT 58.634 37.500 0.00 0.00 0.00 2.52
3097 3250 5.334182 CCTCAACTTTTTCCGAGCTAGTTTC 60.334 44.000 0.00 0.00 0.00 2.78
3098 3251 4.515567 CCTCAACTTTTTCCGAGCTAGTTT 59.484 41.667 0.00 0.00 0.00 2.66
3099 3252 4.065789 CCTCAACTTTTTCCGAGCTAGTT 58.934 43.478 0.00 0.00 0.00 2.24
3100 3253 3.071167 ACCTCAACTTTTTCCGAGCTAGT 59.929 43.478 0.00 0.00 0.00 2.57
3101 3254 3.665190 ACCTCAACTTTTTCCGAGCTAG 58.335 45.455 0.00 0.00 0.00 3.42
3102 3255 3.323979 AGACCTCAACTTTTTCCGAGCTA 59.676 43.478 0.00 0.00 0.00 3.32
3103 3256 2.104963 AGACCTCAACTTTTTCCGAGCT 59.895 45.455 0.00 0.00 0.00 4.09
3104 3257 2.480802 GAGACCTCAACTTTTTCCGAGC 59.519 50.000 0.00 0.00 0.00 5.03
3105 3258 3.067833 GGAGACCTCAACTTTTTCCGAG 58.932 50.000 0.00 0.00 0.00 4.63
3106 3259 2.436542 TGGAGACCTCAACTTTTTCCGA 59.563 45.455 0.00 0.00 0.00 4.55
3107 3260 2.846193 TGGAGACCTCAACTTTTTCCG 58.154 47.619 0.00 0.00 0.00 4.30
3108 3261 5.069119 ACAAATGGAGACCTCAACTTTTTCC 59.931 40.000 0.00 0.00 0.00 3.13
3109 3262 6.149129 ACAAATGGAGACCTCAACTTTTTC 57.851 37.500 0.00 0.00 0.00 2.29
3110 3263 6.544928 AACAAATGGAGACCTCAACTTTTT 57.455 33.333 0.00 0.00 0.00 1.94
3111 3264 7.839680 ATAACAAATGGAGACCTCAACTTTT 57.160 32.000 0.00 0.00 0.00 2.27
3112 3265 9.533831 AATATAACAAATGGAGACCTCAACTTT 57.466 29.630 0.00 0.00 0.00 2.66
3113 3266 8.960591 CAATATAACAAATGGAGACCTCAACTT 58.039 33.333 0.00 0.00 0.00 2.66
3114 3267 8.109634 ACAATATAACAAATGGAGACCTCAACT 58.890 33.333 0.00 0.00 0.00 3.16
3115 3268 8.281212 ACAATATAACAAATGGAGACCTCAAC 57.719 34.615 0.00 0.00 0.00 3.18
3116 3269 8.877864 AACAATATAACAAATGGAGACCTCAA 57.122 30.769 0.00 0.00 0.00 3.02
3182 3335 0.898320 GGCCAGACAACTCTGCTAGA 59.102 55.000 0.00 0.00 42.55 2.43
3183 3336 0.610174 TGGCCAGACAACTCTGCTAG 59.390 55.000 0.00 0.00 42.55 3.42
3184 3337 1.055849 TTGGCCAGACAACTCTGCTA 58.944 50.000 5.11 0.00 42.55 3.49
3185 3338 0.183492 TTTGGCCAGACAACTCTGCT 59.817 50.000 5.11 0.00 42.55 4.24
3186 3339 1.200948 GATTTGGCCAGACAACTCTGC 59.799 52.381 5.11 0.00 42.55 4.26
3187 3340 1.466167 CGATTTGGCCAGACAACTCTG 59.534 52.381 5.11 0.00 43.40 3.35
3188 3341 1.813513 CGATTTGGCCAGACAACTCT 58.186 50.000 5.11 0.00 30.50 3.24
3189 3342 0.169009 GCGATTTGGCCAGACAACTC 59.831 55.000 5.11 0.00 0.00 3.01
3190 3343 2.257353 GCGATTTGGCCAGACAACT 58.743 52.632 5.11 0.00 0.00 3.16
3191 3344 4.868195 GCGATTTGGCCAGACAAC 57.132 55.556 5.11 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.