Multiple sequence alignment - TraesCS1D01G165200

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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 TraesCS1D01G165200 chr1D 100.000 3293 0 0 1 3293 236274457 236277749 0 6082
1 TraesCS1D01G165200 chr1B 96.614 2983 63 14 3 2964 341522294 341525259 0 4915
2 TraesCS1D01G165200 chr1A 93.795 3062 93 33 3 3017 309742630 309739619 0 4512


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 TraesCS1D01G165200 chr1D 236274457 236277749 3292 False 6082 6082 100.000 1 3293 1 chr1D.!!$F1 3292
1 TraesCS1D01G165200 chr1B 341522294 341525259 2965 False 4915 4915 96.614 3 2964 1 chr1B.!!$F1 2961
2 TraesCS1D01G165200 chr1A 309739619 309742630 3011 True 4512 4512 93.795 3 3017 1 chr1A.!!$R1 3014

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
773 776 1.952621 TGGTGTTAGAGCCTAGCCTT 58.047 50.0 0.00 0.0 0.0 4.35 F
1924 1929 5.105351 CCTTGATCAACCTACCCAAATTTCC 60.105 44.0 3.38 0.0 0.0 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 2095 0.267658 TAAGGGAGGCATAGGAGGCA 59.732 55.0 0.00 0.0 36.37 4.75 R
3067 3128 0.034380 AGACAACCGGGAGAGATCGA 60.034 55.0 6.32 0.0 0.00 3.59 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
218 219 7.595819 TGGTAATGTTTCACCTTCATTTCTT 57.404 32.000 0.00 0.00 35.73 2.52
523 526 7.125792 AGAATAGATTTAACATCGACCACCT 57.874 36.000 0.00 0.00 0.00 4.00
524 527 7.565680 AGAATAGATTTAACATCGACCACCTT 58.434 34.615 0.00 0.00 0.00 3.50
525 528 7.711339 AGAATAGATTTAACATCGACCACCTTC 59.289 37.037 0.00 0.00 0.00 3.46
560 563 9.449719 AGAAAAACTTGACCGATAGATAACAAT 57.550 29.630 0.00 0.00 39.76 2.71
729 732 3.827008 ATGACGTGGCACATCTATTCT 57.173 42.857 19.09 0.00 44.52 2.40
773 776 1.952621 TGGTGTTAGAGCCTAGCCTT 58.047 50.000 0.00 0.00 0.00 4.35
784 787 8.399425 GTTAGAGCCTAGCCTTTTCTATTTTTC 58.601 37.037 0.00 0.00 0.00 2.29
1863 1868 7.315142 TGGCTAACAAAATTGAAGAGCAATAG 58.685 34.615 15.25 0.00 46.25 1.73
1924 1929 5.105351 CCTTGATCAACCTACCCAAATTTCC 60.105 44.000 3.38 0.00 0.00 3.13
2088 2095 2.581354 GGCTGCATCCTGACGACT 59.419 61.111 0.50 0.00 0.00 4.18
2097 2104 0.259065 TCCTGACGACTGCCTCCTAT 59.741 55.000 0.00 0.00 0.00 2.57
2133 2140 1.656587 TCCTGTACTGCCAGAACCAT 58.343 50.000 0.00 0.00 34.23 3.55
2202 2212 2.358247 GCCTCCAAGAACGCCGAA 60.358 61.111 0.00 0.00 0.00 4.30
2253 2263 2.182030 CCAGAAGCCGTCGAGGAC 59.818 66.667 6.70 0.00 45.00 3.85
2258 2268 4.680537 AGCCGTCGAGGACCAGGT 62.681 66.667 6.70 0.00 45.00 4.00
2476 2486 5.114764 TGAATTCTGTATCTCATTGCCCA 57.885 39.130 7.05 0.00 0.00 5.36
2484 2495 0.259356 TCTCATTGCCCATGCCATCA 59.741 50.000 0.00 0.00 36.33 3.07
2487 2498 1.044611 CATTGCCCATGCCATCATCA 58.955 50.000 0.00 0.00 36.33 3.07
2536 2555 4.452455 AGTTTGTTCTATCTTGGTCTTGCG 59.548 41.667 0.00 0.00 0.00 4.85
2553 2572 2.766313 TGCGATTCCAAGGATATTCGG 58.234 47.619 14.38 0.00 0.00 4.30
2558 2604 4.686554 CGATTCCAAGGATATTCGGAAGAC 59.313 45.833 0.00 0.00 40.71 3.01
2602 2648 5.491635 AACACTGTTCTTCTTGCTCTTTC 57.508 39.130 0.00 0.00 0.00 2.62
2650 2696 8.744008 TTAGAAGACAATTCAAACTCTAGACG 57.256 34.615 0.00 0.00 0.00 4.18
2673 2727 2.642254 CCCGGTCGCCACTGTTCTA 61.642 63.158 0.00 0.00 0.00 2.10
2808 2864 2.643551 CGGCAAATCCAATCTACCAGT 58.356 47.619 0.00 0.00 34.01 4.00
2907 2967 5.713792 TCTGTAGAGAAAACAGACTCAGG 57.286 43.478 1.92 0.00 46.38 3.86
2908 2968 5.141182 TCTGTAGAGAAAACAGACTCAGGT 58.859 41.667 1.92 0.00 46.38 4.00
2954 3015 4.154918 AGCGCTGTATCTTTCCTCAAAAAG 59.845 41.667 10.39 0.00 37.55 2.27
2980 3041 1.493311 CGCGCTCTTTCAACCAGTC 59.507 57.895 5.56 0.00 0.00 3.51
3011 3072 1.532437 TGCAGAGCACATTTCGACTTG 59.468 47.619 0.00 0.00 31.71 3.16
3017 3078 4.455533 AGAGCACATTTCGACTTGCATTAA 59.544 37.500 8.84 0.00 37.44 1.40
3018 3079 5.124457 AGAGCACATTTCGACTTGCATTAAT 59.876 36.000 8.84 0.00 37.44 1.40
3019 3080 6.316140 AGAGCACATTTCGACTTGCATTAATA 59.684 34.615 8.84 0.00 37.44 0.98
3020 3081 6.851609 AGCACATTTCGACTTGCATTAATAA 58.148 32.000 8.84 0.00 37.44 1.40
3021 3082 7.312154 AGCACATTTCGACTTGCATTAATAAA 58.688 30.769 8.84 0.00 37.44 1.40
3022 3083 7.812191 AGCACATTTCGACTTGCATTAATAAAA 59.188 29.630 8.84 0.00 37.44 1.52
3023 3084 7.892731 GCACATTTCGACTTGCATTAATAAAAC 59.107 33.333 0.00 0.00 34.97 2.43
3024 3085 9.128107 CACATTTCGACTTGCATTAATAAAACT 57.872 29.630 0.00 0.00 0.00 2.66
3025 3086 9.341899 ACATTTCGACTTGCATTAATAAAACTC 57.658 29.630 0.00 0.00 0.00 3.01
3026 3087 9.559958 CATTTCGACTTGCATTAATAAAACTCT 57.440 29.630 0.00 0.00 0.00 3.24
3027 3088 8.948853 TTTCGACTTGCATTAATAAAACTCTG 57.051 30.769 0.00 0.00 0.00 3.35
3028 3089 6.542852 TCGACTTGCATTAATAAAACTCTGC 58.457 36.000 0.00 0.00 0.00 4.26
3029 3090 6.371548 TCGACTTGCATTAATAAAACTCTGCT 59.628 34.615 0.00 0.00 0.00 4.24
3030 3091 7.023575 CGACTTGCATTAATAAAACTCTGCTT 58.976 34.615 0.00 0.00 0.00 3.91
3031 3092 7.217070 CGACTTGCATTAATAAAACTCTGCTTC 59.783 37.037 0.00 0.00 0.00 3.86
3032 3093 7.023575 ACTTGCATTAATAAAACTCTGCTTCG 58.976 34.615 0.00 0.00 0.00 3.79
3033 3094 6.735678 TGCATTAATAAAACTCTGCTTCGA 57.264 33.333 0.00 0.00 0.00 3.71
3034 3095 6.775088 TGCATTAATAAAACTCTGCTTCGAG 58.225 36.000 0.00 0.00 37.07 4.04
3035 3096 6.183360 TGCATTAATAAAACTCTGCTTCGAGG 60.183 38.462 0.00 0.00 35.33 4.63
3036 3097 6.183360 GCATTAATAAAACTCTGCTTCGAGGT 60.183 38.462 0.00 0.00 35.33 3.85
3037 3098 7.011109 GCATTAATAAAACTCTGCTTCGAGGTA 59.989 37.037 0.00 0.00 35.33 3.08
3038 3099 8.879759 CATTAATAAAACTCTGCTTCGAGGTAA 58.120 33.333 0.00 0.00 35.33 2.85
3039 3100 8.836268 TTAATAAAACTCTGCTTCGAGGTAAA 57.164 30.769 0.00 0.00 35.33 2.01
3040 3101 6.969828 ATAAAACTCTGCTTCGAGGTAAAG 57.030 37.500 0.00 0.00 35.33 1.85
3041 3102 3.320673 AACTCTGCTTCGAGGTAAAGG 57.679 47.619 0.00 0.00 35.33 3.11
3042 3103 1.066787 ACTCTGCTTCGAGGTAAAGGC 60.067 52.381 0.00 0.00 35.33 4.35
3043 3104 0.973632 TCTGCTTCGAGGTAAAGGCA 59.026 50.000 0.00 0.00 0.00 4.75
3044 3105 1.555075 TCTGCTTCGAGGTAAAGGCAT 59.445 47.619 0.00 0.00 0.00 4.40
3045 3106 1.667724 CTGCTTCGAGGTAAAGGCATG 59.332 52.381 0.00 0.00 0.00 4.06
3046 3107 1.017387 GCTTCGAGGTAAAGGCATGG 58.983 55.000 0.00 0.00 0.00 3.66
3047 3108 1.679032 GCTTCGAGGTAAAGGCATGGT 60.679 52.381 0.00 0.00 0.00 3.55
3048 3109 2.419574 GCTTCGAGGTAAAGGCATGGTA 60.420 50.000 0.00 0.00 0.00 3.25
3049 3110 3.869065 CTTCGAGGTAAAGGCATGGTAA 58.131 45.455 0.00 0.00 0.00 2.85
3050 3111 3.985019 TCGAGGTAAAGGCATGGTAAA 57.015 42.857 0.00 0.00 0.00 2.01
3051 3112 3.869065 TCGAGGTAAAGGCATGGTAAAG 58.131 45.455 0.00 0.00 0.00 1.85
3052 3113 2.354821 CGAGGTAAAGGCATGGTAAAGC 59.645 50.000 0.00 0.00 0.00 3.51
3053 3114 3.352648 GAGGTAAAGGCATGGTAAAGCA 58.647 45.455 0.00 0.00 0.00 3.91
3054 3115 3.954258 GAGGTAAAGGCATGGTAAAGCAT 59.046 43.478 0.00 0.00 0.00 3.79
3055 3116 4.352893 AGGTAAAGGCATGGTAAAGCATT 58.647 39.130 0.00 0.00 36.17 3.56
3056 3117 4.777366 AGGTAAAGGCATGGTAAAGCATTT 59.223 37.500 0.00 0.00 45.27 2.32
3057 3118 5.248248 AGGTAAAGGCATGGTAAAGCATTTT 59.752 36.000 2.42 0.00 41.29 1.82
3058 3119 5.580691 GGTAAAGGCATGGTAAAGCATTTTC 59.419 40.000 2.42 0.00 41.29 2.29
3059 3120 4.888326 AAGGCATGGTAAAGCATTTTCA 57.112 36.364 0.00 0.00 40.09 2.69
3060 3121 5.425196 AAGGCATGGTAAAGCATTTTCAT 57.575 34.783 0.00 0.00 40.09 2.57
3061 3122 5.425196 AGGCATGGTAAAGCATTTTCATT 57.575 34.783 0.00 0.00 40.09 2.57
3062 3123 6.543430 AGGCATGGTAAAGCATTTTCATTA 57.457 33.333 0.00 0.00 40.09 1.90
3063 3124 6.340522 AGGCATGGTAAAGCATTTTCATTAC 58.659 36.000 0.00 0.00 40.09 1.89
3064 3125 6.070881 AGGCATGGTAAAGCATTTTCATTACA 60.071 34.615 0.00 0.00 40.09 2.41
3065 3126 6.762661 GGCATGGTAAAGCATTTTCATTACAT 59.237 34.615 0.00 0.00 40.09 2.29
3066 3127 7.280652 GGCATGGTAAAGCATTTTCATTACATT 59.719 33.333 0.00 0.00 40.09 2.71
3067 3128 8.667463 GCATGGTAAAGCATTTTCATTACATTT 58.333 29.630 0.00 0.00 40.09 2.32
3069 3130 8.459521 TGGTAAAGCATTTTCATTACATTTCG 57.540 30.769 0.00 0.00 40.09 3.46
3070 3131 8.300286 TGGTAAAGCATTTTCATTACATTTCGA 58.700 29.630 0.00 0.00 40.09 3.71
3071 3132 9.301153 GGTAAAGCATTTTCATTACATTTCGAT 57.699 29.630 0.00 0.00 40.09 3.59
3074 3135 8.847444 AAGCATTTTCATTACATTTCGATCTC 57.153 30.769 0.00 0.00 0.00 2.75
3075 3136 8.218338 AGCATTTTCATTACATTTCGATCTCT 57.782 30.769 0.00 0.00 0.00 3.10
3076 3137 8.341173 AGCATTTTCATTACATTTCGATCTCTC 58.659 33.333 0.00 0.00 0.00 3.20
3077 3138 7.589221 GCATTTTCATTACATTTCGATCTCTCC 59.411 37.037 0.00 0.00 0.00 3.71
3078 3139 7.553881 TTTTCATTACATTTCGATCTCTCCC 57.446 36.000 0.00 0.00 0.00 4.30
3079 3140 4.871513 TCATTACATTTCGATCTCTCCCG 58.128 43.478 0.00 0.00 0.00 5.14
3080 3141 3.728076 TTACATTTCGATCTCTCCCGG 57.272 47.619 0.00 0.00 0.00 5.73
3081 3142 1.486211 ACATTTCGATCTCTCCCGGT 58.514 50.000 0.00 0.00 0.00 5.28
3082 3143 1.831736 ACATTTCGATCTCTCCCGGTT 59.168 47.619 0.00 0.00 0.00 4.44
3083 3144 2.205074 CATTTCGATCTCTCCCGGTTG 58.795 52.381 0.00 0.00 0.00 3.77
3084 3145 1.263356 TTTCGATCTCTCCCGGTTGT 58.737 50.000 0.00 0.00 0.00 3.32
3085 3146 0.815734 TTCGATCTCTCCCGGTTGTC 59.184 55.000 0.00 0.00 0.00 3.18
3086 3147 0.034380 TCGATCTCTCCCGGTTGTCT 60.034 55.000 0.00 0.00 0.00 3.41
3087 3148 1.211212 TCGATCTCTCCCGGTTGTCTA 59.789 52.381 0.00 0.00 0.00 2.59
3088 3149 2.022195 CGATCTCTCCCGGTTGTCTAA 58.978 52.381 0.00 0.00 0.00 2.10
3089 3150 2.426024 CGATCTCTCCCGGTTGTCTAAA 59.574 50.000 0.00 0.00 0.00 1.85
3090 3151 3.119245 CGATCTCTCCCGGTTGTCTAAAA 60.119 47.826 0.00 0.00 0.00 1.52
3091 3152 4.619863 CGATCTCTCCCGGTTGTCTAAAAA 60.620 45.833 0.00 0.00 0.00 1.94
3092 3153 4.267349 TCTCTCCCGGTTGTCTAAAAAG 57.733 45.455 0.00 0.00 0.00 2.27
3093 3154 3.644738 TCTCTCCCGGTTGTCTAAAAAGT 59.355 43.478 0.00 0.00 0.00 2.66
3094 3155 3.735591 TCTCCCGGTTGTCTAAAAAGTG 58.264 45.455 0.00 0.00 0.00 3.16
3095 3156 2.812011 CTCCCGGTTGTCTAAAAAGTGG 59.188 50.000 0.00 0.00 0.00 4.00
3096 3157 2.173143 TCCCGGTTGTCTAAAAAGTGGT 59.827 45.455 0.00 0.00 0.00 4.16
3097 3158 3.390639 TCCCGGTTGTCTAAAAAGTGGTA 59.609 43.478 0.00 0.00 0.00 3.25
3098 3159 4.136051 CCCGGTTGTCTAAAAAGTGGTAA 58.864 43.478 0.00 0.00 0.00 2.85
3099 3160 4.579753 CCCGGTTGTCTAAAAAGTGGTAAA 59.420 41.667 0.00 0.00 0.00 2.01
3100 3161 5.242171 CCCGGTTGTCTAAAAAGTGGTAAAT 59.758 40.000 0.00 0.00 0.00 1.40
3101 3162 6.376177 CCGGTTGTCTAAAAAGTGGTAAATC 58.624 40.000 0.00 0.00 0.00 2.17
3102 3163 6.206048 CCGGTTGTCTAAAAAGTGGTAAATCT 59.794 38.462 0.00 0.00 0.00 2.40
3103 3164 7.295930 CGGTTGTCTAAAAAGTGGTAAATCTC 58.704 38.462 0.00 0.00 0.00 2.75
3104 3165 7.041644 CGGTTGTCTAAAAAGTGGTAAATCTCA 60.042 37.037 0.00 0.00 0.00 3.27
3105 3166 8.290325 GGTTGTCTAAAAAGTGGTAAATCTCAG 58.710 37.037 0.00 0.00 0.00 3.35
3106 3167 7.435068 TGTCTAAAAAGTGGTAAATCTCAGC 57.565 36.000 0.00 0.00 0.00 4.26
3107 3168 6.430000 TGTCTAAAAAGTGGTAAATCTCAGCC 59.570 38.462 0.00 0.00 0.00 4.85
3108 3169 6.430000 GTCTAAAAAGTGGTAAATCTCAGCCA 59.570 38.462 0.00 0.00 0.00 4.75
3115 3176 3.193267 TGGTAAATCTCAGCCACATTTGC 59.807 43.478 0.00 0.00 0.00 3.68
3116 3177 3.445096 GGTAAATCTCAGCCACATTTGCT 59.555 43.478 0.00 0.00 40.41 3.91
3117 3178 4.640201 GGTAAATCTCAGCCACATTTGCTA 59.360 41.667 0.00 0.00 36.81 3.49
3118 3179 4.978083 AAATCTCAGCCACATTTGCTAG 57.022 40.909 0.00 0.00 36.81 3.42
3119 3180 3.920231 ATCTCAGCCACATTTGCTAGA 57.080 42.857 0.00 0.00 36.81 2.43
3120 3181 3.701205 TCTCAGCCACATTTGCTAGAA 57.299 42.857 0.00 0.00 36.81 2.10
3121 3182 4.019792 TCTCAGCCACATTTGCTAGAAA 57.980 40.909 0.00 0.00 36.81 2.52
3122 3183 4.592942 TCTCAGCCACATTTGCTAGAAAT 58.407 39.130 0.00 0.00 36.81 2.17
3123 3184 4.637534 TCTCAGCCACATTTGCTAGAAATC 59.362 41.667 0.00 0.00 36.81 2.17
3124 3185 3.696051 TCAGCCACATTTGCTAGAAATCC 59.304 43.478 0.00 0.00 36.81 3.01
3125 3186 3.444742 CAGCCACATTTGCTAGAAATCCA 59.555 43.478 0.00 0.00 36.81 3.41
3126 3187 4.082081 CAGCCACATTTGCTAGAAATCCAA 60.082 41.667 0.00 0.00 36.81 3.53
3127 3188 4.527816 AGCCACATTTGCTAGAAATCCAAA 59.472 37.500 0.00 0.00 37.28 3.28
3128 3189 4.866486 GCCACATTTGCTAGAAATCCAAAG 59.134 41.667 0.00 0.00 32.65 2.77
3129 3190 4.866486 CCACATTTGCTAGAAATCCAAAGC 59.134 41.667 0.00 0.00 32.65 3.51
3130 3191 4.866486 CACATTTGCTAGAAATCCAAAGCC 59.134 41.667 0.00 0.00 33.99 4.35
3131 3192 4.774200 ACATTTGCTAGAAATCCAAAGCCT 59.226 37.500 0.00 0.00 33.99 4.58
3132 3193 5.951747 ACATTTGCTAGAAATCCAAAGCCTA 59.048 36.000 0.00 0.00 33.99 3.93
3133 3194 6.608808 ACATTTGCTAGAAATCCAAAGCCTAT 59.391 34.615 0.00 0.00 33.99 2.57
3134 3195 6.455360 TTTGCTAGAAATCCAAAGCCTATG 57.545 37.500 0.00 0.00 33.99 2.23
3135 3196 5.116084 TGCTAGAAATCCAAAGCCTATGT 57.884 39.130 0.00 0.00 33.99 2.29
3136 3197 5.126067 TGCTAGAAATCCAAAGCCTATGTC 58.874 41.667 0.00 0.00 33.99 3.06
3137 3198 4.212214 GCTAGAAATCCAAAGCCTATGTCG 59.788 45.833 0.00 0.00 0.00 4.35
3138 3199 3.545703 AGAAATCCAAAGCCTATGTCGG 58.454 45.455 0.00 0.00 0.00 4.79
3147 3208 2.015736 GCCTATGTCGGCCATATGAG 57.984 55.000 2.24 0.00 44.41 2.90
3148 3209 1.550524 GCCTATGTCGGCCATATGAGA 59.449 52.381 2.24 0.00 44.41 3.27
3149 3210 2.169352 GCCTATGTCGGCCATATGAGAT 59.831 50.000 2.24 0.00 44.41 2.75
3150 3211 3.384789 GCCTATGTCGGCCATATGAGATA 59.615 47.826 2.24 0.00 44.41 1.98
3151 3212 4.141937 GCCTATGTCGGCCATATGAGATAA 60.142 45.833 2.24 0.00 44.41 1.75
3152 3213 5.453903 GCCTATGTCGGCCATATGAGATAAT 60.454 44.000 2.24 2.73 44.41 1.28
3153 3214 6.219473 CCTATGTCGGCCATATGAGATAATC 58.781 44.000 2.24 0.00 35.50 1.75
3154 3215 4.110036 TGTCGGCCATATGAGATAATCG 57.890 45.455 2.24 0.00 0.00 3.34
3155 3216 3.761752 TGTCGGCCATATGAGATAATCGA 59.238 43.478 2.24 0.00 0.00 3.59
3156 3217 4.402474 TGTCGGCCATATGAGATAATCGAT 59.598 41.667 2.24 0.00 0.00 3.59
3157 3218 5.105351 TGTCGGCCATATGAGATAATCGATT 60.105 40.000 16.15 16.15 0.00 3.34
3158 3219 5.233050 GTCGGCCATATGAGATAATCGATTG 59.767 44.000 20.87 0.87 0.00 2.67
3159 3220 4.025396 CGGCCATATGAGATAATCGATTGC 60.025 45.833 20.87 12.17 0.00 3.56
3160 3221 4.025396 GGCCATATGAGATAATCGATTGCG 60.025 45.833 20.87 0.27 39.35 4.85
3161 3222 4.568359 GCCATATGAGATAATCGATTGCGT 59.432 41.667 20.87 10.56 38.98 5.24
3162 3223 5.501413 GCCATATGAGATAATCGATTGCGTG 60.501 44.000 20.87 7.72 38.98 5.34
3163 3224 5.807011 CCATATGAGATAATCGATTGCGTGA 59.193 40.000 20.87 0.00 38.98 4.35
3164 3225 6.478016 CCATATGAGATAATCGATTGCGTGAT 59.522 38.462 20.87 5.47 38.98 3.06
3165 3226 5.774878 ATGAGATAATCGATTGCGTGATG 57.225 39.130 20.87 0.00 38.98 3.07
3166 3227 4.870363 TGAGATAATCGATTGCGTGATGA 58.130 39.130 20.87 0.00 38.98 2.92
3167 3228 5.288804 TGAGATAATCGATTGCGTGATGAA 58.711 37.500 20.87 0.00 38.98 2.57
3168 3229 5.752955 TGAGATAATCGATTGCGTGATGAAA 59.247 36.000 20.87 0.00 38.98 2.69
3169 3230 5.978878 AGATAATCGATTGCGTGATGAAAC 58.021 37.500 20.87 0.00 38.98 2.78
3170 3231 3.405170 AATCGATTGCGTGATGAAACC 57.595 42.857 10.50 0.00 38.98 3.27
3171 3232 2.093306 TCGATTGCGTGATGAAACCT 57.907 45.000 0.00 0.00 38.98 3.50
3172 3233 3.239587 TCGATTGCGTGATGAAACCTA 57.760 42.857 0.00 0.00 38.98 3.08
3173 3234 3.591023 TCGATTGCGTGATGAAACCTAA 58.409 40.909 0.00 0.00 38.98 2.69
3174 3235 3.369756 TCGATTGCGTGATGAAACCTAAC 59.630 43.478 0.00 0.00 38.98 2.34
3175 3236 3.670203 GATTGCGTGATGAAACCTAACG 58.330 45.455 0.00 0.00 37.32 3.18
3176 3237 2.442212 TGCGTGATGAAACCTAACGA 57.558 45.000 0.00 0.00 36.38 3.85
3177 3238 2.063266 TGCGTGATGAAACCTAACGAC 58.937 47.619 0.00 0.00 36.38 4.34
3178 3239 1.392510 GCGTGATGAAACCTAACGACC 59.607 52.381 0.00 0.00 36.38 4.79
3179 3240 2.929592 GCGTGATGAAACCTAACGACCT 60.930 50.000 0.00 0.00 36.38 3.85
3180 3241 3.323243 CGTGATGAAACCTAACGACCTT 58.677 45.455 0.00 0.00 36.38 3.50
3181 3242 3.367025 CGTGATGAAACCTAACGACCTTC 59.633 47.826 0.00 0.00 36.38 3.46
3182 3243 4.312443 GTGATGAAACCTAACGACCTTCA 58.688 43.478 0.00 0.00 0.00 3.02
3183 3244 4.753107 GTGATGAAACCTAACGACCTTCAA 59.247 41.667 0.00 0.00 30.37 2.69
3184 3245 5.237779 GTGATGAAACCTAACGACCTTCAAA 59.762 40.000 0.00 0.00 30.37 2.69
3185 3246 5.468746 TGATGAAACCTAACGACCTTCAAAG 59.531 40.000 0.00 0.00 30.37 2.77
3186 3247 4.773013 TGAAACCTAACGACCTTCAAAGT 58.227 39.130 0.00 0.00 0.00 2.66
3187 3248 5.916318 TGAAACCTAACGACCTTCAAAGTA 58.084 37.500 0.00 0.00 0.00 2.24
3188 3249 6.347696 TGAAACCTAACGACCTTCAAAGTAA 58.652 36.000 0.00 0.00 0.00 2.24
3189 3250 6.822676 TGAAACCTAACGACCTTCAAAGTAAA 59.177 34.615 0.00 0.00 0.00 2.01
3190 3251 6.609237 AACCTAACGACCTTCAAAGTAAAC 57.391 37.500 0.00 0.00 0.00 2.01
3191 3252 4.746611 ACCTAACGACCTTCAAAGTAAACG 59.253 41.667 0.00 0.00 0.00 3.60
3192 3253 3.597377 AACGACCTTCAAAGTAAACGC 57.403 42.857 0.00 0.00 0.00 4.84
3193 3254 1.869132 ACGACCTTCAAAGTAAACGCC 59.131 47.619 0.00 0.00 0.00 5.68
3194 3255 2.140717 CGACCTTCAAAGTAAACGCCT 58.859 47.619 0.00 0.00 0.00 5.52
3195 3256 3.243839 ACGACCTTCAAAGTAAACGCCTA 60.244 43.478 0.00 0.00 0.00 3.93
3196 3257 3.122445 CGACCTTCAAAGTAAACGCCTAC 59.878 47.826 0.00 0.00 0.00 3.18
3197 3258 4.060205 GACCTTCAAAGTAAACGCCTACA 58.940 43.478 0.00 0.00 0.00 2.74
3198 3259 4.648651 ACCTTCAAAGTAAACGCCTACAT 58.351 39.130 0.00 0.00 0.00 2.29
3199 3260 5.067954 ACCTTCAAAGTAAACGCCTACATT 58.932 37.500 0.00 0.00 0.00 2.71
3200 3261 5.533528 ACCTTCAAAGTAAACGCCTACATTT 59.466 36.000 0.00 0.00 0.00 2.32
3201 3262 6.040054 ACCTTCAAAGTAAACGCCTACATTTT 59.960 34.615 0.00 0.00 0.00 1.82
3202 3263 6.921307 CCTTCAAAGTAAACGCCTACATTTTT 59.079 34.615 0.00 0.00 0.00 1.94
3203 3264 7.114388 CCTTCAAAGTAAACGCCTACATTTTTC 59.886 37.037 0.00 0.00 0.00 2.29
3204 3265 7.028926 TCAAAGTAAACGCCTACATTTTTCA 57.971 32.000 0.00 0.00 0.00 2.69
3205 3266 7.481642 TCAAAGTAAACGCCTACATTTTTCAA 58.518 30.769 0.00 0.00 0.00 2.69
3206 3267 7.646130 TCAAAGTAAACGCCTACATTTTTCAAG 59.354 33.333 0.00 0.00 0.00 3.02
3207 3268 5.458015 AGTAAACGCCTACATTTTTCAAGC 58.542 37.500 0.00 0.00 0.00 4.01
3208 3269 3.297830 AACGCCTACATTTTTCAAGCC 57.702 42.857 0.00 0.00 0.00 4.35
3209 3270 2.235016 ACGCCTACATTTTTCAAGCCA 58.765 42.857 0.00 0.00 0.00 4.75
3210 3271 2.825532 ACGCCTACATTTTTCAAGCCAT 59.174 40.909 0.00 0.00 0.00 4.40
3211 3272 3.181397 CGCCTACATTTTTCAAGCCATG 58.819 45.455 0.00 0.00 0.00 3.66
3212 3273 3.119531 CGCCTACATTTTTCAAGCCATGA 60.120 43.478 0.00 0.00 35.85 3.07
3213 3274 4.617995 CGCCTACATTTTTCAAGCCATGAA 60.618 41.667 0.00 0.00 46.22 2.57
3228 3289 1.808945 CATGAATATGGGCGCTTCTCC 59.191 52.381 7.64 0.00 0.00 3.71
3229 3290 0.836606 TGAATATGGGCGCTTCTCCA 59.163 50.000 7.64 6.44 37.46 3.86
3230 3291 1.421268 TGAATATGGGCGCTTCTCCAT 59.579 47.619 18.12 18.12 44.97 3.41
3231 3292 1.808945 GAATATGGGCGCTTCTCCATG 59.191 52.381 21.73 0.00 43.05 3.66
3232 3293 0.767375 ATATGGGCGCTTCTCCATGT 59.233 50.000 21.73 14.60 43.05 3.21
3233 3294 0.179048 TATGGGCGCTTCTCCATGTG 60.179 55.000 21.73 0.00 43.05 3.21
3234 3295 2.045926 GGGCGCTTCTCCATGTGT 60.046 61.111 7.64 0.00 0.00 3.72
3235 3296 1.220749 GGGCGCTTCTCCATGTGTA 59.779 57.895 7.64 0.00 0.00 2.90
3236 3297 1.090052 GGGCGCTTCTCCATGTGTAC 61.090 60.000 7.64 0.00 0.00 2.90
3237 3298 0.108138 GGCGCTTCTCCATGTGTACT 60.108 55.000 7.64 0.00 0.00 2.73
3238 3299 1.136305 GGCGCTTCTCCATGTGTACTA 59.864 52.381 7.64 0.00 0.00 1.82
3239 3300 2.418197 GGCGCTTCTCCATGTGTACTAA 60.418 50.000 7.64 0.00 0.00 2.24
3240 3301 3.259064 GCGCTTCTCCATGTGTACTAAA 58.741 45.455 0.00 0.00 0.00 1.85
3241 3302 3.871594 GCGCTTCTCCATGTGTACTAAAT 59.128 43.478 0.00 0.00 0.00 1.40
3242 3303 4.025647 GCGCTTCTCCATGTGTACTAAATC 60.026 45.833 0.00 0.00 0.00 2.17
3243 3304 5.109210 CGCTTCTCCATGTGTACTAAATCA 58.891 41.667 0.00 0.00 0.00 2.57
3244 3305 5.580691 CGCTTCTCCATGTGTACTAAATCAA 59.419 40.000 0.00 0.00 0.00 2.57
3245 3306 6.258727 CGCTTCTCCATGTGTACTAAATCAAT 59.741 38.462 0.00 0.00 0.00 2.57
3246 3307 7.438160 CGCTTCTCCATGTGTACTAAATCAATA 59.562 37.037 0.00 0.00 0.00 1.90
3247 3308 9.277783 GCTTCTCCATGTGTACTAAATCAATAT 57.722 33.333 0.00 0.00 0.00 1.28
3273 3334 5.895636 ATATCTGACATCATCTCTCGACC 57.104 43.478 0.00 0.00 0.00 4.79
3274 3335 3.004752 TCTGACATCATCTCTCGACCA 57.995 47.619 0.00 0.00 0.00 4.02
3275 3336 3.560105 TCTGACATCATCTCTCGACCAT 58.440 45.455 0.00 0.00 0.00 3.55
3276 3337 3.567585 TCTGACATCATCTCTCGACCATC 59.432 47.826 0.00 0.00 0.00 3.51
3277 3338 2.291741 TGACATCATCTCTCGACCATCG 59.708 50.000 0.00 0.00 42.10 3.84
3278 3339 1.000827 ACATCATCTCTCGACCATCGC 60.001 52.381 0.00 0.00 40.21 4.58
3279 3340 0.239613 ATCATCTCTCGACCATCGCG 59.760 55.000 0.00 0.00 40.21 5.87
3280 3341 2.013483 CATCTCTCGACCATCGCGC 61.013 63.158 0.00 0.00 40.21 6.86
3281 3342 3.200887 ATCTCTCGACCATCGCGCC 62.201 63.158 0.00 0.00 40.21 6.53
3284 3345 4.246206 CTCGACCATCGCGCCGTA 62.246 66.667 0.00 0.00 40.21 4.02
3285 3346 3.744749 CTCGACCATCGCGCCGTAA 62.745 63.158 0.00 0.00 40.21 3.18
3286 3347 2.881827 CGACCATCGCGCCGTAAA 60.882 61.111 0.00 0.00 31.14 2.01
3287 3348 2.235016 CGACCATCGCGCCGTAAAT 61.235 57.895 0.00 0.00 31.14 1.40
3288 3349 1.275657 GACCATCGCGCCGTAAATG 59.724 57.895 0.00 0.00 0.00 2.32
3289 3350 1.149361 GACCATCGCGCCGTAAATGA 61.149 55.000 0.00 0.00 0.00 2.57
3290 3351 0.531974 ACCATCGCGCCGTAAATGAT 60.532 50.000 0.00 0.00 0.00 2.45
3291 3352 0.163788 CCATCGCGCCGTAAATGATC 59.836 55.000 0.00 0.00 0.00 2.92
3292 3353 1.139989 CATCGCGCCGTAAATGATCT 58.860 50.000 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 189 7.118496 TGAAGGTGAAACATTACCAATTTGT 57.882 32.000 0.00 0.00 43.10 2.83
218 219 9.273016 CTTTAGTCTATGAACTGGAGAAACAAA 57.727 33.333 0.00 0.00 0.00 2.83
322 323 3.066621 AGAAACAAAGAAACGATGCAGCA 59.933 39.130 1.53 0.00 0.00 4.41
550 553 7.497579 TGCGAAATTAGAAGGCATTGTTATCTA 59.502 33.333 0.00 0.00 0.00 1.98
560 563 5.880332 AGAAGTATTGCGAAATTAGAAGGCA 59.120 36.000 0.00 0.00 0.00 4.75
643 646 7.335627 TGTGGTTATTCTCCTATACAAAGTGG 58.664 38.462 0.00 0.00 0.00 4.00
729 732 3.008375 CCACAGGAAAAGGTCAGAGATGA 59.992 47.826 0.00 0.00 0.00 2.92
773 776 5.946377 GGAGAGGCAGAAGGAAAAATAGAAA 59.054 40.000 0.00 0.00 0.00 2.52
784 787 1.409381 GGATTTGGGAGAGGCAGAAGG 60.409 57.143 0.00 0.00 0.00 3.46
1659 1664 3.836562 GTTTGGGACCTTAGACTGTAGGA 59.163 47.826 11.30 0.00 35.45 2.94
1852 1857 4.288531 GCATGTGCATTCTATTGCTCTTC 58.711 43.478 0.00 0.00 43.18 2.87
1924 1929 4.556233 TGTCGTGTCCAAAGATTACTCAG 58.444 43.478 0.00 0.00 0.00 3.35
2088 2095 0.267658 TAAGGGAGGCATAGGAGGCA 59.732 55.000 0.00 0.00 36.37 4.75
2133 2140 1.133823 TCCTTGAACAGCTGCCAGAAA 60.134 47.619 15.27 0.63 0.00 2.52
2253 2263 4.335647 ACGGCTTCTGGCACCTGG 62.336 66.667 0.00 0.00 44.01 4.45
2258 2268 4.069232 CCTCGACGGCTTCTGGCA 62.069 66.667 0.00 0.00 44.01 4.92
2399 2409 3.046087 CACTGCGTGCCTCTGTGG 61.046 66.667 0.00 0.00 39.35 4.17
2476 2486 1.951602 CCATTCACGTGATGATGGCAT 59.048 47.619 27.80 12.43 37.11 4.40
2484 2495 3.610040 TTCTGCTACCATTCACGTGAT 57.390 42.857 20.80 6.87 0.00 3.06
2487 2498 4.685169 CAAATTCTGCTACCATTCACGT 57.315 40.909 0.00 0.00 0.00 4.49
2536 2555 4.686554 CGTCTTCCGAATATCCTTGGAATC 59.313 45.833 0.00 0.00 39.60 2.52
2553 2572 3.032667 GCTTCCCTCCCCCGTCTTC 62.033 68.421 0.00 0.00 0.00 2.87
2558 2604 4.778143 CAACGCTTCCCTCCCCCG 62.778 72.222 0.00 0.00 0.00 5.73
2572 2618 5.456822 GCAAGAAGAACAGTGTTTGATCAAC 59.543 40.000 10.45 4.45 31.42 3.18
2673 2727 1.625616 GCACGTTACGATACTGCAGT 58.374 50.000 25.12 25.12 0.00 4.40
2808 2864 0.473755 AGCATCCACACACAACCTGA 59.526 50.000 0.00 0.00 0.00 3.86
2907 2967 5.007332 TGTTTTAGCTTCTCAGGAAACGAAC 59.993 40.000 0.00 0.00 31.53 3.95
2908 2968 5.120399 TGTTTTAGCTTCTCAGGAAACGAA 58.880 37.500 0.00 0.00 31.53 3.85
2954 3015 2.050077 AAAGAGCGCGCTTTTGCC 60.050 55.556 36.87 22.02 43.93 4.52
2980 3041 0.179163 TGCTCTGCACGTAGACGATG 60.179 55.000 9.41 4.85 43.39 3.84
3011 3072 6.183360 ACCTCGAAGCAGAGTTTTATTAATGC 60.183 38.462 0.00 0.00 36.56 3.56
3017 3078 5.875359 CCTTTACCTCGAAGCAGAGTTTTAT 59.125 40.000 0.00 0.00 36.56 1.40
3018 3079 5.235516 CCTTTACCTCGAAGCAGAGTTTTA 58.764 41.667 0.00 0.00 36.56 1.52
3019 3080 4.065789 CCTTTACCTCGAAGCAGAGTTTT 58.934 43.478 0.00 0.00 36.56 2.43
3020 3081 3.665190 CCTTTACCTCGAAGCAGAGTTT 58.335 45.455 0.00 0.00 36.56 2.66
3021 3082 2.613223 GCCTTTACCTCGAAGCAGAGTT 60.613 50.000 0.00 0.00 36.56 3.01
3022 3083 1.066787 GCCTTTACCTCGAAGCAGAGT 60.067 52.381 0.00 0.00 36.56 3.24
3023 3084 1.066858 TGCCTTTACCTCGAAGCAGAG 60.067 52.381 0.00 0.00 37.97 3.35
3024 3085 0.973632 TGCCTTTACCTCGAAGCAGA 59.026 50.000 0.00 0.00 0.00 4.26
3025 3086 1.667724 CATGCCTTTACCTCGAAGCAG 59.332 52.381 0.00 0.00 0.00 4.24
3026 3087 1.678728 CCATGCCTTTACCTCGAAGCA 60.679 52.381 0.00 0.00 0.00 3.91
3027 3088 1.017387 CCATGCCTTTACCTCGAAGC 58.983 55.000 0.00 0.00 0.00 3.86
3028 3089 2.403252 ACCATGCCTTTACCTCGAAG 57.597 50.000 0.00 0.00 0.00 3.79
3029 3090 3.985019 TTACCATGCCTTTACCTCGAA 57.015 42.857 0.00 0.00 0.00 3.71
3030 3091 3.869065 CTTTACCATGCCTTTACCTCGA 58.131 45.455 0.00 0.00 0.00 4.04
3031 3092 2.354821 GCTTTACCATGCCTTTACCTCG 59.645 50.000 0.00 0.00 0.00 4.63
3032 3093 3.352648 TGCTTTACCATGCCTTTACCTC 58.647 45.455 0.00 0.00 0.00 3.85
3033 3094 3.449746 TGCTTTACCATGCCTTTACCT 57.550 42.857 0.00 0.00 0.00 3.08
3034 3095 4.736126 AATGCTTTACCATGCCTTTACC 57.264 40.909 0.00 0.00 0.00 2.85
3035 3096 6.162777 TGAAAATGCTTTACCATGCCTTTAC 58.837 36.000 0.00 0.00 0.00 2.01
3036 3097 6.352016 TGAAAATGCTTTACCATGCCTTTA 57.648 33.333 0.00 0.00 0.00 1.85
3037 3098 5.226194 TGAAAATGCTTTACCATGCCTTT 57.774 34.783 0.00 0.00 0.00 3.11
3038 3099 4.888326 TGAAAATGCTTTACCATGCCTT 57.112 36.364 0.00 0.00 0.00 4.35
3039 3100 5.425196 AATGAAAATGCTTTACCATGCCT 57.575 34.783 0.00 0.00 0.00 4.75
3040 3101 6.105333 TGTAATGAAAATGCTTTACCATGCC 58.895 36.000 0.00 0.00 31.21 4.40
3041 3102 7.775397 ATGTAATGAAAATGCTTTACCATGC 57.225 32.000 0.00 0.00 31.21 4.06
3043 3104 9.086336 CGAAATGTAATGAAAATGCTTTACCAT 57.914 29.630 0.00 0.00 31.21 3.55
3044 3105 8.300286 TCGAAATGTAATGAAAATGCTTTACCA 58.700 29.630 0.00 0.00 31.21 3.25
3045 3106 8.682128 TCGAAATGTAATGAAAATGCTTTACC 57.318 30.769 0.00 0.00 31.21 2.85
3048 3109 9.294030 GAGATCGAAATGTAATGAAAATGCTTT 57.706 29.630 0.00 0.00 0.00 3.51
3049 3110 8.680903 AGAGATCGAAATGTAATGAAAATGCTT 58.319 29.630 0.00 0.00 0.00 3.91
3050 3111 8.218338 AGAGATCGAAATGTAATGAAAATGCT 57.782 30.769 0.00 0.00 0.00 3.79
3051 3112 7.589221 GGAGAGATCGAAATGTAATGAAAATGC 59.411 37.037 0.00 0.00 0.00 3.56
3052 3113 8.072567 GGGAGAGATCGAAATGTAATGAAAATG 58.927 37.037 0.00 0.00 0.00 2.32
3053 3114 7.041780 CGGGAGAGATCGAAATGTAATGAAAAT 60.042 37.037 0.00 0.00 0.00 1.82
3054 3115 6.257849 CGGGAGAGATCGAAATGTAATGAAAA 59.742 38.462 0.00 0.00 0.00 2.29
3055 3116 5.753438 CGGGAGAGATCGAAATGTAATGAAA 59.247 40.000 0.00 0.00 0.00 2.69
3056 3117 5.289595 CGGGAGAGATCGAAATGTAATGAA 58.710 41.667 0.00 0.00 0.00 2.57
3057 3118 4.262036 CCGGGAGAGATCGAAATGTAATGA 60.262 45.833 0.00 0.00 0.00 2.57
3058 3119 3.990469 CCGGGAGAGATCGAAATGTAATG 59.010 47.826 0.00 0.00 0.00 1.90
3059 3120 3.641906 ACCGGGAGAGATCGAAATGTAAT 59.358 43.478 6.32 0.00 0.00 1.89
3060 3121 3.028850 ACCGGGAGAGATCGAAATGTAA 58.971 45.455 6.32 0.00 0.00 2.41
3061 3122 2.662866 ACCGGGAGAGATCGAAATGTA 58.337 47.619 6.32 0.00 0.00 2.29
3062 3123 1.486211 ACCGGGAGAGATCGAAATGT 58.514 50.000 6.32 0.00 0.00 2.71
3063 3124 2.205074 CAACCGGGAGAGATCGAAATG 58.795 52.381 6.32 0.00 0.00 2.32
3064 3125 1.831736 ACAACCGGGAGAGATCGAAAT 59.168 47.619 6.32 0.00 0.00 2.17
3065 3126 1.203994 GACAACCGGGAGAGATCGAAA 59.796 52.381 6.32 0.00 0.00 3.46
3066 3127 0.815734 GACAACCGGGAGAGATCGAA 59.184 55.000 6.32 0.00 0.00 3.71
3067 3128 0.034380 AGACAACCGGGAGAGATCGA 60.034 55.000 6.32 0.00 0.00 3.59
3068 3129 1.676746 TAGACAACCGGGAGAGATCG 58.323 55.000 6.32 0.00 0.00 3.69
3069 3130 4.467198 TTTTAGACAACCGGGAGAGATC 57.533 45.455 6.32 0.00 0.00 2.75
3070 3131 4.286291 ACTTTTTAGACAACCGGGAGAGAT 59.714 41.667 6.32 0.00 0.00 2.75
3071 3132 3.644738 ACTTTTTAGACAACCGGGAGAGA 59.355 43.478 6.32 0.00 0.00 3.10
3072 3133 3.746492 CACTTTTTAGACAACCGGGAGAG 59.254 47.826 6.32 0.00 0.00 3.20
3073 3134 3.495453 CCACTTTTTAGACAACCGGGAGA 60.495 47.826 6.32 0.00 0.00 3.71
3074 3135 2.812011 CCACTTTTTAGACAACCGGGAG 59.188 50.000 6.32 0.00 0.00 4.30
3075 3136 2.173143 ACCACTTTTTAGACAACCGGGA 59.827 45.455 6.32 0.00 0.00 5.14
3076 3137 2.578786 ACCACTTTTTAGACAACCGGG 58.421 47.619 6.32 0.00 0.00 5.73
3077 3138 5.754543 TTTACCACTTTTTAGACAACCGG 57.245 39.130 0.00 0.00 0.00 5.28
3078 3139 7.041644 TGAGATTTACCACTTTTTAGACAACCG 60.042 37.037 0.00 0.00 0.00 4.44
3079 3140 8.161699 TGAGATTTACCACTTTTTAGACAACC 57.838 34.615 0.00 0.00 0.00 3.77
3080 3141 7.803659 GCTGAGATTTACCACTTTTTAGACAAC 59.196 37.037 0.00 0.00 0.00 3.32
3081 3142 7.040686 GGCTGAGATTTACCACTTTTTAGACAA 60.041 37.037 0.00 0.00 0.00 3.18
3082 3143 6.430000 GGCTGAGATTTACCACTTTTTAGACA 59.570 38.462 0.00 0.00 0.00 3.41
3083 3144 6.430000 TGGCTGAGATTTACCACTTTTTAGAC 59.570 38.462 0.00 0.00 0.00 2.59
3084 3145 6.539173 TGGCTGAGATTTACCACTTTTTAGA 58.461 36.000 0.00 0.00 0.00 2.10
3085 3146 6.817765 TGGCTGAGATTTACCACTTTTTAG 57.182 37.500 0.00 0.00 0.00 1.85
3093 3154 3.193267 GCAAATGTGGCTGAGATTTACCA 59.807 43.478 0.00 0.00 0.00 3.25
3094 3155 3.445096 AGCAAATGTGGCTGAGATTTACC 59.555 43.478 0.00 0.00 40.80 2.85
3095 3156 4.708726 AGCAAATGTGGCTGAGATTTAC 57.291 40.909 0.00 0.00 40.80 2.01
3096 3157 5.744171 TCTAGCAAATGTGGCTGAGATTTA 58.256 37.500 0.00 0.00 42.62 1.40
3097 3158 4.592942 TCTAGCAAATGTGGCTGAGATTT 58.407 39.130 0.00 0.00 42.62 2.17
3098 3159 4.226427 TCTAGCAAATGTGGCTGAGATT 57.774 40.909 0.00 0.00 42.62 2.40
3099 3160 3.920231 TCTAGCAAATGTGGCTGAGAT 57.080 42.857 0.00 0.00 42.62 2.75
3100 3161 3.701205 TTCTAGCAAATGTGGCTGAGA 57.299 42.857 0.00 0.00 42.62 3.27
3101 3162 4.201990 GGATTTCTAGCAAATGTGGCTGAG 60.202 45.833 0.00 0.00 42.62 3.35
3102 3163 3.696051 GGATTTCTAGCAAATGTGGCTGA 59.304 43.478 0.00 0.00 42.62 4.26
3103 3164 3.444742 TGGATTTCTAGCAAATGTGGCTG 59.555 43.478 0.00 0.00 42.62 4.85
3104 3165 3.700538 TGGATTTCTAGCAAATGTGGCT 58.299 40.909 5.29 0.00 45.18 4.75
3105 3166 4.454728 TTGGATTTCTAGCAAATGTGGC 57.545 40.909 5.29 0.00 0.00 5.01
3106 3167 4.866486 GCTTTGGATTTCTAGCAAATGTGG 59.134 41.667 5.29 0.00 33.88 4.17
3107 3168 4.866486 GGCTTTGGATTTCTAGCAAATGTG 59.134 41.667 0.00 0.00 35.36 3.21
3108 3169 4.774200 AGGCTTTGGATTTCTAGCAAATGT 59.226 37.500 0.00 0.00 35.36 2.71
3109 3170 5.334724 AGGCTTTGGATTTCTAGCAAATG 57.665 39.130 0.00 0.00 35.36 2.32
3110 3171 6.608808 ACATAGGCTTTGGATTTCTAGCAAAT 59.391 34.615 9.76 1.33 35.36 2.32
3111 3172 5.951747 ACATAGGCTTTGGATTTCTAGCAAA 59.048 36.000 9.76 0.00 35.36 3.68
3112 3173 5.509498 ACATAGGCTTTGGATTTCTAGCAA 58.491 37.500 9.76 0.00 35.36 3.91
3113 3174 5.116084 ACATAGGCTTTGGATTTCTAGCA 57.884 39.130 9.76 0.00 35.36 3.49
3114 3175 4.212214 CGACATAGGCTTTGGATTTCTAGC 59.788 45.833 9.76 0.00 0.00 3.42
3115 3176 4.752101 CCGACATAGGCTTTGGATTTCTAG 59.248 45.833 9.76 0.00 0.00 2.43
3116 3177 4.703897 CCGACATAGGCTTTGGATTTCTA 58.296 43.478 9.76 0.00 0.00 2.10
3117 3178 3.545703 CCGACATAGGCTTTGGATTTCT 58.454 45.455 9.76 0.00 0.00 2.52
3118 3179 3.971032 CCGACATAGGCTTTGGATTTC 57.029 47.619 9.76 0.00 0.00 2.17
3129 3190 5.598416 TTATCTCATATGGCCGACATAGG 57.402 43.478 2.13 0.00 44.79 2.57
3130 3191 5.917447 CGATTATCTCATATGGCCGACATAG 59.083 44.000 2.13 0.00 44.79 2.23
3131 3192 5.592688 TCGATTATCTCATATGGCCGACATA 59.407 40.000 2.13 0.00 45.60 2.29
3132 3193 4.402474 TCGATTATCTCATATGGCCGACAT 59.598 41.667 2.13 0.00 43.68 3.06
3133 3194 3.761752 TCGATTATCTCATATGGCCGACA 59.238 43.478 2.13 0.00 0.00 4.35
3134 3195 4.371855 TCGATTATCTCATATGGCCGAC 57.628 45.455 2.13 0.00 0.00 4.79
3135 3196 5.351458 CAATCGATTATCTCATATGGCCGA 58.649 41.667 10.97 2.81 0.00 5.54
3136 3197 4.025396 GCAATCGATTATCTCATATGGCCG 60.025 45.833 10.97 0.00 0.00 6.13
3137 3198 4.025396 CGCAATCGATTATCTCATATGGCC 60.025 45.833 10.97 0.00 38.10 5.36
3138 3199 4.568359 ACGCAATCGATTATCTCATATGGC 59.432 41.667 10.97 5.09 39.41 4.40
3139 3200 5.807011 TCACGCAATCGATTATCTCATATGG 59.193 40.000 10.97 0.00 39.41 2.74
3140 3201 6.875926 TCACGCAATCGATTATCTCATATG 57.124 37.500 10.97 0.00 39.41 1.78
3141 3202 7.260603 TCATCACGCAATCGATTATCTCATAT 58.739 34.615 10.97 0.00 39.41 1.78
3142 3203 6.620678 TCATCACGCAATCGATTATCTCATA 58.379 36.000 10.97 0.00 39.41 2.15
3143 3204 5.473039 TCATCACGCAATCGATTATCTCAT 58.527 37.500 10.97 0.00 39.41 2.90
3144 3205 4.870363 TCATCACGCAATCGATTATCTCA 58.130 39.130 10.97 0.00 39.41 3.27
3145 3206 5.829233 TTCATCACGCAATCGATTATCTC 57.171 39.130 10.97 0.00 39.41 2.75
3146 3207 5.050091 GGTTTCATCACGCAATCGATTATCT 60.050 40.000 10.97 0.00 39.41 1.98
3147 3208 5.050091 AGGTTTCATCACGCAATCGATTATC 60.050 40.000 10.97 4.98 39.41 1.75
3148 3209 4.816385 AGGTTTCATCACGCAATCGATTAT 59.184 37.500 10.97 0.00 39.41 1.28
3149 3210 4.188462 AGGTTTCATCACGCAATCGATTA 58.812 39.130 10.97 0.00 39.41 1.75
3150 3211 3.009723 AGGTTTCATCACGCAATCGATT 58.990 40.909 4.39 4.39 39.41 3.34
3151 3212 2.632377 AGGTTTCATCACGCAATCGAT 58.368 42.857 0.00 0.00 39.41 3.59
3152 3213 2.093306 AGGTTTCATCACGCAATCGA 57.907 45.000 0.00 0.00 39.41 3.59
3153 3214 3.670203 GTTAGGTTTCATCACGCAATCG 58.330 45.455 0.00 0.00 42.43 3.34
3154 3215 3.369756 TCGTTAGGTTTCATCACGCAATC 59.630 43.478 0.00 0.00 0.00 2.67
3155 3216 3.124636 GTCGTTAGGTTTCATCACGCAAT 59.875 43.478 0.00 0.00 0.00 3.56
3156 3217 2.477375 GTCGTTAGGTTTCATCACGCAA 59.523 45.455 0.00 0.00 0.00 4.85
3157 3218 2.063266 GTCGTTAGGTTTCATCACGCA 58.937 47.619 0.00 0.00 0.00 5.24
3158 3219 1.392510 GGTCGTTAGGTTTCATCACGC 59.607 52.381 0.00 0.00 0.00 5.34
3159 3220 2.955614 AGGTCGTTAGGTTTCATCACG 58.044 47.619 0.00 0.00 0.00 4.35
3160 3221 4.312443 TGAAGGTCGTTAGGTTTCATCAC 58.688 43.478 0.00 0.00 0.00 3.06
3161 3222 4.610605 TGAAGGTCGTTAGGTTTCATCA 57.389 40.909 0.00 0.00 0.00 3.07
3162 3223 5.469084 ACTTTGAAGGTCGTTAGGTTTCATC 59.531 40.000 0.00 0.00 0.00 2.92
3163 3224 5.374071 ACTTTGAAGGTCGTTAGGTTTCAT 58.626 37.500 0.00 0.00 0.00 2.57
3164 3225 4.773013 ACTTTGAAGGTCGTTAGGTTTCA 58.227 39.130 0.00 0.00 0.00 2.69
3165 3226 6.849588 TTACTTTGAAGGTCGTTAGGTTTC 57.150 37.500 0.00 0.00 0.00 2.78
3166 3227 6.238184 CGTTTACTTTGAAGGTCGTTAGGTTT 60.238 38.462 0.00 0.00 0.00 3.27
3167 3228 5.234972 CGTTTACTTTGAAGGTCGTTAGGTT 59.765 40.000 0.00 0.00 0.00 3.50
3168 3229 4.746611 CGTTTACTTTGAAGGTCGTTAGGT 59.253 41.667 0.00 0.00 0.00 3.08
3169 3230 4.376717 GCGTTTACTTTGAAGGTCGTTAGG 60.377 45.833 0.00 0.00 0.00 2.69
3170 3231 4.376717 GGCGTTTACTTTGAAGGTCGTTAG 60.377 45.833 0.00 0.00 0.00 2.34
3171 3232 3.494251 GGCGTTTACTTTGAAGGTCGTTA 59.506 43.478 0.00 0.00 0.00 3.18
3172 3233 2.288729 GGCGTTTACTTTGAAGGTCGTT 59.711 45.455 0.00 0.00 0.00 3.85
3173 3234 1.869132 GGCGTTTACTTTGAAGGTCGT 59.131 47.619 0.00 0.00 0.00 4.34
3174 3235 2.140717 AGGCGTTTACTTTGAAGGTCG 58.859 47.619 0.00 0.00 0.00 4.79
3175 3236 4.060205 TGTAGGCGTTTACTTTGAAGGTC 58.940 43.478 0.00 0.00 0.00 3.85
3176 3237 4.075963 TGTAGGCGTTTACTTTGAAGGT 57.924 40.909 0.00 0.00 0.00 3.50
3177 3238 5.622770 AATGTAGGCGTTTACTTTGAAGG 57.377 39.130 0.00 0.00 0.00 3.46
3178 3239 7.646130 TGAAAAATGTAGGCGTTTACTTTGAAG 59.354 33.333 0.00 0.00 33.79 3.02
3179 3240 7.481642 TGAAAAATGTAGGCGTTTACTTTGAA 58.518 30.769 0.00 0.00 33.79 2.69
3180 3241 7.028926 TGAAAAATGTAGGCGTTTACTTTGA 57.971 32.000 0.00 0.00 33.79 2.69
3181 3242 7.566868 GCTTGAAAAATGTAGGCGTTTACTTTG 60.567 37.037 0.00 0.00 33.79 2.77
3182 3243 6.419710 GCTTGAAAAATGTAGGCGTTTACTTT 59.580 34.615 0.00 0.00 33.79 2.66
3183 3244 5.918576 GCTTGAAAAATGTAGGCGTTTACTT 59.081 36.000 0.00 0.00 33.79 2.24
3184 3245 5.458015 GCTTGAAAAATGTAGGCGTTTACT 58.542 37.500 0.00 0.00 33.79 2.24
3185 3246 4.619760 GGCTTGAAAAATGTAGGCGTTTAC 59.380 41.667 0.00 0.00 33.79 2.01
3186 3247 4.278669 TGGCTTGAAAAATGTAGGCGTTTA 59.721 37.500 0.00 0.00 36.10 2.01
3187 3248 3.068873 TGGCTTGAAAAATGTAGGCGTTT 59.931 39.130 0.00 0.00 36.10 3.60
3188 3249 2.625790 TGGCTTGAAAAATGTAGGCGTT 59.374 40.909 0.00 0.00 36.10 4.84
3189 3250 2.235016 TGGCTTGAAAAATGTAGGCGT 58.765 42.857 0.00 0.00 36.10 5.68
3190 3251 3.119531 TCATGGCTTGAAAAATGTAGGCG 60.120 43.478 0.00 0.00 36.10 5.52
3191 3252 4.454728 TCATGGCTTGAAAAATGTAGGC 57.545 40.909 0.00 0.00 0.00 3.93
3208 3269 1.808945 GGAGAAGCGCCCATATTCATG 59.191 52.381 2.29 0.00 0.00 3.07
3209 3270 1.421268 TGGAGAAGCGCCCATATTCAT 59.579 47.619 2.29 0.00 0.00 2.57
3210 3271 0.836606 TGGAGAAGCGCCCATATTCA 59.163 50.000 2.29 0.00 0.00 2.57
3211 3272 1.808945 CATGGAGAAGCGCCCATATTC 59.191 52.381 14.47 6.88 40.95 1.75
3212 3273 1.143684 ACATGGAGAAGCGCCCATATT 59.856 47.619 14.47 3.80 40.95 1.28
3213 3274 0.767375 ACATGGAGAAGCGCCCATAT 59.233 50.000 14.47 2.09 40.95 1.78
3214 3275 0.179048 CACATGGAGAAGCGCCCATA 60.179 55.000 14.47 0.00 40.95 2.74
3215 3276 1.452651 CACATGGAGAAGCGCCCAT 60.453 57.895 2.29 6.98 43.51 4.00
3216 3277 1.549243 TACACATGGAGAAGCGCCCA 61.549 55.000 2.29 4.24 36.79 5.36
3217 3278 1.090052 GTACACATGGAGAAGCGCCC 61.090 60.000 2.29 0.00 0.00 6.13
3218 3279 0.108138 AGTACACATGGAGAAGCGCC 60.108 55.000 2.29 0.00 0.00 6.53
3219 3280 2.579207 TAGTACACATGGAGAAGCGC 57.421 50.000 0.00 0.00 0.00 5.92
3220 3281 5.109210 TGATTTAGTACACATGGAGAAGCG 58.891 41.667 0.00 0.00 0.00 4.68
3221 3282 6.985188 TTGATTTAGTACACATGGAGAAGC 57.015 37.500 0.00 0.00 0.00 3.86
3247 3308 9.114952 GGTCGAGAGATGATGTCAGATATATTA 57.885 37.037 0.00 0.00 45.19 0.98
3248 3309 7.613411 TGGTCGAGAGATGATGTCAGATATATT 59.387 37.037 0.00 0.00 45.19 1.28
3249 3310 7.115414 TGGTCGAGAGATGATGTCAGATATAT 58.885 38.462 0.00 0.00 45.19 0.86
3250 3311 6.476378 TGGTCGAGAGATGATGTCAGATATA 58.524 40.000 0.00 0.00 45.19 0.86
3251 3312 5.320277 TGGTCGAGAGATGATGTCAGATAT 58.680 41.667 0.00 0.00 45.19 1.63
3252 3313 4.718961 TGGTCGAGAGATGATGTCAGATA 58.281 43.478 0.00 0.00 45.19 1.98
3253 3314 3.560105 TGGTCGAGAGATGATGTCAGAT 58.440 45.455 0.00 0.00 45.19 2.90
3254 3315 3.004752 TGGTCGAGAGATGATGTCAGA 57.995 47.619 0.00 0.00 45.19 3.27
3255 3316 3.608941 CGATGGTCGAGAGATGATGTCAG 60.609 52.174 0.00 0.00 43.74 3.51
3256 3317 2.291741 CGATGGTCGAGAGATGATGTCA 59.708 50.000 0.00 0.00 43.74 3.58
3257 3318 2.920227 GCGATGGTCGAGAGATGATGTC 60.920 54.545 3.20 0.00 43.74 3.06
3258 3319 1.000827 GCGATGGTCGAGAGATGATGT 60.001 52.381 3.20 0.00 43.74 3.06
3259 3320 1.695813 GCGATGGTCGAGAGATGATG 58.304 55.000 3.20 0.00 43.74 3.07
3260 3321 0.239613 CGCGATGGTCGAGAGATGAT 59.760 55.000 0.00 0.00 43.74 2.45
3261 3322 1.649267 CGCGATGGTCGAGAGATGA 59.351 57.895 0.00 0.00 43.74 2.92
3262 3323 2.013483 GCGCGATGGTCGAGAGATG 61.013 63.158 12.10 0.00 43.74 2.90
3263 3324 2.333225 GCGCGATGGTCGAGAGAT 59.667 61.111 12.10 0.00 43.74 2.75
3264 3325 3.889044 GGCGCGATGGTCGAGAGA 61.889 66.667 12.10 0.00 43.74 3.10
3267 3328 3.744749 TTACGGCGCGATGGTCGAG 62.745 63.158 12.10 0.83 43.74 4.04
3268 3329 2.616786 ATTTACGGCGCGATGGTCGA 62.617 55.000 12.10 0.00 43.74 4.20
3269 3330 2.235016 ATTTACGGCGCGATGGTCG 61.235 57.895 12.10 7.51 43.89 4.79
3270 3331 1.149361 TCATTTACGGCGCGATGGTC 61.149 55.000 12.10 0.00 0.00 4.02
3271 3332 0.531974 ATCATTTACGGCGCGATGGT 60.532 50.000 12.10 6.30 0.00 3.55
3272 3333 0.163788 GATCATTTACGGCGCGATGG 59.836 55.000 12.10 0.00 0.00 3.51
3273 3334 1.139989 AGATCATTTACGGCGCGATG 58.860 50.000 12.10 9.13 0.00 3.84
3274 3335 3.588277 AGATCATTTACGGCGCGAT 57.412 47.368 12.10 0.99 0.00 4.58


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

AutoCloner maintained by Alex Coulton.