Multiple sequence alignment - TraesCS5D01G078800

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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 TraesCS5D01G078800 chr5D 100.000 3260 0 0 1 3260 78803257 78806516 0.000000e+00 6021
1 TraesCS5D01G078800 chr5A 94.861 3016 103 21 1 2977 74947196 74950198 0.000000e+00 4663
2 TraesCS5D01G078800 chr5B 95.049 2969 94 15 1 2926 88357405 88360363 0.000000e+00 4619
3 TraesCS5D01G078800 chr5B 73.842 367 66 19 1635 1989 88745401 88745749 5.710000e-23 119
4 TraesCS5D01G078800 chr6A 91.770 972 73 5 360 1326 173604972 173605941 0.000000e+00 1345
5 TraesCS5D01G078800 chr4B 72.685 648 127 42 1620 2241 78604477 78603854 1.560000e-38 171
6 TraesCS5D01G078800 chr4D 72.377 648 129 42 1620 2241 53751926 53751303 3.370000e-35 159
7 TraesCS5D01G078800 chr4A 72.160 625 120 44 1635 2241 543375294 543375882 1.220000e-29 141


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 TraesCS5D01G078800 chr5D 78803257 78806516 3259 False 6021 6021 100.000 1 3260 1 chr5D.!!$F1 3259
1 TraesCS5D01G078800 chr5A 74947196 74950198 3002 False 4663 4663 94.861 1 2977 1 chr5A.!!$F1 2976
2 TraesCS5D01G078800 chr5B 88357405 88360363 2958 False 4619 4619 95.049 1 2926 1 chr5B.!!$F1 2925
3 TraesCS5D01G078800 chr6A 173604972 173605941 969 False 1345 1345 91.770 360 1326 1 chr6A.!!$F1 966

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
765 776 0.029834 CATGGCTGTTGCTAATCGCC 59.970 55.0 0.0 0.0 41.06 5.54 F
1014 1025 0.043183 TCTCAATGGAGGCTGGAGGA 59.957 55.0 0.0 0.0 41.69 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2175 2191 0.464870 CATCAGAGCTGAGGACCTGG 59.535 60.0 0.00 0.0 43.36 4.45 R
3005 3062 0.037046 GGAAAACCGGAGCGTCCTAA 60.037 55.0 9.46 0.0 33.30 2.69 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
99 101 2.422597 TCAGTACATTTTGCTGGTCCG 58.577 47.619 0.00 0.00 38.44 4.79
101 103 3.007074 TCAGTACATTTTGCTGGTCCGTA 59.993 43.478 0.00 0.00 38.44 4.02
102 104 3.938963 CAGTACATTTTGCTGGTCCGTAT 59.061 43.478 0.00 0.00 34.41 3.06
103 105 4.394920 CAGTACATTTTGCTGGTCCGTATT 59.605 41.667 0.00 0.00 34.41 1.89
117 119 4.156008 GGTCCGTATTTCACTGCATTTCTT 59.844 41.667 0.00 0.00 0.00 2.52
125 127 4.057406 TCACTGCATTTCTTTGGTTTGG 57.943 40.909 0.00 0.00 0.00 3.28
152 154 6.479990 GCTGTTGGCAGAAACTTATTTTTCTT 59.520 34.615 0.00 0.00 42.09 2.52
156 158 9.308318 GTTGGCAGAAACTTATTTTTCTTTGTA 57.692 29.630 0.00 0.00 42.09 2.41
250 255 5.016831 GGATACCAACCTCCAAAATCTTGT 58.983 41.667 0.00 0.00 0.00 3.16
385 394 9.579932 AGTTCTTAAGAATGTTCAGATTCCTTT 57.420 29.630 20.41 0.00 36.33 3.11
708 719 6.566197 ACCAGCAGTTGAAATTCTCTAAAG 57.434 37.500 0.00 0.00 0.00 1.85
765 776 0.029834 CATGGCTGTTGCTAATCGCC 59.970 55.000 0.00 0.00 41.06 5.54
898 909 4.455877 ACAGTATAAAAGCACCTGAACTGC 59.544 41.667 0.00 0.00 37.25 4.40
955 966 2.460853 CCAACCACACTCCCCAGGT 61.461 63.158 0.00 0.00 35.47 4.00
963 974 1.072930 ACTCCCCAGGTCACCCTTT 60.073 57.895 0.00 0.00 39.89 3.11
1014 1025 0.043183 TCTCAATGGAGGCTGGAGGA 59.957 55.000 0.00 0.00 41.69 3.71
1056 1067 0.893270 CCATGTTTGACTTCCCGCCA 60.893 55.000 0.00 0.00 0.00 5.69
1104 1115 2.437897 CTGCTTGGCACCTTCCCT 59.562 61.111 0.00 0.00 33.79 4.20
1171 1182 3.431415 TCCCATCCATCCTACTATGACG 58.569 50.000 0.00 0.00 0.00 4.35
1212 1223 2.621338 TGTAGTGACAGCAATGCTAGC 58.379 47.619 7.70 8.10 36.40 3.42
1233 1244 0.881118 GCTTTGCTGTTCCATCCGAA 59.119 50.000 0.00 0.00 0.00 4.30
1285 1296 4.489771 CCCTGGGCATCACGTCCC 62.490 72.222 0.00 3.07 39.41 4.46
1286 1297 3.402681 CCTGGGCATCACGTCCCT 61.403 66.667 11.08 0.00 39.41 4.20
1326 1340 4.704833 GTCCAGGAGCAAGGCGCA 62.705 66.667 10.83 0.00 46.13 6.09
1350 1364 4.656112 ACCGAGTTTCTGAATATGATCCCT 59.344 41.667 0.00 0.00 0.00 4.20
1352 1366 6.015010 ACCGAGTTTCTGAATATGATCCCTAG 60.015 42.308 0.00 0.00 0.00 3.02
1370 1384 5.103728 TCCCTAGCATTTCCCATGATTTGTA 60.104 40.000 0.00 0.00 0.00 2.41
1372 1386 5.010012 CCTAGCATTTCCCATGATTTGTACC 59.990 44.000 0.00 0.00 0.00 3.34
1768 1784 1.486310 CCTCTATGCAAGGGTACTGCA 59.514 52.381 10.32 10.32 43.04 4.41
1795 1811 4.462508 TCATCTCTTTCGCATCTGAAGT 57.537 40.909 0.00 0.00 0.00 3.01
1796 1812 5.582689 TCATCTCTTTCGCATCTGAAGTA 57.417 39.130 0.00 0.00 0.00 2.24
1797 1813 5.344066 TCATCTCTTTCGCATCTGAAGTAC 58.656 41.667 0.00 0.00 0.00 2.73
1798 1814 5.126222 TCATCTCTTTCGCATCTGAAGTACT 59.874 40.000 0.00 0.00 0.00 2.73
2109 2125 3.492313 GCAGTTGCTCAATTTAGTTCGG 58.508 45.455 0.00 0.00 38.21 4.30
2148 2164 3.891400 CCATGGCGGACATTGCGG 61.891 66.667 0.00 0.00 37.84 5.69
2167 2183 3.518634 GGCTGACGAATTTCTCTCTCT 57.481 47.619 0.00 0.00 0.00 3.10
2168 2184 3.855858 GGCTGACGAATTTCTCTCTCTT 58.144 45.455 0.00 0.00 0.00 2.85
2169 2185 5.000012 GGCTGACGAATTTCTCTCTCTTA 58.000 43.478 0.00 0.00 0.00 2.10
2175 2191 9.965748 CTGACGAATTTCTCTCTCTTAAATTTC 57.034 33.333 0.00 0.00 33.99 2.17
2241 2257 1.544724 ACAACGGGATGAACATTGGG 58.455 50.000 0.00 0.00 0.00 4.12
2335 2358 5.292101 CGAGTTCTCCACTAACCATTCAATC 59.708 44.000 0.00 0.00 35.01 2.67
2425 2448 2.755952 AAACTTGTGAAGAGGCCCTT 57.244 45.000 0.00 1.90 37.93 3.95
2634 2673 9.066892 ACTTTAAGATAAATGACTGAAACTGCA 57.933 29.630 0.00 0.00 0.00 4.41
2641 2680 6.833342 AAATGACTGAAACTGCAAAATCAC 57.167 33.333 0.00 0.00 0.00 3.06
2679 2718 6.022315 TCATAATTTTTGGGGGACACAATCT 58.978 36.000 0.00 0.00 0.00 2.40
2784 2840 2.795231 AACCATGCATGTAGCTGACT 57.205 45.000 24.58 0.58 45.94 3.41
2918 2974 4.619863 GCACAAATCATGCACTCTCCATTT 60.620 41.667 0.00 0.00 42.88 2.32
2928 2984 5.229423 TGCACTCTCCATTTTAACATTTGC 58.771 37.500 0.00 0.00 0.00 3.68
2977 3034 6.538945 TGAAAATAGGGTTTATTTCAGGCC 57.461 37.500 0.00 0.00 36.99 5.19
2978 3035 5.126384 TGAAAATAGGGTTTATTTCAGGCCG 59.874 40.000 0.00 0.00 36.99 6.13
2979 3036 2.721425 TAGGGTTTATTTCAGGCCGG 57.279 50.000 0.00 0.00 0.00 6.13
2980 3037 0.683179 AGGGTTTATTTCAGGCCGGC 60.683 55.000 21.18 21.18 0.00 6.13
2981 3038 1.672854 GGGTTTATTTCAGGCCGGCC 61.673 60.000 39.29 39.29 0.00 6.13
2982 3039 0.968393 GGTTTATTTCAGGCCGGCCA 60.968 55.000 45.13 27.20 38.92 5.36
2983 3040 0.172578 GTTTATTTCAGGCCGGCCAC 59.827 55.000 45.13 28.37 38.92 5.01
2984 3041 0.251386 TTTATTTCAGGCCGGCCACA 60.251 50.000 45.13 29.30 38.92 4.17
2985 3042 0.963355 TTATTTCAGGCCGGCCACAC 60.963 55.000 45.13 20.70 38.92 3.82
2986 3043 2.130821 TATTTCAGGCCGGCCACACA 62.131 55.000 45.13 27.21 38.92 3.72
2987 3044 2.992817 ATTTCAGGCCGGCCACACAA 62.993 55.000 45.13 30.54 38.92 3.33
2988 3045 4.641645 TCAGGCCGGCCACACAAG 62.642 66.667 45.13 26.22 38.92 3.16
2991 3048 4.740822 GGCCGGCCACACAAGGAT 62.741 66.667 40.73 0.00 35.81 3.24
2992 3049 3.443045 GCCGGCCACACAAGGATG 61.443 66.667 18.11 0.00 0.00 3.51
2993 3050 3.443045 CCGGCCACACAAGGATGC 61.443 66.667 2.24 0.00 0.00 3.91
2994 3051 3.803082 CGGCCACACAAGGATGCG 61.803 66.667 2.24 0.00 0.00 4.73
2995 3052 2.359850 GGCCACACAAGGATGCGA 60.360 61.111 0.00 0.00 0.00 5.10
2996 3053 1.750399 GGCCACACAAGGATGCGAT 60.750 57.895 0.00 0.00 0.00 4.58
2997 3054 1.718757 GGCCACACAAGGATGCGATC 61.719 60.000 0.00 0.00 0.00 3.69
2998 3055 1.026182 GCCACACAAGGATGCGATCA 61.026 55.000 0.00 0.00 0.00 2.92
2999 3056 1.671979 CCACACAAGGATGCGATCAT 58.328 50.000 0.00 0.00 35.17 2.45
3000 3057 2.019249 CCACACAAGGATGCGATCATT 58.981 47.619 0.00 0.00 32.89 2.57
3001 3058 2.424601 CCACACAAGGATGCGATCATTT 59.575 45.455 0.00 0.00 29.75 2.32
3002 3059 3.488047 CCACACAAGGATGCGATCATTTC 60.488 47.826 0.00 0.00 29.75 2.17
3003 3060 3.127376 CACACAAGGATGCGATCATTTCA 59.873 43.478 0.00 0.00 29.75 2.69
3004 3061 3.758023 ACACAAGGATGCGATCATTTCAA 59.242 39.130 0.00 0.00 29.75 2.69
3005 3062 4.400251 ACACAAGGATGCGATCATTTCAAT 59.600 37.500 0.00 0.00 29.75 2.57
3006 3063 5.105635 ACACAAGGATGCGATCATTTCAATT 60.106 36.000 0.00 0.00 29.75 2.32
3007 3064 6.095300 ACACAAGGATGCGATCATTTCAATTA 59.905 34.615 0.00 0.00 29.75 1.40
3008 3065 6.635641 CACAAGGATGCGATCATTTCAATTAG 59.364 38.462 0.00 0.00 29.75 1.73
3009 3066 5.954296 AGGATGCGATCATTTCAATTAGG 57.046 39.130 0.00 0.00 31.96 2.69
3010 3067 5.624159 AGGATGCGATCATTTCAATTAGGA 58.376 37.500 0.00 0.00 31.96 2.94
3011 3068 5.471456 AGGATGCGATCATTTCAATTAGGAC 59.529 40.000 0.00 0.00 31.96 3.85
3012 3069 4.794248 TGCGATCATTTCAATTAGGACG 57.206 40.909 0.00 0.00 0.00 4.79
3013 3070 3.002246 TGCGATCATTTCAATTAGGACGC 59.998 43.478 0.00 0.00 42.05 5.19
3014 3071 3.248602 GCGATCATTTCAATTAGGACGCT 59.751 43.478 0.00 0.00 39.38 5.07
3015 3072 4.609336 GCGATCATTTCAATTAGGACGCTC 60.609 45.833 0.00 0.00 39.38 5.03
3016 3073 4.084328 CGATCATTTCAATTAGGACGCTCC 60.084 45.833 0.00 0.00 36.58 4.70
3017 3074 3.194861 TCATTTCAATTAGGACGCTCCG 58.805 45.455 0.00 0.00 42.75 4.63
3018 3075 2.018542 TTTCAATTAGGACGCTCCGG 57.981 50.000 0.00 0.00 42.75 5.14
3019 3076 0.899720 TTCAATTAGGACGCTCCGGT 59.100 50.000 0.00 0.00 42.75 5.28
3020 3077 0.899720 TCAATTAGGACGCTCCGGTT 59.100 50.000 0.00 0.00 42.75 4.44
3021 3078 1.276989 TCAATTAGGACGCTCCGGTTT 59.723 47.619 0.00 0.00 42.75 3.27
3022 3079 2.081462 CAATTAGGACGCTCCGGTTTT 58.919 47.619 0.00 0.00 42.75 2.43
3023 3080 2.019948 ATTAGGACGCTCCGGTTTTC 57.980 50.000 0.00 0.00 42.75 2.29
3024 3081 0.037046 TTAGGACGCTCCGGTTTTCC 60.037 55.000 0.00 3.59 42.75 3.13
3025 3082 0.901580 TAGGACGCTCCGGTTTTCCT 60.902 55.000 17.04 17.04 42.75 3.36
3026 3083 2.033194 GGACGCTCCGGTTTTCCTG 61.033 63.158 0.00 0.00 37.95 3.86
3027 3084 2.032071 ACGCTCCGGTTTTCCTGG 59.968 61.111 0.00 0.00 37.95 4.45
3028 3085 3.431725 CGCTCCGGTTTTCCTGGC 61.432 66.667 0.00 0.00 37.95 4.85
3029 3086 2.034221 GCTCCGGTTTTCCTGGCT 59.966 61.111 0.00 0.00 37.95 4.75
3030 3087 2.041115 GCTCCGGTTTTCCTGGCTC 61.041 63.158 0.00 0.00 37.95 4.70
3031 3088 1.741770 CTCCGGTTTTCCTGGCTCG 60.742 63.158 0.00 0.00 37.95 5.03
3032 3089 3.431725 CCGGTTTTCCTGGCTCGC 61.432 66.667 0.00 0.00 37.95 5.03
3033 3090 2.358737 CGGTTTTCCTGGCTCGCT 60.359 61.111 0.00 0.00 37.95 4.93
3034 3091 2.680913 CGGTTTTCCTGGCTCGCTG 61.681 63.158 0.00 0.00 37.95 5.18
3035 3092 2.335712 GGTTTTCCTGGCTCGCTGG 61.336 63.158 0.00 0.00 36.94 4.85
3036 3093 1.600916 GTTTTCCTGGCTCGCTGGT 60.601 57.895 0.00 0.00 0.00 4.00
3037 3094 1.302511 TTTTCCTGGCTCGCTGGTC 60.303 57.895 0.00 0.00 0.00 4.02
3038 3095 2.050836 TTTTCCTGGCTCGCTGGTCA 62.051 55.000 0.00 0.00 0.00 4.02
3039 3096 2.050836 TTTCCTGGCTCGCTGGTCAA 62.051 55.000 0.00 0.00 0.00 3.18
3040 3097 2.435586 CCTGGCTCGCTGGTCAAG 60.436 66.667 0.00 0.00 0.00 3.02
3041 3098 2.435586 CTGGCTCGCTGGTCAAGG 60.436 66.667 0.00 0.00 0.00 3.61
3042 3099 3.241530 TGGCTCGCTGGTCAAGGT 61.242 61.111 0.00 0.00 0.00 3.50
3043 3100 2.032681 GGCTCGCTGGTCAAGGTT 59.967 61.111 0.00 0.00 0.00 3.50
3044 3101 2.328099 GGCTCGCTGGTCAAGGTTG 61.328 63.158 0.00 0.00 0.00 3.77
3045 3102 1.301716 GCTCGCTGGTCAAGGTTGA 60.302 57.895 0.00 0.00 34.20 3.18
3053 3110 3.973458 TCAAGGTTGACCGGTCCA 58.027 55.556 31.19 18.97 42.08 4.02
3054 3111 1.448497 TCAAGGTTGACCGGTCCAC 59.552 57.895 31.19 28.73 42.08 4.02
3055 3112 1.052124 TCAAGGTTGACCGGTCCACT 61.052 55.000 31.13 23.07 42.08 4.00
3056 3113 0.682852 CAAGGTTGACCGGTCCACTA 59.317 55.000 31.13 13.04 42.08 2.74
3057 3114 1.278127 CAAGGTTGACCGGTCCACTAT 59.722 52.381 31.13 20.47 42.08 2.12
3058 3115 1.652947 AGGTTGACCGGTCCACTATT 58.347 50.000 31.13 18.01 42.08 1.73
3059 3116 1.278127 AGGTTGACCGGTCCACTATTG 59.722 52.381 31.13 0.00 42.08 1.90
3060 3117 1.276989 GGTTGACCGGTCCACTATTGA 59.723 52.381 31.13 10.51 0.00 2.57
3061 3118 2.344025 GTTGACCGGTCCACTATTGAC 58.656 52.381 31.19 12.60 0.00 3.18
3073 3130 6.842163 GTCCACTATTGACCATTTACTGTTG 58.158 40.000 0.00 0.00 0.00 3.33
3074 3131 6.653320 GTCCACTATTGACCATTTACTGTTGA 59.347 38.462 0.00 0.00 0.00 3.18
3075 3132 6.653320 TCCACTATTGACCATTTACTGTTGAC 59.347 38.462 0.00 0.00 0.00 3.18
3076 3133 6.655003 CCACTATTGACCATTTACTGTTGACT 59.345 38.462 0.00 0.00 0.00 3.41
3077 3134 7.174946 CCACTATTGACCATTTACTGTTGACTT 59.825 37.037 0.00 0.00 0.00 3.01
3078 3135 8.567948 CACTATTGACCATTTACTGTTGACTTT 58.432 33.333 0.00 0.00 0.00 2.66
3079 3136 9.131791 ACTATTGACCATTTACTGTTGACTTTT 57.868 29.630 0.00 0.00 0.00 2.27
3080 3137 9.612620 CTATTGACCATTTACTGTTGACTTTTC 57.387 33.333 0.00 0.00 0.00 2.29
3081 3138 7.397892 TTGACCATTTACTGTTGACTTTTCA 57.602 32.000 0.00 0.00 0.00 2.69
3082 3139 7.397892 TGACCATTTACTGTTGACTTTTCAA 57.602 32.000 0.00 0.00 39.55 2.69
3083 3140 7.479980 TGACCATTTACTGTTGACTTTTCAAG 58.520 34.615 0.00 0.00 42.60 3.02
3084 3141 7.122055 TGACCATTTACTGTTGACTTTTCAAGT 59.878 33.333 0.00 0.00 42.60 3.16
3085 3142 7.836842 ACCATTTACTGTTGACTTTTCAAGTT 58.163 30.769 0.00 0.00 42.60 2.66
3086 3143 8.311109 ACCATTTACTGTTGACTTTTCAAGTTT 58.689 29.630 0.00 0.00 42.60 2.66
3087 3144 9.150348 CCATTTACTGTTGACTTTTCAAGTTTT 57.850 29.630 0.00 0.00 42.60 2.43
3140 3197 9.579610 GTTTGTGAAAATTCAAAATAATCACGG 57.420 29.630 0.00 0.00 39.21 4.94
3141 3198 8.879342 TTGTGAAAATTCAAAATAATCACGGT 57.121 26.923 0.00 0.00 39.21 4.83
3142 3199 8.879342 TGTGAAAATTCAAAATAATCACGGTT 57.121 26.923 0.00 0.00 39.21 4.44
3143 3200 9.319143 TGTGAAAATTCAAAATAATCACGGTTT 57.681 25.926 0.00 0.00 39.21 3.27
3144 3201 9.791838 GTGAAAATTCAAAATAATCACGGTTTC 57.208 29.630 0.00 0.00 39.21 2.78
3145 3202 9.534565 TGAAAATTCAAAATAATCACGGTTTCA 57.465 25.926 0.00 0.00 33.55 2.69
3255 3312 9.814899 TCAAGAACTTGAAAAATTCATGCTTAA 57.185 25.926 13.78 0.00 45.56 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 6.448852 TCATTCATTGTCATCAGTTGGTTTG 58.551 36.000 0.00 0.00 0.00 2.93
99 101 7.307337 CCAAACCAAAGAAATGCAGTGAAATAC 60.307 37.037 0.00 0.00 0.00 1.89
101 103 5.528320 CCAAACCAAAGAAATGCAGTGAAAT 59.472 36.000 0.00 0.00 0.00 2.17
102 104 4.874966 CCAAACCAAAGAAATGCAGTGAAA 59.125 37.500 0.00 0.00 0.00 2.69
103 105 4.081198 ACCAAACCAAAGAAATGCAGTGAA 60.081 37.500 0.00 0.00 0.00 3.18
117 119 1.519719 GCCAACAGCACCAAACCAA 59.480 52.632 0.00 0.00 42.97 3.67
250 255 4.520111 AGCAGCATTGATGTTCAACACTTA 59.480 37.500 3.56 0.00 39.45 2.24
334 342 8.985315 TCAAAAGAGGATATATGAAAGCACAT 57.015 30.769 0.00 0.00 0.00 3.21
385 394 1.965930 GCCTGCACGAACATGGTGA 60.966 57.895 4.93 0.00 37.60 4.02
708 719 1.000163 TGGAGAGCTGAAGACGACAAC 60.000 52.381 0.00 0.00 0.00 3.32
765 776 2.289631 TGAAGTGTGTGGTGATAGGCTG 60.290 50.000 0.00 0.00 0.00 4.85
898 909 1.270550 GGGGTGAAGACAAATGCACAG 59.729 52.381 0.00 0.00 33.09 3.66
935 946 1.073199 CTGGGGAGTGTGGTTGGAC 59.927 63.158 0.00 0.00 0.00 4.02
955 966 1.460255 CCTTGGAGGCAAAGGGTGA 59.540 57.895 5.90 0.00 40.54 4.02
1014 1025 1.078143 GCCAGCCTCCGAAATCAGT 60.078 57.895 0.00 0.00 0.00 3.41
1056 1067 2.280404 TATCGGACTCCTCGCCCTGT 62.280 60.000 0.00 0.00 0.00 4.00
1104 1115 0.033208 GGGCTTCATCACCATGGGAA 60.033 55.000 18.09 8.79 0.00 3.97
1171 1182 6.369059 ACATGCACTTGTATTAAGATCAGC 57.631 37.500 0.00 0.00 0.00 4.26
1233 1244 2.177669 ACCCAAATAGTAGCCCATGCAT 59.822 45.455 0.00 0.00 41.13 3.96
1280 1291 4.742201 CCTGTGGTGCGAGGGACG 62.742 72.222 0.00 0.00 45.66 4.79
1281 1292 3.311110 TCCTGTGGTGCGAGGGAC 61.311 66.667 0.00 0.00 0.00 4.46
1285 1296 2.047844 CAGGTCCTGTGGTGCGAG 60.048 66.667 11.09 0.00 0.00 5.03
1286 1297 2.137528 TTCAGGTCCTGTGGTGCGA 61.138 57.895 18.65 0.00 32.61 5.10
1326 1340 5.131142 AGGGATCATATTCAGAAACTCGGTT 59.869 40.000 0.00 0.00 0.00 4.44
1350 1364 4.578516 CGGTACAAATCATGGGAAATGCTA 59.421 41.667 0.00 0.00 0.00 3.49
1352 1366 3.490761 CCGGTACAAATCATGGGAAATGC 60.491 47.826 0.00 0.00 0.00 3.56
1372 1386 3.479269 GCTTGACTCGCCGTTCCG 61.479 66.667 0.00 0.00 0.00 4.30
1730 1746 3.036429 GCTCTGGGGATCGGTTGCT 62.036 63.158 0.00 0.00 0.00 3.91
1768 1784 8.442632 TTCAGATGCGAAAGAGATGATTATTT 57.557 30.769 0.00 0.00 0.00 1.40
1796 1812 9.630098 CACATTCAGTTGCAAAAGATAATTAGT 57.370 29.630 0.00 0.00 0.00 2.24
1797 1813 9.844790 TCACATTCAGTTGCAAAAGATAATTAG 57.155 29.630 0.00 0.00 0.00 1.73
2109 2125 5.147162 GGAACAATTTGTCTGATGTCGAAC 58.853 41.667 1.83 0.00 0.00 3.95
2148 2164 6.952935 TTTAAGAGAGAGAAATTCGTCAGC 57.047 37.500 2.15 0.00 0.00 4.26
2165 2181 4.289672 AGCTGAGGACCTGGAAATTTAAGA 59.710 41.667 0.00 0.00 0.00 2.10
2166 2182 4.593956 AGCTGAGGACCTGGAAATTTAAG 58.406 43.478 0.00 0.00 0.00 1.85
2167 2183 4.289672 AGAGCTGAGGACCTGGAAATTTAA 59.710 41.667 0.00 0.00 0.00 1.52
2168 2184 3.846588 AGAGCTGAGGACCTGGAAATTTA 59.153 43.478 0.00 0.00 0.00 1.40
2169 2185 2.646798 AGAGCTGAGGACCTGGAAATTT 59.353 45.455 0.00 0.00 0.00 1.82
2175 2191 0.464870 CATCAGAGCTGAGGACCTGG 59.535 60.000 0.00 0.00 43.36 4.45
2241 2257 6.279123 TCATCTCTACATGTTCAGATCAAGC 58.721 40.000 2.30 0.00 0.00 4.01
2527 2550 7.818930 ACATGCCAACAAAAGAACTATATTTGG 59.181 33.333 0.00 0.00 38.14 3.28
2634 2673 6.349243 TGAAGCTCATTCCAATGTGATTTT 57.651 33.333 6.37 0.00 38.25 1.82
2641 2680 8.609176 CCAAAAATTATGAAGCTCATTCCAATG 58.391 33.333 4.35 0.00 38.26 2.82
2784 2840 4.225984 GCAAATTCTAATGCACGTCAACA 58.774 39.130 0.00 0.00 42.12 3.33
2918 2974 6.495181 TGAGGATTTGTTAGGGCAAATGTTAA 59.505 34.615 8.51 0.00 45.68 2.01
2928 2984 7.665974 AGAAGTTAGTTTGAGGATTTGTTAGGG 59.334 37.037 0.00 0.00 0.00 3.53
2977 3034 3.803082 CGCATCCTTGTGTGGCCG 61.803 66.667 0.00 0.00 0.00 6.13
2978 3035 1.718757 GATCGCATCCTTGTGTGGCC 61.719 60.000 0.00 0.00 34.86 5.36
2979 3036 1.026182 TGATCGCATCCTTGTGTGGC 61.026 55.000 0.00 0.00 34.86 5.01
2980 3037 1.671979 ATGATCGCATCCTTGTGTGG 58.328 50.000 0.00 0.00 34.86 4.17
2981 3038 3.127376 TGAAATGATCGCATCCTTGTGTG 59.873 43.478 0.00 0.00 34.86 3.82
2982 3039 3.346315 TGAAATGATCGCATCCTTGTGT 58.654 40.909 0.00 0.00 34.86 3.72
2983 3040 4.359971 TTGAAATGATCGCATCCTTGTG 57.640 40.909 0.00 0.00 32.35 3.33
2984 3041 5.587388 AATTGAAATGATCGCATCCTTGT 57.413 34.783 0.00 0.00 32.35 3.16
2985 3042 6.016860 TCCTAATTGAAATGATCGCATCCTTG 60.017 38.462 0.00 0.00 32.35 3.61
2986 3043 6.016777 GTCCTAATTGAAATGATCGCATCCTT 60.017 38.462 0.00 0.00 32.35 3.36
2987 3044 5.471456 GTCCTAATTGAAATGATCGCATCCT 59.529 40.000 0.00 0.00 32.35 3.24
2988 3045 5.615544 CGTCCTAATTGAAATGATCGCATCC 60.616 44.000 0.00 0.00 32.35 3.51
2989 3046 5.377358 CGTCCTAATTGAAATGATCGCATC 58.623 41.667 0.00 0.00 32.35 3.91
2990 3047 4.319766 GCGTCCTAATTGAAATGATCGCAT 60.320 41.667 0.00 0.00 39.72 4.73
2991 3048 3.002246 GCGTCCTAATTGAAATGATCGCA 59.998 43.478 0.00 0.00 39.72 5.10
2992 3049 3.248602 AGCGTCCTAATTGAAATGATCGC 59.751 43.478 0.00 0.00 40.14 4.58
2993 3050 4.084328 GGAGCGTCCTAATTGAAATGATCG 60.084 45.833 0.00 0.00 32.53 3.69
2994 3051 4.084328 CGGAGCGTCCTAATTGAAATGATC 60.084 45.833 0.00 0.00 33.30 2.92
2995 3052 3.809832 CGGAGCGTCCTAATTGAAATGAT 59.190 43.478 0.00 0.00 33.30 2.45
2996 3053 3.194861 CGGAGCGTCCTAATTGAAATGA 58.805 45.455 0.00 0.00 33.30 2.57
2997 3054 2.287915 CCGGAGCGTCCTAATTGAAATG 59.712 50.000 0.00 0.00 33.30 2.32
2998 3055 2.093128 ACCGGAGCGTCCTAATTGAAAT 60.093 45.455 9.46 0.00 33.30 2.17
2999 3056 1.276989 ACCGGAGCGTCCTAATTGAAA 59.723 47.619 9.46 0.00 33.30 2.69
3000 3057 0.899720 ACCGGAGCGTCCTAATTGAA 59.100 50.000 9.46 0.00 33.30 2.69
3001 3058 0.899720 AACCGGAGCGTCCTAATTGA 59.100 50.000 9.46 0.00 33.30 2.57
3002 3059 1.734163 AAACCGGAGCGTCCTAATTG 58.266 50.000 9.46 0.00 33.30 2.32
3003 3060 2.353323 GAAAACCGGAGCGTCCTAATT 58.647 47.619 9.46 0.00 33.30 1.40
3004 3061 1.406477 GGAAAACCGGAGCGTCCTAAT 60.406 52.381 9.46 0.00 33.30 1.73
3005 3062 0.037046 GGAAAACCGGAGCGTCCTAA 60.037 55.000 9.46 0.00 33.30 2.69
3006 3063 0.901580 AGGAAAACCGGAGCGTCCTA 60.902 55.000 9.46 0.00 36.94 2.94
3007 3064 2.214920 AGGAAAACCGGAGCGTCCT 61.215 57.895 9.46 11.75 33.30 3.85
3008 3065 2.033194 CAGGAAAACCGGAGCGTCC 61.033 63.158 9.46 9.37 0.00 4.79
3009 3066 2.033194 CCAGGAAAACCGGAGCGTC 61.033 63.158 9.46 0.00 0.00 5.19
3010 3067 2.032071 CCAGGAAAACCGGAGCGT 59.968 61.111 9.46 0.00 0.00 5.07
3011 3068 3.431725 GCCAGGAAAACCGGAGCG 61.432 66.667 9.46 0.00 0.00 5.03
3012 3069 2.034221 AGCCAGGAAAACCGGAGC 59.966 61.111 9.46 0.00 0.00 4.70
3013 3070 1.741770 CGAGCCAGGAAAACCGGAG 60.742 63.158 9.46 0.00 0.00 4.63
3014 3071 2.345991 CGAGCCAGGAAAACCGGA 59.654 61.111 9.46 0.00 0.00 5.14
3015 3072 3.431725 GCGAGCCAGGAAAACCGG 61.432 66.667 0.00 0.00 0.00 5.28
3016 3073 2.358737 AGCGAGCCAGGAAAACCG 60.359 61.111 0.00 0.00 0.00 4.44
3017 3074 2.335712 CCAGCGAGCCAGGAAAACC 61.336 63.158 0.00 0.00 0.00 3.27
3018 3075 1.578206 GACCAGCGAGCCAGGAAAAC 61.578 60.000 10.52 0.00 0.00 2.43
3019 3076 1.302511 GACCAGCGAGCCAGGAAAA 60.303 57.895 10.52 0.00 0.00 2.29
3020 3077 2.050836 TTGACCAGCGAGCCAGGAAA 62.051 55.000 10.52 3.16 0.00 3.13
3021 3078 2.454832 CTTGACCAGCGAGCCAGGAA 62.455 60.000 10.52 0.00 0.00 3.36
3022 3079 2.922503 TTGACCAGCGAGCCAGGA 60.923 61.111 10.52 0.00 0.00 3.86
3023 3080 2.435586 CTTGACCAGCGAGCCAGG 60.436 66.667 3.10 3.10 0.00 4.45
3024 3081 2.435586 CCTTGACCAGCGAGCCAG 60.436 66.667 0.00 0.00 0.00 4.85
3025 3082 2.818169 AACCTTGACCAGCGAGCCA 61.818 57.895 0.00 0.00 0.00 4.75
3026 3083 2.032681 AACCTTGACCAGCGAGCC 59.967 61.111 0.00 0.00 0.00 4.70
3027 3084 1.301716 TCAACCTTGACCAGCGAGC 60.302 57.895 0.00 0.00 31.01 5.03
3036 3093 1.052124 AGTGGACCGGTCAACCTTGA 61.052 55.000 34.00 7.96 34.02 3.02
3037 3094 0.682852 TAGTGGACCGGTCAACCTTG 59.317 55.000 34.00 0.00 34.02 3.61
3038 3095 1.652947 ATAGTGGACCGGTCAACCTT 58.347 50.000 34.00 21.44 34.02 3.50
3039 3096 1.278127 CAATAGTGGACCGGTCAACCT 59.722 52.381 34.00 26.09 34.02 3.50
3040 3097 1.276989 TCAATAGTGGACCGGTCAACC 59.723 52.381 34.00 20.15 34.02 3.77
3041 3098 2.344025 GTCAATAGTGGACCGGTCAAC 58.656 52.381 31.48 31.48 33.71 3.18
3042 3099 1.276989 GGTCAATAGTGGACCGGTCAA 59.723 52.381 34.40 23.48 44.80 3.18
3043 3100 0.899720 GGTCAATAGTGGACCGGTCA 59.100 55.000 34.40 18.59 44.80 4.02
3044 3101 3.754766 GGTCAATAGTGGACCGGTC 57.245 57.895 27.04 27.04 44.80 4.79
3049 3106 6.653320 TCAACAGTAAATGGTCAATAGTGGAC 59.347 38.462 0.00 0.00 34.52 4.02
3050 3107 6.653320 GTCAACAGTAAATGGTCAATAGTGGA 59.347 38.462 0.00 0.00 0.00 4.02
3051 3108 6.655003 AGTCAACAGTAAATGGTCAATAGTGG 59.345 38.462 0.00 0.00 0.00 4.00
3052 3109 7.672983 AGTCAACAGTAAATGGTCAATAGTG 57.327 36.000 0.00 0.00 0.00 2.74
3053 3110 8.691661 AAAGTCAACAGTAAATGGTCAATAGT 57.308 30.769 0.00 0.00 0.00 2.12
3054 3111 9.612620 GAAAAGTCAACAGTAAATGGTCAATAG 57.387 33.333 0.00 0.00 0.00 1.73
3055 3112 9.126151 TGAAAAGTCAACAGTAAATGGTCAATA 57.874 29.630 0.00 0.00 0.00 1.90
3056 3113 8.006298 TGAAAAGTCAACAGTAAATGGTCAAT 57.994 30.769 0.00 0.00 0.00 2.57
3057 3114 7.397892 TGAAAAGTCAACAGTAAATGGTCAA 57.602 32.000 0.00 0.00 0.00 3.18
3058 3115 7.397892 TTGAAAAGTCAACAGTAAATGGTCA 57.602 32.000 0.00 0.00 38.88 4.02
3059 3116 7.914537 CTTGAAAAGTCAACAGTAAATGGTC 57.085 36.000 0.00 0.00 38.88 4.02
3114 3171 9.579610 CCGTGATTATTTTGAATTTTCACAAAC 57.420 29.630 0.00 0.00 36.83 2.93
3115 3172 9.319143 ACCGTGATTATTTTGAATTTTCACAAA 57.681 25.926 0.00 0.00 36.83 2.83
3116 3173 8.879342 ACCGTGATTATTTTGAATTTTCACAA 57.121 26.923 0.00 0.00 36.83 3.33
3117 3174 8.879342 AACCGTGATTATTTTGAATTTTCACA 57.121 26.923 0.00 0.00 36.83 3.58
3118 3175 9.791838 GAAACCGTGATTATTTTGAATTTTCAC 57.208 29.630 0.00 0.00 36.83 3.18
3119 3176 9.534565 TGAAACCGTGATTATTTTGAATTTTCA 57.465 25.926 0.00 0.00 34.92 2.69
3225 3282 8.606602 GCATGAATTTTTCAAGTTCTTGAACTT 58.393 29.630 22.33 19.42 43.95 2.66
3226 3283 7.983484 AGCATGAATTTTTCAAGTTCTTGAACT 59.017 29.630 22.33 9.93 43.95 3.01
3227 3284 8.134905 AGCATGAATTTTTCAAGTTCTTGAAC 57.865 30.769 22.33 13.68 43.95 3.18
3228 3285 8.721019 AAGCATGAATTTTTCAAGTTCTTGAA 57.279 26.923 19.77 19.77 43.95 2.69
3229 3286 9.814899 TTAAGCATGAATTTTTCAAGTTCTTGA 57.185 25.926 10.67 10.67 43.95 3.02


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

AutoCloner maintained by Alex Coulton.