Multiple sequence alignment - TraesCS1D01G294800

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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 TraesCS1D01G294800 chr1D 100.000 3108 0 0 1 3108 393928118 393931225 0.000000e+00 5740
1 TraesCS1D01G294800 chr1D 95.385 130 6 0 2979 3108 355655746 355655875 1.130000e-49 207
2 TraesCS1D01G294800 chr1D 96.032 126 5 0 2982 3107 301131919 301131794 4.060000e-49 206
3 TraesCS1D01G294800 chr1B 93.279 3050 134 34 1 2989 528399178 528396139 0.000000e+00 4431
4 TraesCS1D01G294800 chr1A 91.690 2118 96 24 13 2069 491313093 491310995 0.000000e+00 2863
5 TraesCS1D01G294800 chr1A 91.937 893 42 16 2110 2979 491310985 491310100 0.000000e+00 1223
6 TraesCS1D01G294800 chr1A 94.656 131 7 0 2978 3108 171397896 171398026 1.460000e-48 204
7 TraesCS1D01G294800 chr7A 95.385 130 6 0 2979 3108 589484813 589484684 1.130000e-49 207
8 TraesCS1D01G294800 chr3A 96.063 127 5 0 2982 3108 391606110 391605984 1.130000e-49 207
9 TraesCS1D01G294800 chr6A 94.656 131 7 0 2978 3108 222957227 222957097 1.460000e-48 204
10 TraesCS1D01G294800 chr6A 94.656 131 7 0 2978 3108 296450410 296450280 1.460000e-48 204
11 TraesCS1D01G294800 chr6D 95.276 127 6 0 2979 3105 165493559 165493685 5.260000e-48 202
12 TraesCS1D01G294800 chr4D 94.615 130 7 0 2979 3108 60255741 60255870 5.260000e-48 202


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 TraesCS1D01G294800 chr1D 393928118 393931225 3107 False 5740 5740 100.0000 1 3108 1 chr1D.!!$F2 3107
1 TraesCS1D01G294800 chr1B 528396139 528399178 3039 True 4431 4431 93.2790 1 2989 1 chr1B.!!$R1 2988
2 TraesCS1D01G294800 chr1A 491310100 491313093 2993 True 2043 2863 91.8135 13 2979 2 chr1A.!!$R1 2966

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
798 835 1.070786 TTATCGAAGCGGGGATGCC 59.929 57.895 0.0 0.0 34.65 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2640 2757 0.099613 ATACACGCGTGAGAGCTGAG 59.9 55.0 42.94 16.02 34.4 3.35 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
35 36 6.150396 ACATCGGTTAATTTTCCAACAACA 57.850 33.333 0.00 0.00 0.00 3.33
103 110 8.954950 AAAAATGTGAACATGTCCATACAAAA 57.045 26.923 0.00 0.00 39.58 2.44
131 143 7.833285 AAGCCATAACTAAGGAAAACTCAAA 57.167 32.000 0.00 0.00 0.00 2.69
136 148 7.962918 CCATAACTAAGGAAAACTCAAATCACG 59.037 37.037 0.00 0.00 0.00 4.35
265 282 7.546250 ACCAAGAGATGAAAGAAGAAGAGTA 57.454 36.000 0.00 0.00 0.00 2.59
281 299 8.567285 AAGAAGAGTATCGAAAAATGATGGTT 57.433 30.769 0.00 0.00 42.67 3.67
440 458 3.513515 AGGCCACAACAAACTGAAAAAGA 59.486 39.130 5.01 0.00 0.00 2.52
523 542 2.034842 CGGAAGCGAACACGATAATCAC 60.035 50.000 0.00 0.00 0.00 3.06
585 622 5.355596 CAGCTAAGGAAGGTAATGACTCTG 58.644 45.833 0.00 0.00 33.59 3.35
613 650 1.167851 TACCCTCCGCGTAATATCGG 58.832 55.000 4.92 0.00 46.52 4.18
670 707 1.603802 CCGCATTAACGCTCCATTCAT 59.396 47.619 0.00 0.00 0.00 2.57
729 766 4.863548 TCGAGGTCTCCTTCCAATACTAA 58.136 43.478 0.00 0.00 31.76 2.24
735 772 7.699878 AGGTCTCCTTCCAATACTAAATTTGT 58.300 34.615 0.00 0.00 0.00 2.83
776 813 4.976116 GCACTCAAGTTTAATGCGTTTCTT 59.024 37.500 0.00 0.00 0.00 2.52
798 835 1.070786 TTATCGAAGCGGGGATGCC 59.929 57.895 0.00 0.00 34.65 4.40
835 872 4.562789 CGATCTCACAAAATCTAAGCACGA 59.437 41.667 0.00 0.00 0.00 4.35
863 900 7.483691 CGCCTATTTTGTGTTATAGTCCAAAAC 59.516 37.037 0.00 0.00 38.98 2.43
929 966 9.214957 TGTGTATCTTATCGAATTCTTTTGTGT 57.785 29.630 3.52 0.00 0.00 3.72
935 972 9.226606 TCTTATCGAATTCTTTTGTGTTATGGT 57.773 29.630 3.52 0.00 0.00 3.55
957 1005 6.378564 TGGTAAATTGAAAGTTTGTGAGGTGA 59.621 34.615 0.00 0.00 0.00 4.02
962 1010 5.913137 TGAAAGTTTGTGAGGTGATGTTT 57.087 34.783 0.00 0.00 0.00 2.83
977 1025 5.869344 GGTGATGTTTCCTAAAATTCTTGGC 59.131 40.000 0.00 0.00 0.00 4.52
986 1036 5.187576 TCCTAAAATTCTTGGCAAATCCCTG 59.812 40.000 0.00 0.00 0.00 4.45
1024 1074 6.987404 TGTTTAAATAGGCTGGGTTTTCAAAC 59.013 34.615 0.00 5.54 38.17 2.93
1091 1148 2.070654 AAAGCGCAGACAAAACCCCG 62.071 55.000 11.47 0.00 0.00 5.73
1165 1226 4.664677 AAGACGCGCGCTTCCAGT 62.665 61.111 30.84 20.38 0.00 4.00
1181 1242 1.616994 CCAGTTCCAAATCCTCCCCAC 60.617 57.143 0.00 0.00 0.00 4.61
1239 1300 0.909610 TTCTCCATCGCCTCCCACTT 60.910 55.000 0.00 0.00 0.00 3.16
1399 1460 1.139947 GGAGCTAGAGGTGCACGTC 59.860 63.158 27.81 27.81 33.94 4.34
1786 1850 2.358247 GACGGGAGCGGCAAGAAA 60.358 61.111 1.45 0.00 0.00 2.52
2013 2080 1.257743 TGCCCAGCTCGATATACTCC 58.742 55.000 0.00 0.00 0.00 3.85
2054 2121 7.121315 AGTCAAACTAGTTCAAACTTCAAAGCT 59.879 33.333 8.95 0.00 40.37 3.74
2076 2143 2.423538 GGTTACACCATTGGCTTAGCTG 59.576 50.000 3.59 0.00 38.42 4.24
2085 2152 1.995626 GGCTTAGCTGGGGTCTGGA 60.996 63.158 3.59 0.00 0.00 3.86
2094 2161 0.401395 TGGGGTCTGGACAGGAGTTT 60.401 55.000 3.10 0.00 0.00 2.66
2161 2233 3.097342 AGATTTGCTGCTCATTTCCCT 57.903 42.857 0.00 0.00 0.00 4.20
2202 2274 1.616865 TGGACGAACCAGACGAGAATT 59.383 47.619 0.00 0.00 44.64 2.17
2357 2455 2.310966 TGTTTGCGCACGCGACATA 61.311 52.632 15.93 5.37 45.51 2.29
2417 2515 3.394836 GGCGTGAAGGGGAGAGCT 61.395 66.667 0.00 0.00 0.00 4.09
2428 2526 1.344191 GGGAGAGCTTCATCTGGCCT 61.344 60.000 3.32 0.00 0.00 5.19
2429 2527 0.106521 GGAGAGCTTCATCTGGCCTC 59.893 60.000 3.32 0.00 0.00 4.70
2430 2528 1.122227 GAGAGCTTCATCTGGCCTCT 58.878 55.000 3.32 0.00 0.00 3.69
2431 2529 1.069049 GAGAGCTTCATCTGGCCTCTC 59.931 57.143 3.32 0.01 0.00 3.20
2604 2719 1.059913 GTAGGGTGGGATCATGGGAG 58.940 60.000 0.00 0.00 0.00 4.30
2614 2729 2.639065 GATCATGGGAGTTTAACGGCA 58.361 47.619 0.00 0.00 0.00 5.69
2640 2757 3.718210 GATGGGTCTCGTCGTGCCC 62.718 68.421 15.53 15.53 41.42 5.36
2694 2815 2.973899 GTCTGCGGCAGGAAGAGA 59.026 61.111 28.18 6.70 31.51 3.10
2696 2817 0.739112 GTCTGCGGCAGGAAGAGAAG 60.739 60.000 28.18 1.86 31.51 2.85
2853 2976 2.595463 GCTTGGCTCACAGCACCA 60.595 61.111 0.00 0.00 44.75 4.17
2903 3027 1.301637 CACACGCACCTGGTCATCA 60.302 57.895 0.00 0.00 0.00 3.07
2911 3035 0.761187 ACCTGGTCATCATGGATCGG 59.239 55.000 0.00 0.00 0.00 4.18
2939 3063 3.255379 GCGCGCCACACTACTAGC 61.255 66.667 23.24 0.00 0.00 3.42
2941 3065 2.577059 GCGCCACACTACTAGCCA 59.423 61.111 0.00 0.00 0.00 4.75
2974 3098 1.354337 GCTCGATCGTGCTTGCTTCA 61.354 55.000 29.31 0.46 0.00 3.02
2980 3104 0.391228 TCGTGCTTGCTTCACTGGTA 59.609 50.000 0.00 0.00 32.54 3.25
2982 3106 0.519077 GTGCTTGCTTCACTGGTAGC 59.481 55.000 0.00 0.00 37.87 3.58
2985 3109 1.609061 GCTTGCTTCACTGGTAGCTCA 60.609 52.381 0.00 0.00 38.18 4.26
2989 3113 2.104792 TGCTTCACTGGTAGCTCACTTT 59.895 45.455 0.00 0.00 38.18 2.66
2990 3114 3.323691 TGCTTCACTGGTAGCTCACTTTA 59.676 43.478 0.00 0.00 38.18 1.85
2991 3115 4.020218 TGCTTCACTGGTAGCTCACTTTAT 60.020 41.667 0.00 0.00 38.18 1.40
2992 3116 4.568760 GCTTCACTGGTAGCTCACTTTATC 59.431 45.833 0.00 0.00 34.87 1.75
2993 3117 4.737855 TCACTGGTAGCTCACTTTATCC 57.262 45.455 0.00 0.00 0.00 2.59
2994 3118 3.451178 TCACTGGTAGCTCACTTTATCCC 59.549 47.826 0.00 0.00 0.00 3.85
2995 3119 3.197766 CACTGGTAGCTCACTTTATCCCA 59.802 47.826 0.00 0.00 0.00 4.37
2996 3120 3.452627 ACTGGTAGCTCACTTTATCCCAG 59.547 47.826 0.00 0.00 43.02 4.45
2997 3121 3.450904 TGGTAGCTCACTTTATCCCAGT 58.549 45.455 0.00 0.00 0.00 4.00
2998 3122 3.197766 TGGTAGCTCACTTTATCCCAGTG 59.802 47.826 0.00 0.00 42.74 3.66
2999 3123 3.451178 GGTAGCTCACTTTATCCCAGTGA 59.549 47.826 0.00 2.91 46.81 3.41
3005 3129 5.055265 TCACTTTATCCCAGTGAAAACCA 57.945 39.130 0.21 0.00 46.16 3.67
3006 3130 5.640147 TCACTTTATCCCAGTGAAAACCAT 58.360 37.500 0.21 0.00 46.16 3.55
3007 3131 6.074648 TCACTTTATCCCAGTGAAAACCATT 58.925 36.000 0.21 0.00 46.16 3.16
3008 3132 6.553100 TCACTTTATCCCAGTGAAAACCATTT 59.447 34.615 0.21 0.00 46.16 2.32
3009 3133 7.726291 TCACTTTATCCCAGTGAAAACCATTTA 59.274 33.333 0.21 0.00 46.16 1.40
3010 3134 8.531146 CACTTTATCCCAGTGAAAACCATTTAT 58.469 33.333 0.00 0.00 43.90 1.40
3011 3135 9.762381 ACTTTATCCCAGTGAAAACCATTTATA 57.238 29.630 0.00 0.00 0.00 0.98
3013 3137 6.693315 ATCCCAGTGAAAACCATTTATACG 57.307 37.500 0.00 0.00 0.00 3.06
3014 3138 5.806818 TCCCAGTGAAAACCATTTATACGA 58.193 37.500 0.00 0.00 0.00 3.43
3015 3139 5.878116 TCCCAGTGAAAACCATTTATACGAG 59.122 40.000 0.00 0.00 0.00 4.18
3016 3140 5.646360 CCCAGTGAAAACCATTTATACGAGT 59.354 40.000 0.00 0.00 0.00 4.18
3017 3141 6.403200 CCCAGTGAAAACCATTTATACGAGTG 60.403 42.308 0.00 0.00 0.00 3.51
3018 3142 6.021596 CAGTGAAAACCATTTATACGAGTGC 58.978 40.000 0.00 0.00 0.00 4.40
3019 3143 5.019498 GTGAAAACCATTTATACGAGTGCG 58.981 41.667 0.00 0.00 44.79 5.34
3020 3144 4.930405 TGAAAACCATTTATACGAGTGCGA 59.070 37.500 0.00 0.00 41.64 5.10
3021 3145 5.408909 TGAAAACCATTTATACGAGTGCGAA 59.591 36.000 0.00 0.00 41.64 4.70
3022 3146 5.464965 AAACCATTTATACGAGTGCGAAG 57.535 39.130 0.00 0.00 41.64 3.79
3023 3147 4.119442 ACCATTTATACGAGTGCGAAGT 57.881 40.909 0.00 0.00 41.64 3.01
3024 3148 4.501071 ACCATTTATACGAGTGCGAAGTT 58.499 39.130 0.00 0.00 41.64 2.66
3025 3149 4.328983 ACCATTTATACGAGTGCGAAGTTG 59.671 41.667 0.00 0.00 41.64 3.16
3026 3150 4.260212 CCATTTATACGAGTGCGAAGTTGG 60.260 45.833 0.00 0.00 41.64 3.77
3027 3151 1.917273 TATACGAGTGCGAAGTTGGC 58.083 50.000 2.45 2.45 41.64 4.52
3028 3152 0.739813 ATACGAGTGCGAAGTTGGCC 60.740 55.000 7.45 0.00 41.64 5.36
3029 3153 2.089887 TACGAGTGCGAAGTTGGCCA 62.090 55.000 0.00 0.00 41.64 5.36
3030 3154 2.250939 CGAGTGCGAAGTTGGCCAA 61.251 57.895 16.05 16.05 40.82 4.52
3031 3155 1.576421 GAGTGCGAAGTTGGCCAAG 59.424 57.895 21.21 8.42 0.00 3.61
3032 3156 0.884704 GAGTGCGAAGTTGGCCAAGA 60.885 55.000 21.21 0.00 0.00 3.02
3033 3157 0.250901 AGTGCGAAGTTGGCCAAGAT 60.251 50.000 21.21 10.97 0.00 2.40
3034 3158 1.003118 AGTGCGAAGTTGGCCAAGATA 59.997 47.619 21.21 0.00 0.00 1.98
3035 3159 2.017049 GTGCGAAGTTGGCCAAGATAT 58.983 47.619 21.21 5.06 0.00 1.63
3036 3160 3.118408 AGTGCGAAGTTGGCCAAGATATA 60.118 43.478 21.21 0.89 0.00 0.86
3037 3161 3.815401 GTGCGAAGTTGGCCAAGATATAT 59.185 43.478 21.21 0.99 0.00 0.86
3038 3162 4.994852 GTGCGAAGTTGGCCAAGATATATA 59.005 41.667 21.21 0.00 0.00 0.86
3039 3163 5.643777 GTGCGAAGTTGGCCAAGATATATAT 59.356 40.000 21.21 0.00 0.00 0.86
3040 3164 5.643348 TGCGAAGTTGGCCAAGATATATATG 59.357 40.000 21.21 3.27 0.00 1.78
3041 3165 5.874810 GCGAAGTTGGCCAAGATATATATGA 59.125 40.000 21.21 0.00 0.00 2.15
3042 3166 6.540189 GCGAAGTTGGCCAAGATATATATGAT 59.460 38.462 21.21 0.00 0.00 2.45
3043 3167 7.254590 GCGAAGTTGGCCAAGATATATATGATC 60.255 40.741 21.21 1.63 0.00 2.92
3044 3168 7.765819 CGAAGTTGGCCAAGATATATATGATCA 59.234 37.037 21.21 0.00 0.00 2.92
3045 3169 9.107177 GAAGTTGGCCAAGATATATATGATCAG 57.893 37.037 21.21 0.00 0.00 2.90
3046 3170 7.571919 AGTTGGCCAAGATATATATGATCAGG 58.428 38.462 21.21 0.00 0.00 3.86
3047 3171 7.404104 AGTTGGCCAAGATATATATGATCAGGA 59.596 37.037 21.21 0.00 0.00 3.86
3048 3172 7.942733 TGGCCAAGATATATATGATCAGGAT 57.057 36.000 0.61 0.00 0.00 3.24
3049 3173 7.971201 TGGCCAAGATATATATGATCAGGATC 58.029 38.462 0.61 2.30 38.29 3.36
3050 3174 7.095910 GGCCAAGATATATATGATCAGGATCG 58.904 42.308 0.09 0.00 40.63 3.69
3051 3175 7.256119 GGCCAAGATATATATGATCAGGATCGT 60.256 40.741 0.09 8.87 40.63 3.73
3052 3176 8.797438 GCCAAGATATATATGATCAGGATCGTA 58.203 37.037 12.29 12.29 41.83 3.43
3059 3183 3.650070 TGATCAGGATCGTATGTCTGC 57.350 47.619 4.93 0.00 40.63 4.26
3060 3184 2.958355 TGATCAGGATCGTATGTCTGCA 59.042 45.455 4.93 0.00 40.63 4.41
3061 3185 3.575687 TGATCAGGATCGTATGTCTGCAT 59.424 43.478 4.93 0.00 40.63 3.96
3062 3186 3.375782 TCAGGATCGTATGTCTGCATG 57.624 47.619 0.00 0.00 36.58 4.06
3063 3187 2.036346 TCAGGATCGTATGTCTGCATGG 59.964 50.000 0.00 0.00 36.58 3.66
3064 3188 2.036346 CAGGATCGTATGTCTGCATGGA 59.964 50.000 0.00 0.00 36.58 3.41
3065 3189 2.298446 AGGATCGTATGTCTGCATGGAG 59.702 50.000 8.12 8.12 36.58 3.86
3066 3190 2.036475 GGATCGTATGTCTGCATGGAGT 59.964 50.000 14.43 0.00 36.58 3.85
3067 3191 3.493350 GGATCGTATGTCTGCATGGAGTT 60.493 47.826 14.43 3.50 36.58 3.01
3068 3192 3.165058 TCGTATGTCTGCATGGAGTTC 57.835 47.619 14.43 9.28 36.58 3.01
3069 3193 2.760650 TCGTATGTCTGCATGGAGTTCT 59.239 45.455 14.43 2.64 36.58 3.01
3070 3194 2.862536 CGTATGTCTGCATGGAGTTCTG 59.137 50.000 14.43 0.00 36.58 3.02
3071 3195 3.429410 CGTATGTCTGCATGGAGTTCTGA 60.429 47.826 14.43 0.00 36.58 3.27
3072 3196 2.756840 TGTCTGCATGGAGTTCTGAG 57.243 50.000 14.43 0.00 0.00 3.35
3073 3197 1.277273 TGTCTGCATGGAGTTCTGAGG 59.723 52.381 14.43 0.00 0.00 3.86
3074 3198 1.552337 GTCTGCATGGAGTTCTGAGGA 59.448 52.381 14.43 0.00 0.00 3.71
3075 3199 1.552337 TCTGCATGGAGTTCTGAGGAC 59.448 52.381 14.43 0.00 0.00 3.85
3076 3200 0.615331 TGCATGGAGTTCTGAGGACC 59.385 55.000 0.00 0.00 0.00 4.46
3077 3201 0.615331 GCATGGAGTTCTGAGGACCA 59.385 55.000 0.00 0.00 35.09 4.02
3078 3202 1.211457 GCATGGAGTTCTGAGGACCAT 59.789 52.381 0.00 0.00 41.25 3.55
3079 3203 2.744494 GCATGGAGTTCTGAGGACCATC 60.744 54.545 0.00 0.00 38.99 3.51
3080 3204 1.186200 TGGAGTTCTGAGGACCATCG 58.814 55.000 0.00 0.00 0.00 3.84
3081 3205 1.187087 GGAGTTCTGAGGACCATCGT 58.813 55.000 0.00 0.00 0.00 3.73
3082 3206 2.291346 TGGAGTTCTGAGGACCATCGTA 60.291 50.000 0.00 0.00 0.00 3.43
3083 3207 2.959707 GGAGTTCTGAGGACCATCGTAT 59.040 50.000 0.00 0.00 0.00 3.06
3084 3208 3.004944 GGAGTTCTGAGGACCATCGTATC 59.995 52.174 0.00 0.00 0.00 2.24
3085 3209 3.632333 AGTTCTGAGGACCATCGTATCA 58.368 45.455 0.00 0.00 0.00 2.15
3086 3210 3.634448 AGTTCTGAGGACCATCGTATCAG 59.366 47.826 0.00 0.00 37.30 2.90
3087 3211 3.577805 TCTGAGGACCATCGTATCAGA 57.422 47.619 5.07 5.07 40.24 3.27
3088 3212 4.105754 TCTGAGGACCATCGTATCAGAT 57.894 45.455 5.07 0.00 38.81 2.90
3089 3213 5.242795 TCTGAGGACCATCGTATCAGATA 57.757 43.478 5.07 0.00 38.81 1.98
3090 3214 5.249420 TCTGAGGACCATCGTATCAGATAG 58.751 45.833 5.07 0.00 38.81 2.08
3091 3215 4.336280 TGAGGACCATCGTATCAGATAGG 58.664 47.826 4.00 4.00 0.00 2.57
3092 3216 3.697045 GAGGACCATCGTATCAGATAGGG 59.303 52.174 9.73 3.77 0.00 3.53
3093 3217 2.761208 GGACCATCGTATCAGATAGGGG 59.239 54.545 9.73 6.98 0.00 4.79
3094 3218 2.761208 GACCATCGTATCAGATAGGGGG 59.239 54.545 9.73 12.77 0.00 5.40
3095 3219 2.382305 ACCATCGTATCAGATAGGGGGA 59.618 50.000 19.95 6.06 0.00 4.81
3096 3220 2.761208 CCATCGTATCAGATAGGGGGAC 59.239 54.545 9.73 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.013464 TGTTGTTGGAAAATTAACCGATGTACT 59.987 33.333 0.00 0.00 0.00 2.73
131 143 5.630415 TCCCTATTTTCTTGATCCGTGAT 57.370 39.130 0.00 0.00 0.00 3.06
136 148 7.255277 GCATGTACTTCCCTATTTTCTTGATCC 60.255 40.741 0.00 0.00 0.00 3.36
265 282 9.226606 TCAGTTTACTAACCATCATTTTTCGAT 57.773 29.630 0.00 0.00 34.71 3.59
281 299 4.420522 AAACCCGGTGTTCAGTTTACTA 57.579 40.909 0.00 0.00 35.67 1.82
440 458 4.821805 ACCTTTGATTGAATTGTGACGACT 59.178 37.500 0.00 0.00 0.00 4.18
523 542 1.653114 CAATTATTGGTTTGCGCCACG 59.347 47.619 4.18 0.00 38.42 4.94
585 622 1.861971 CGCGGAGGGTAAAATAGTCC 58.138 55.000 0.00 0.00 34.98 3.85
613 650 4.647964 TGCGCATAAAGACTTTCGAATTC 58.352 39.130 5.66 0.00 0.00 2.17
670 707 8.774183 ACCATTAAAATGTACCCACTATCTACA 58.226 33.333 2.25 0.00 34.60 2.74
735 772 8.840833 TTGAGTGCGCTATATCCAAATAATTA 57.159 30.769 9.73 0.00 0.00 1.40
776 813 1.052124 ATCCCCGCTTCGATAACCCA 61.052 55.000 0.00 0.00 0.00 4.51
835 872 5.121105 GGACTATAACACAAAATAGGCGGT 58.879 41.667 0.00 0.00 34.96 5.68
928 965 9.191995 CCTCACAAACTTTCAATTTACCATAAC 57.808 33.333 0.00 0.00 0.00 1.89
929 966 8.919145 ACCTCACAAACTTTCAATTTACCATAA 58.081 29.630 0.00 0.00 0.00 1.90
931 968 7.069331 TCACCTCACAAACTTTCAATTTACCAT 59.931 33.333 0.00 0.00 0.00 3.55
932 969 6.378564 TCACCTCACAAACTTTCAATTTACCA 59.621 34.615 0.00 0.00 0.00 3.25
933 970 6.801575 TCACCTCACAAACTTTCAATTTACC 58.198 36.000 0.00 0.00 0.00 2.85
934 971 7.920682 ACATCACCTCACAAACTTTCAATTTAC 59.079 33.333 0.00 0.00 0.00 2.01
935 972 8.006298 ACATCACCTCACAAACTTTCAATTTA 57.994 30.769 0.00 0.00 0.00 1.40
957 1005 7.607607 GGATTTGCCAAGAATTTTAGGAAACAT 59.392 33.333 0.00 0.00 36.34 2.71
962 1010 5.187576 CAGGGATTTGCCAAGAATTTTAGGA 59.812 40.000 0.00 0.00 38.95 2.94
1024 1074 3.523668 GGGTTTTATGGGGCGCGG 61.524 66.667 8.83 0.00 0.00 6.46
1026 1076 2.717044 GGTGGGTTTTATGGGGCGC 61.717 63.158 0.00 0.00 0.00 6.53
1165 1226 0.778078 TGGGTGGGGAGGATTTGGAA 60.778 55.000 0.00 0.00 0.00 3.53
1239 1300 0.326618 GATGTCCTTGAGGGAGGGGA 60.327 60.000 0.00 0.00 46.10 4.81
1399 1460 1.668101 GGGAGGTGGAGTAGAGCACG 61.668 65.000 0.00 0.00 0.00 5.34
1606 1667 4.671590 TGGACCTCCTCGACGCCA 62.672 66.667 0.00 0.00 36.82 5.69
1778 1842 0.944311 TCGTCGCTCTGTTTCTTGCC 60.944 55.000 0.00 0.00 0.00 4.52
1786 1850 3.432588 CCGTCCTCGTCGCTCTGT 61.433 66.667 0.00 0.00 35.01 3.41
1846 1913 3.011517 AAGAGGCAGTCCGGGCAT 61.012 61.111 9.71 0.00 37.47 4.40
1897 1964 0.888619 TCAGTTACTGGACAGCCGAG 59.111 55.000 12.79 0.00 36.79 4.63
2035 2102 5.757850 ACCAGCTTTGAAGTTTGAACTAG 57.242 39.130 0.00 0.00 38.57 2.57
2076 2143 0.771755 AAAACTCCTGTCCAGACCCC 59.228 55.000 0.00 0.00 0.00 4.95
2108 2177 9.284968 AGTTGTAATGCCGAAGCTAAATTATAT 57.715 29.630 0.00 0.00 40.80 0.86
2357 2455 1.694150 AGCTGCATGGGTATATCGTGT 59.306 47.619 1.02 0.00 0.00 4.49
2417 2515 0.841961 CATGGGAGAGGCCAGATGAA 59.158 55.000 5.01 0.00 38.95 2.57
2428 2526 0.109153 CATCGGGCAATCATGGGAGA 59.891 55.000 0.00 0.00 0.00 3.71
2429 2527 0.179009 ACATCGGGCAATCATGGGAG 60.179 55.000 0.00 0.00 0.00 4.30
2430 2528 0.258484 AACATCGGGCAATCATGGGA 59.742 50.000 0.00 0.00 0.00 4.37
2431 2529 1.067516 GAAACATCGGGCAATCATGGG 59.932 52.381 0.00 0.00 0.00 4.00
2604 2719 1.240256 TCATGTGGGTGCCGTTAAAC 58.760 50.000 0.00 0.00 0.00 2.01
2640 2757 0.099613 ATACACGCGTGAGAGCTGAG 59.900 55.000 42.94 16.02 34.40 3.35
2853 2976 1.748122 CATGGCGCAGAAGGCTCTT 60.748 57.895 10.83 0.00 41.67 2.85
2903 3027 4.552365 CGTGCTGGGCCGATCCAT 62.552 66.667 0.00 0.00 36.05 3.41
2932 3056 1.139058 ACGAATGGGCTTGGCTAGTAG 59.861 52.381 0.00 0.00 0.00 2.57
2939 3063 1.982073 GAGCGAACGAATGGGCTTGG 61.982 60.000 0.00 0.00 35.54 3.61
2941 3065 2.100631 CGAGCGAACGAATGGGCTT 61.101 57.895 0.00 0.00 35.54 4.35
2974 3098 3.450904 TGGGATAAAGTGAGCTACCAGT 58.549 45.455 0.00 0.00 0.00 4.00
2985 3109 6.994421 AAATGGTTTTCACTGGGATAAAGT 57.006 33.333 0.00 0.00 0.00 2.66
2989 3113 7.566569 TCGTATAAATGGTTTTCACTGGGATA 58.433 34.615 0.00 0.00 0.00 2.59
2990 3114 6.419791 TCGTATAAATGGTTTTCACTGGGAT 58.580 36.000 0.00 0.00 0.00 3.85
2991 3115 5.806818 TCGTATAAATGGTTTTCACTGGGA 58.193 37.500 0.00 0.00 0.00 4.37
2992 3116 5.646360 ACTCGTATAAATGGTTTTCACTGGG 59.354 40.000 0.00 0.00 0.00 4.45
2993 3117 6.542852 CACTCGTATAAATGGTTTTCACTGG 58.457 40.000 0.00 0.00 0.00 4.00
2994 3118 6.021596 GCACTCGTATAAATGGTTTTCACTG 58.978 40.000 0.00 0.00 0.00 3.66
2995 3119 5.163893 CGCACTCGTATAAATGGTTTTCACT 60.164 40.000 0.00 0.00 0.00 3.41
2996 3120 5.019498 CGCACTCGTATAAATGGTTTTCAC 58.981 41.667 0.00 0.00 0.00 3.18
2997 3121 4.930405 TCGCACTCGTATAAATGGTTTTCA 59.070 37.500 0.00 0.00 36.96 2.69
2998 3122 5.459110 TCGCACTCGTATAAATGGTTTTC 57.541 39.130 0.00 0.00 36.96 2.29
2999 3123 5.410439 ACTTCGCACTCGTATAAATGGTTTT 59.590 36.000 0.00 0.00 36.96 2.43
3000 3124 4.933400 ACTTCGCACTCGTATAAATGGTTT 59.067 37.500 0.00 0.00 36.96 3.27
3001 3125 4.501071 ACTTCGCACTCGTATAAATGGTT 58.499 39.130 0.00 0.00 36.96 3.67
3002 3126 4.119442 ACTTCGCACTCGTATAAATGGT 57.881 40.909 0.00 0.00 36.96 3.55
3003 3127 4.260212 CCAACTTCGCACTCGTATAAATGG 60.260 45.833 0.00 0.00 36.96 3.16
3004 3128 4.782195 GCCAACTTCGCACTCGTATAAATG 60.782 45.833 0.00 0.00 36.96 2.32
3005 3129 3.308866 GCCAACTTCGCACTCGTATAAAT 59.691 43.478 0.00 0.00 36.96 1.40
3006 3130 2.669434 GCCAACTTCGCACTCGTATAAA 59.331 45.455 0.00 0.00 36.96 1.40
3007 3131 2.264813 GCCAACTTCGCACTCGTATAA 58.735 47.619 0.00 0.00 36.96 0.98
3008 3132 1.470285 GGCCAACTTCGCACTCGTATA 60.470 52.381 0.00 0.00 36.96 1.47
3009 3133 0.739813 GGCCAACTTCGCACTCGTAT 60.740 55.000 0.00 0.00 36.96 3.06
3010 3134 1.373748 GGCCAACTTCGCACTCGTA 60.374 57.895 0.00 0.00 36.96 3.43
3011 3135 2.665185 GGCCAACTTCGCACTCGT 60.665 61.111 0.00 0.00 36.96 4.18
3012 3136 2.175184 CTTGGCCAACTTCGCACTCG 62.175 60.000 16.05 0.00 0.00 4.18
3013 3137 0.884704 TCTTGGCCAACTTCGCACTC 60.885 55.000 16.05 0.00 0.00 3.51
3014 3138 0.250901 ATCTTGGCCAACTTCGCACT 60.251 50.000 16.05 0.00 0.00 4.40
3015 3139 1.448985 TATCTTGGCCAACTTCGCAC 58.551 50.000 16.05 0.00 0.00 5.34
3016 3140 2.418368 ATATCTTGGCCAACTTCGCA 57.582 45.000 16.05 0.00 0.00 5.10
3017 3141 5.874810 TCATATATATCTTGGCCAACTTCGC 59.125 40.000 16.05 0.00 0.00 4.70
3018 3142 7.765819 TGATCATATATATCTTGGCCAACTTCG 59.234 37.037 16.05 4.90 0.00 3.79
3019 3143 9.107177 CTGATCATATATATCTTGGCCAACTTC 57.893 37.037 16.05 0.00 0.00 3.01
3020 3144 8.051535 CCTGATCATATATATCTTGGCCAACTT 58.948 37.037 16.05 7.40 0.00 2.66
3021 3145 7.404104 TCCTGATCATATATATCTTGGCCAACT 59.596 37.037 16.05 7.60 0.00 3.16
3022 3146 7.568349 TCCTGATCATATATATCTTGGCCAAC 58.432 38.462 16.05 0.00 0.00 3.77
3023 3147 7.754091 TCCTGATCATATATATCTTGGCCAA 57.246 36.000 19.25 19.25 0.00 4.52
3024 3148 7.256083 CGATCCTGATCATATATATCTTGGCCA 60.256 40.741 0.00 0.00 37.69 5.36
3025 3149 7.095910 CGATCCTGATCATATATATCTTGGCC 58.904 42.308 0.00 0.00 37.69 5.36
3026 3150 7.665690 ACGATCCTGATCATATATATCTTGGC 58.334 38.462 7.82 0.00 37.69 4.52
3033 3157 8.787852 GCAGACATACGATCCTGATCATATATA 58.212 37.037 7.82 0.00 37.69 0.86
3034 3158 7.286316 TGCAGACATACGATCCTGATCATATAT 59.714 37.037 7.82 0.00 37.69 0.86
3035 3159 6.603201 TGCAGACATACGATCCTGATCATATA 59.397 38.462 7.82 0.00 37.69 0.86
3036 3160 5.420104 TGCAGACATACGATCCTGATCATAT 59.580 40.000 7.82 0.00 37.69 1.78
3037 3161 4.766891 TGCAGACATACGATCCTGATCATA 59.233 41.667 7.82 0.00 37.69 2.15
3038 3162 3.575687 TGCAGACATACGATCCTGATCAT 59.424 43.478 7.82 0.00 37.69 2.45
3039 3163 2.958355 TGCAGACATACGATCCTGATCA 59.042 45.455 7.82 0.00 37.69 2.92
3040 3164 3.650070 TGCAGACATACGATCCTGATC 57.350 47.619 0.00 0.00 34.56 2.92
3041 3165 3.306571 CCATGCAGACATACGATCCTGAT 60.307 47.826 0.00 0.00 33.67 2.90
3042 3166 2.036346 CCATGCAGACATACGATCCTGA 59.964 50.000 0.00 0.00 33.67 3.86
3043 3167 2.036346 TCCATGCAGACATACGATCCTG 59.964 50.000 0.00 0.00 33.67 3.86
3044 3168 2.298446 CTCCATGCAGACATACGATCCT 59.702 50.000 0.00 0.00 33.67 3.24
3045 3169 2.036475 ACTCCATGCAGACATACGATCC 59.964 50.000 0.00 0.00 33.67 3.36
3046 3170 3.377346 ACTCCATGCAGACATACGATC 57.623 47.619 0.00 0.00 33.67 3.69
3047 3171 3.386078 AGAACTCCATGCAGACATACGAT 59.614 43.478 0.00 0.00 33.67 3.73
3048 3172 2.760650 AGAACTCCATGCAGACATACGA 59.239 45.455 0.00 0.00 33.67 3.43
3049 3173 2.862536 CAGAACTCCATGCAGACATACG 59.137 50.000 0.00 0.00 33.67 3.06
3050 3174 4.118410 CTCAGAACTCCATGCAGACATAC 58.882 47.826 0.00 0.00 33.67 2.39
3051 3175 3.133542 CCTCAGAACTCCATGCAGACATA 59.866 47.826 0.00 0.00 33.67 2.29
3052 3176 2.093075 CCTCAGAACTCCATGCAGACAT 60.093 50.000 0.00 0.00 36.79 3.06
3053 3177 1.277273 CCTCAGAACTCCATGCAGACA 59.723 52.381 0.00 0.00 0.00 3.41
3054 3178 1.552337 TCCTCAGAACTCCATGCAGAC 59.448 52.381 0.00 0.00 0.00 3.51
3055 3179 1.552337 GTCCTCAGAACTCCATGCAGA 59.448 52.381 0.00 0.00 0.00 4.26
3056 3180 1.406614 GGTCCTCAGAACTCCATGCAG 60.407 57.143 0.00 0.00 0.00 4.41
3057 3181 0.615331 GGTCCTCAGAACTCCATGCA 59.385 55.000 0.00 0.00 0.00 3.96
3058 3182 0.615331 TGGTCCTCAGAACTCCATGC 59.385 55.000 0.00 0.00 0.00 4.06
3059 3183 2.482664 CGATGGTCCTCAGAACTCCATG 60.483 54.545 0.00 0.00 38.74 3.66
3060 3184 1.759445 CGATGGTCCTCAGAACTCCAT 59.241 52.381 0.00 0.00 40.92 3.41
3061 3185 1.186200 CGATGGTCCTCAGAACTCCA 58.814 55.000 0.00 0.00 0.00 3.86
3062 3186 1.187087 ACGATGGTCCTCAGAACTCC 58.813 55.000 0.00 0.00 0.00 3.85
3063 3187 3.632604 TGATACGATGGTCCTCAGAACTC 59.367 47.826 0.00 0.00 0.00 3.01
3064 3188 3.632333 TGATACGATGGTCCTCAGAACT 58.368 45.455 0.00 0.00 0.00 3.01
3065 3189 3.632604 TCTGATACGATGGTCCTCAGAAC 59.367 47.826 15.96 0.00 39.86 3.01
3066 3190 3.898482 TCTGATACGATGGTCCTCAGAA 58.102 45.455 15.96 5.24 39.86 3.02
3067 3191 3.577805 TCTGATACGATGGTCCTCAGA 57.422 47.619 14.93 14.93 40.20 3.27
3068 3192 4.397730 CCTATCTGATACGATGGTCCTCAG 59.602 50.000 11.75 11.75 37.39 3.35
3069 3193 4.336280 CCTATCTGATACGATGGTCCTCA 58.664 47.826 0.00 0.00 0.00 3.86
3070 3194 3.697045 CCCTATCTGATACGATGGTCCTC 59.303 52.174 0.00 0.00 0.00 3.71
3071 3195 3.564571 CCCCTATCTGATACGATGGTCCT 60.565 52.174 0.00 0.00 0.00 3.85
3072 3196 2.761208 CCCCTATCTGATACGATGGTCC 59.239 54.545 0.00 0.00 0.00 4.46
3073 3197 2.761208 CCCCCTATCTGATACGATGGTC 59.239 54.545 0.00 0.00 0.00 4.02
3074 3198 2.382305 TCCCCCTATCTGATACGATGGT 59.618 50.000 0.00 0.00 0.00 3.55
3075 3199 2.761208 GTCCCCCTATCTGATACGATGG 59.239 54.545 0.00 0.00 0.00 3.51
3076 3200 2.761208 GGTCCCCCTATCTGATACGATG 59.239 54.545 0.00 0.00 0.00 3.84
3077 3201 2.292323 GGGTCCCCCTATCTGATACGAT 60.292 54.545 0.00 0.00 41.34 3.73
3078 3202 1.076677 GGGTCCCCCTATCTGATACGA 59.923 57.143 0.00 0.00 41.34 3.43
3079 3203 1.203137 TGGGTCCCCCTATCTGATACG 60.203 57.143 5.13 0.00 45.70 3.06
3080 3204 2.158143 ACTGGGTCCCCCTATCTGATAC 60.158 54.545 5.13 0.00 45.70 2.24
3081 3205 2.161624 ACTGGGTCCCCCTATCTGATA 58.838 52.381 5.13 0.00 45.70 2.15
3082 3206 0.952659 ACTGGGTCCCCCTATCTGAT 59.047 55.000 5.13 0.00 45.70 2.90
3083 3207 0.722676 AACTGGGTCCCCCTATCTGA 59.277 55.000 5.13 0.00 45.70 3.27
3084 3208 1.596496 AAACTGGGTCCCCCTATCTG 58.404 55.000 5.13 0.00 45.70 2.90
3085 3209 2.321296 AGTAAACTGGGTCCCCCTATCT 59.679 50.000 5.13 0.00 45.70 1.98
3086 3210 2.772930 AGTAAACTGGGTCCCCCTATC 58.227 52.381 5.13 0.00 45.70 2.08
3087 3211 2.984989 AGTAAACTGGGTCCCCCTAT 57.015 50.000 5.13 0.00 45.70 2.57
3088 3212 2.747083 AAGTAAACTGGGTCCCCCTA 57.253 50.000 5.13 0.00 45.70 3.53
3089 3213 3.610896 AAGTAAACTGGGTCCCCCT 57.389 52.632 5.13 0.00 45.70 4.79


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

AutoCloner maintained by Alex Coulton.