Multiple sequence alignment - TraesCS3D01G247200

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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 TraesCS3D01G247200 chr3D 100.000 4196 0 0 1 4196 346310623 346314818 0.000000e+00 7749.0
1 TraesCS3D01G247200 chr3D 100.000 169 0 0 2908 3076 402850796 402850628 3.150000e-81 313.0
2 TraesCS3D01G247200 chr3D 100.000 167 0 0 2908 3074 433193918 433194084 4.070000e-80 309.0
3 TraesCS3D01G247200 chr3D 97.191 178 3 2 2903 3080 563044231 563044056 2.450000e-77 300.0
4 TraesCS3D01G247200 chr3D 100.000 34 0 0 3598 3631 346314253 346314220 3.500000e-06 63.9
5 TraesCS3D01G247200 chr3B 92.385 2587 135 38 344 2909 445594978 445597523 0.000000e+00 3629.0
6 TraesCS3D01G247200 chr3B 95.131 534 19 4 3070 3602 445597522 445598049 0.000000e+00 835.0
7 TraesCS3D01G247200 chr3B 91.910 581 24 9 3609 4172 445598140 445598714 0.000000e+00 791.0
8 TraesCS3D01G247200 chr3B 93.814 291 11 3 1 286 445594433 445594721 8.330000e-117 431.0
9 TraesCS3D01G247200 chr3B 94.565 92 4 1 277 368 445594884 445594974 1.570000e-29 141.0
10 TraesCS3D01G247200 chr3A 91.980 2444 134 32 496 2909 457487430 457485019 0.000000e+00 3371.0
11 TraesCS3D01G247200 chr3A 93.636 1147 41 20 3070 4196 457485020 457483886 0.000000e+00 1685.0
12 TraesCS3D01G247200 chr3A 94.143 461 25 2 1 461 457487882 457487424 0.000000e+00 701.0
13 TraesCS3D01G247200 chr2D 99.419 172 1 0 2901 3072 75834217 75834388 3.150000e-81 313.0
14 TraesCS3D01G247200 chr2D 96.703 182 3 3 2908 3087 315486972 315487152 2.450000e-77 300.0
15 TraesCS3D01G247200 chr6D 99.412 170 1 0 2905 3074 80743568 80743737 4.070000e-80 309.0
16 TraesCS3D01G247200 chr6D 99.412 170 0 1 2907 3075 85165856 85165687 1.470000e-79 307.0
17 TraesCS3D01G247200 chr6D 97.753 178 3 1 2908 3085 27398891 27399067 5.270000e-79 305.0
18 TraesCS3D01G247200 chr4D 98.295 176 2 1 2901 3076 509818871 509819045 1.470000e-79 307.0


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 TraesCS3D01G247200 chr3D 346310623 346314818 4195 False 7749.0 7749 100.000 1 4196 1 chr3D.!!$F1 4195
1 TraesCS3D01G247200 chr3B 445594433 445598714 4281 False 1165.4 3629 93.561 1 4172 5 chr3B.!!$F1 4171
2 TraesCS3D01G247200 chr3A 457483886 457487882 3996 True 1919.0 3371 93.253 1 4196 3 chr3A.!!$R1 4195

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
945 1156 0.036010 AAACTGAGGGGATGACGCAG 60.036 55.0 0.0 0.0 40.86 5.18 F
1555 1771 0.035630 AGCGGCTTTGCTGATTCTCT 60.036 50.0 0.0 0.0 45.28 3.10 F
2164 2422 0.830648 GGCTGGCTCTGTGTATGGTA 59.169 55.0 0.0 0.0 0.00 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 2130 0.179119 GGAAGCATACTACGCACGGT 60.179 55.0 0.00 0.0 0.00 4.83 R
2600 2859 0.590195 GTTGCAGAGCAGACAGTTGG 59.410 55.0 0.00 0.0 40.61 3.77 R
4001 4372 1.084289 GTTTCGCTTGCTAACCGGAT 58.916 50.0 9.46 0.0 0.00 4.18 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
123 129 8.900983 AAATTAACCTGCAGATTTTAGCAAAA 57.099 26.923 17.39 0.00 40.73 2.44
194 200 2.102420 TGACCCGTAGCACTCCATATTG 59.898 50.000 0.00 0.00 0.00 1.90
326 504 1.337167 GGTGTCCAAAATGAAGCTGGC 60.337 52.381 0.00 0.00 0.00 4.85
368 546 6.328641 ACGGTCATACAGATGGTACTAATC 57.671 41.667 0.00 0.00 34.07 1.75
452 657 2.582052 CAAAGTAACTCCCACAAGGCA 58.418 47.619 0.00 0.00 34.51 4.75
461 666 1.503542 CCACAAGGCAGCGATGTTC 59.496 57.895 1.22 0.00 0.00 3.18
507 712 4.115199 AGGGGCGAACTGATGGGC 62.115 66.667 0.00 0.00 0.00 5.36
719 924 3.003763 AGGCACGGGAGAGGTTCC 61.004 66.667 0.00 0.00 46.00 3.62
756 961 3.525619 CGGTTGGAAGATCCGAACA 57.474 52.632 2.73 0.00 46.05 3.18
850 1061 2.104530 GTCGCGGTAGAGCCTTCC 59.895 66.667 6.13 0.00 34.25 3.46
874 1085 0.960861 CCTTTTCCTCGTGAAGCCCC 60.961 60.000 0.00 0.00 33.63 5.80
914 1125 4.215399 GTCCGATCCAAAATCAACAGTTGA 59.785 41.667 18.42 18.42 45.01 3.18
945 1156 0.036010 AAACTGAGGGGATGACGCAG 60.036 55.000 0.00 0.00 40.86 5.18
949 1160 0.465705 TGAGGGGATGACGCAGAATC 59.534 55.000 0.00 0.00 33.80 2.52
964 1175 6.223852 ACGCAGAATCTTATACCGAATGAAT 58.776 36.000 0.00 0.00 0.00 2.57
965 1176 6.146184 ACGCAGAATCTTATACCGAATGAATG 59.854 38.462 0.00 0.00 0.00 2.67
966 1177 6.366061 CGCAGAATCTTATACCGAATGAATGA 59.634 38.462 0.00 0.00 0.00 2.57
1080 1293 2.690497 TCGAATCATTCTCGGCTCTCTT 59.310 45.455 0.00 0.00 36.93 2.85
1226 1439 2.955660 TCCTGTTTGTTCCACCATTGAC 59.044 45.455 0.00 0.00 0.00 3.18
1239 1452 2.888414 ACCATTGACCCGATTTCGTTTT 59.112 40.909 0.00 0.00 37.74 2.43
1255 1468 2.542824 CGTTTTTGTGTTGCCCTTCGAT 60.543 45.455 0.00 0.00 0.00 3.59
1555 1771 0.035630 AGCGGCTTTGCTGATTCTCT 60.036 50.000 0.00 0.00 45.28 3.10
1589 1838 6.814954 ACTAATCCTTCTCAAGCTTGGATA 57.185 37.500 25.73 9.20 36.61 2.59
1593 1842 3.131223 TCCTTCTCAAGCTTGGATACTCG 59.869 47.826 25.73 8.29 37.61 4.18
1661 1911 2.747799 GCCTTCCTGGACTGGAATCATC 60.748 54.545 16.47 0.00 44.17 2.92
1678 1928 4.274794 TCATCTAAACCTGTAGGGCCTA 57.725 45.455 9.81 9.81 40.27 3.93
1762 2013 5.832539 ACCTATGCCAGCACTAGAATAAT 57.167 39.130 0.00 0.00 0.00 1.28
1766 2017 6.315642 CCTATGCCAGCACTAGAATAATCATG 59.684 42.308 0.00 0.00 0.00 3.07
1850 2101 3.221771 TGGAACTGGAACCAGATGTTTG 58.778 45.455 25.03 0.58 46.30 2.93
1865 2116 5.921976 CAGATGTTTGAGTTGCTGCATTTTA 59.078 36.000 1.84 0.00 0.00 1.52
1877 2128 9.135189 AGTTGCTGCATTTTATATTCAGGATAA 57.865 29.630 1.84 0.00 0.00 1.75
1879 2130 8.922931 TGCTGCATTTTATATTCAGGATAAGA 57.077 30.769 0.00 0.00 0.00 2.10
1884 2135 8.230486 GCATTTTATATTCAGGATAAGACCGTG 58.770 37.037 0.00 0.00 34.73 4.94
1897 2153 1.197910 GACCGTGCGTAGTATGCTTC 58.802 55.000 15.23 7.73 0.00 3.86
1913 2171 7.282585 AGTATGCTTCCTAAGTTGCATTCATA 58.717 34.615 4.65 0.00 42.60 2.15
1970 2228 8.296713 ACCTAGTGTAATATTGTTTGTGCAAAG 58.703 33.333 0.00 0.00 31.63 2.77
2021 2279 4.816392 ACACAATGCAAGTCGACTATGTA 58.184 39.130 20.39 17.73 0.00 2.29
2049 2307 4.282703 ACTTTGCATCTGCTTTTCCAATCT 59.717 37.500 3.53 0.00 42.66 2.40
2071 2329 9.950496 AATCTGACCTAATCATACATTCATACC 57.050 33.333 0.00 0.00 36.48 2.73
2072 2330 8.727100 TCTGACCTAATCATACATTCATACCT 57.273 34.615 0.00 0.00 36.48 3.08
2073 2331 8.588472 TCTGACCTAATCATACATTCATACCTG 58.412 37.037 0.00 0.00 36.48 4.00
2074 2332 8.262601 TGACCTAATCATACATTCATACCTGT 57.737 34.615 0.00 0.00 29.99 4.00
2075 2333 8.150296 TGACCTAATCATACATTCATACCTGTG 58.850 37.037 0.00 0.00 29.99 3.66
2076 2334 8.262601 ACCTAATCATACATTCATACCTGTGA 57.737 34.615 0.00 0.00 0.00 3.58
2077 2335 8.370940 ACCTAATCATACATTCATACCTGTGAG 58.629 37.037 0.00 0.00 0.00 3.51
2078 2336 7.821359 CCTAATCATACATTCATACCTGTGAGG 59.179 40.741 0.00 0.00 42.49 3.86
2089 2347 1.069765 CTGTGAGGCTGTGACCGTT 59.930 57.895 0.00 0.00 33.69 4.44
2157 2415 1.738099 GTGTACGGCTGGCTCTGTG 60.738 63.158 0.00 0.00 0.00 3.66
2159 2417 0.896479 TGTACGGCTGGCTCTGTGTA 60.896 55.000 0.00 0.00 0.00 2.90
2164 2422 0.830648 GGCTGGCTCTGTGTATGGTA 59.169 55.000 0.00 0.00 0.00 3.25
2435 2694 5.221880 TCTCATGCTGCAATTTACAAACAC 58.778 37.500 6.36 0.00 0.00 3.32
2436 2695 3.980134 TCATGCTGCAATTTACAAACACG 59.020 39.130 6.36 0.00 0.00 4.49
2641 2902 6.852420 ACTTCTACTGCTGAAGGTAACATA 57.148 37.500 12.60 0.00 43.59 2.29
2642 2903 7.425224 ACTTCTACTGCTGAAGGTAACATAT 57.575 36.000 12.60 0.00 43.59 1.78
2648 2909 7.383102 ACTGCTGAAGGTAACATATGAAAAG 57.617 36.000 10.38 0.00 41.41 2.27
2686 2947 5.129634 TCTTACACCTGTCATGAGCAAAAA 58.870 37.500 0.00 0.00 0.00 1.94
2787 3048 5.878406 TGAAGATAGAAATCAGGAGGGTC 57.122 43.478 0.00 0.00 34.28 4.46
2908 3169 6.219772 TCTGGGATTGCTACTCCTATATCCTA 59.780 42.308 0.00 0.00 33.64 2.94
2909 3170 6.195700 TGGGATTGCTACTCCTATATCCTAC 58.804 44.000 0.00 0.00 33.64 3.18
2910 3171 6.010650 TGGGATTGCTACTCCTATATCCTACT 60.011 42.308 0.00 0.00 33.64 2.57
2911 3172 6.548251 GGGATTGCTACTCCTATATCCTACTC 59.452 46.154 0.00 0.00 33.64 2.59
2912 3173 6.548251 GGATTGCTACTCCTATATCCTACTCC 59.452 46.154 0.00 0.00 31.11 3.85
2913 3174 5.453866 TGCTACTCCTATATCCTACTCCC 57.546 47.826 0.00 0.00 0.00 4.30
2914 3175 5.109479 TGCTACTCCTATATCCTACTCCCT 58.891 45.833 0.00 0.00 0.00 4.20
2915 3176 5.192121 TGCTACTCCTATATCCTACTCCCTC 59.808 48.000 0.00 0.00 0.00 4.30
2916 3177 5.398239 GCTACTCCTATATCCTACTCCCTCC 60.398 52.000 0.00 0.00 0.00 4.30
2917 3178 3.524380 ACTCCTATATCCTACTCCCTCCG 59.476 52.174 0.00 0.00 0.00 4.63
2918 3179 3.524380 CTCCTATATCCTACTCCCTCCGT 59.476 52.174 0.00 0.00 0.00 4.69
2919 3180 3.921486 TCCTATATCCTACTCCCTCCGTT 59.079 47.826 0.00 0.00 0.00 4.44
2920 3181 4.018597 TCCTATATCCTACTCCCTCCGTTC 60.019 50.000 0.00 0.00 0.00 3.95
2921 3182 2.671896 TATCCTACTCCCTCCGTTCC 57.328 55.000 0.00 0.00 0.00 3.62
2922 3183 0.935194 ATCCTACTCCCTCCGTTCCT 59.065 55.000 0.00 0.00 0.00 3.36
2923 3184 1.600058 TCCTACTCCCTCCGTTCCTA 58.400 55.000 0.00 0.00 0.00 2.94
2924 3185 1.925255 TCCTACTCCCTCCGTTCCTAA 59.075 52.381 0.00 0.00 0.00 2.69
2925 3186 2.312741 TCCTACTCCCTCCGTTCCTAAA 59.687 50.000 0.00 0.00 0.00 1.85
2926 3187 3.052338 TCCTACTCCCTCCGTTCCTAAAT 60.052 47.826 0.00 0.00 0.00 1.40
2927 3188 4.168675 TCCTACTCCCTCCGTTCCTAAATA 59.831 45.833 0.00 0.00 0.00 1.40
2928 3189 4.280425 CCTACTCCCTCCGTTCCTAAATAC 59.720 50.000 0.00 0.00 0.00 1.89
2929 3190 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
2930 3191 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
2931 3192 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
2932 3193 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
2933 3194 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
2934 3195 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
2935 3196 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2936 3197 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
2937 3198 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
2938 3199 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
2939 3200 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
2940 3201 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
2941 3202 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
2942 3203 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
2943 3204 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
2944 3205 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
2945 3206 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
2946 3207 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
2948 3209 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
2949 3210 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
2950 3211 6.319141 ACTTGTCTTTCTAGGCATTTCAAC 57.681 37.500 0.00 0.00 35.56 3.18
2951 3212 5.827797 ACTTGTCTTTCTAGGCATTTCAACA 59.172 36.000 0.00 0.00 35.56 3.33
2952 3213 6.321181 ACTTGTCTTTCTAGGCATTTCAACAA 59.679 34.615 0.00 0.00 35.56 2.83
2953 3214 6.317789 TGTCTTTCTAGGCATTTCAACAAG 57.682 37.500 0.00 0.00 29.10 3.16
2954 3215 5.827797 TGTCTTTCTAGGCATTTCAACAAGT 59.172 36.000 0.00 0.00 29.10 3.16
2955 3216 6.145535 GTCTTTCTAGGCATTTCAACAAGTG 58.854 40.000 0.00 0.00 0.00 3.16
2956 3217 6.017109 GTCTTTCTAGGCATTTCAACAAGTGA 60.017 38.462 0.00 0.00 0.00 3.41
2957 3218 5.689383 TTCTAGGCATTTCAACAAGTGAC 57.311 39.130 0.00 0.00 35.39 3.67
2958 3219 4.973168 TCTAGGCATTTCAACAAGTGACT 58.027 39.130 0.00 0.00 40.60 3.41
2959 3220 6.109156 TCTAGGCATTTCAACAAGTGACTA 57.891 37.500 0.00 0.00 38.51 2.59
2960 3221 5.932303 TCTAGGCATTTCAACAAGTGACTAC 59.068 40.000 0.00 0.00 38.51 2.73
2961 3222 4.460263 AGGCATTTCAACAAGTGACTACA 58.540 39.130 0.00 0.00 35.84 2.74
2962 3223 5.072741 AGGCATTTCAACAAGTGACTACAT 58.927 37.500 0.00 0.00 35.84 2.29
2963 3224 6.237901 AGGCATTTCAACAAGTGACTACATA 58.762 36.000 0.00 0.00 35.84 2.29
2964 3225 6.149474 AGGCATTTCAACAAGTGACTACATAC 59.851 38.462 0.00 0.00 35.84 2.39
2965 3226 6.015504 GCATTTCAACAAGTGACTACATACG 58.984 40.000 0.00 0.00 35.39 3.06
2966 3227 6.534059 CATTTCAACAAGTGACTACATACGG 58.466 40.000 0.00 0.00 35.39 4.02
2967 3228 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2968 3229 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2969 3230 5.010314 TTCAACAAGTGACTACATACGGAGT 59.990 40.000 0.00 0.00 39.84 3.85
2970 3231 6.207221 TTCAACAAGTGACTACATACGGAGTA 59.793 38.462 0.00 0.00 41.66 2.59
2971 3232 7.255555 TTCAACAAGTGACTACATACGGAGTAA 60.256 37.037 0.00 0.00 41.03 2.24
2987 3248 6.931838 ACGGAGTAAAATGAGTGAATCTACA 58.068 36.000 0.00 0.00 41.94 2.74
2988 3249 6.812160 ACGGAGTAAAATGAGTGAATCTACAC 59.188 38.462 0.00 0.00 41.94 2.90
3029 3290 8.763049 CATACATCCGTATGTGATAGTCATTT 57.237 34.615 3.56 0.00 46.70 2.32
3030 3291 8.650714 CATACATCCGTATGTGATAGTCATTTG 58.349 37.037 3.56 0.00 46.70 2.32
3031 3292 6.816136 ACATCCGTATGTGATAGTCATTTGA 58.184 36.000 0.00 0.00 44.79 2.69
3032 3293 7.272244 ACATCCGTATGTGATAGTCATTTGAA 58.728 34.615 0.00 0.00 44.79 2.69
3033 3294 7.768582 ACATCCGTATGTGATAGTCATTTGAAA 59.231 33.333 0.00 0.00 44.79 2.69
3034 3295 8.777413 CATCCGTATGTGATAGTCATTTGAAAT 58.223 33.333 0.00 0.00 0.00 2.17
3035 3296 8.141835 TCCGTATGTGATAGTCATTTGAAATG 57.858 34.615 11.54 11.54 0.00 2.32
3036 3297 6.852853 CCGTATGTGATAGTCATTTGAAATGC 59.147 38.462 12.86 8.33 0.00 3.56
3037 3298 6.852853 CGTATGTGATAGTCATTTGAAATGCC 59.147 38.462 12.86 1.61 0.00 4.40
3038 3299 7.254898 CGTATGTGATAGTCATTTGAAATGCCT 60.255 37.037 12.86 9.73 0.00 4.75
3039 3300 9.056005 GTATGTGATAGTCATTTGAAATGCCTA 57.944 33.333 10.59 10.59 0.00 3.93
3040 3301 7.558161 TGTGATAGTCATTTGAAATGCCTAG 57.442 36.000 13.20 0.00 0.00 3.02
3041 3302 7.337938 TGTGATAGTCATTTGAAATGCCTAGA 58.662 34.615 13.20 1.78 0.00 2.43
3042 3303 7.828717 TGTGATAGTCATTTGAAATGCCTAGAA 59.171 33.333 13.20 2.99 0.00 2.10
3043 3304 8.677300 GTGATAGTCATTTGAAATGCCTAGAAA 58.323 33.333 13.20 0.91 0.00 2.52
3044 3305 8.896744 TGATAGTCATTTGAAATGCCTAGAAAG 58.103 33.333 13.20 0.00 0.00 2.62
3045 3306 9.113838 GATAGTCATTTGAAATGCCTAGAAAGA 57.886 33.333 13.20 0.00 0.00 2.52
3046 3307 7.150783 AGTCATTTGAAATGCCTAGAAAGAC 57.849 36.000 12.86 3.23 0.00 3.01
3047 3308 6.716628 AGTCATTTGAAATGCCTAGAAAGACA 59.283 34.615 12.86 0.00 0.00 3.41
3048 3309 7.231317 AGTCATTTGAAATGCCTAGAAAGACAA 59.769 33.333 12.86 0.00 0.00 3.18
3049 3310 7.540055 GTCATTTGAAATGCCTAGAAAGACAAG 59.460 37.037 12.86 0.00 0.00 3.16
3050 3311 6.959639 TTTGAAATGCCTAGAAAGACAAGT 57.040 33.333 0.00 0.00 0.00 3.16
3051 3312 8.514594 CATTTGAAATGCCTAGAAAGACAAGTA 58.485 33.333 4.82 0.00 0.00 2.24
3052 3313 8.635765 TTTGAAATGCCTAGAAAGACAAGTAT 57.364 30.769 0.00 0.00 0.00 2.12
3053 3314 8.635765 TTGAAATGCCTAGAAAGACAAGTATT 57.364 30.769 0.00 0.00 0.00 1.89
3054 3315 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
3055 3316 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
3057 3318 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
3058 3319 7.490657 TGCCTAGAAAGACAAGTATTTAGGA 57.509 36.000 11.40 0.00 26.70 2.94
3059 3320 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
3060 3321 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
3061 3322 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
3062 3323 7.491696 CCTAGAAAGACAAGTATTTAGGAACGG 59.508 40.741 4.01 0.00 26.70 4.44
3063 3324 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
3064 3325 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
3065 3326 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
3066 3327 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
3067 3328 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
3068 3329 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
3069 3330 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
3143 3404 9.090692 GCAAAATGTTATTCTGTTTGATAGCAT 57.909 29.630 0.00 0.00 32.18 3.79
3162 3424 5.014808 GCATTATGGACTTTTGGAATGCT 57.985 39.130 9.52 0.00 43.59 3.79
3226 3488 9.859692 GGTACATACTAATTTTTCTACGCAATC 57.140 33.333 0.00 0.00 0.00 2.67
3227 3489 9.564041 GTACATACTAATTTTTCTACGCAATCG 57.436 33.333 0.00 0.00 42.43 3.34
3393 3655 7.041721 TGTTTCATGTATAGACAGTTAGGCAG 58.958 38.462 0.00 0.00 39.50 4.85
3429 3691 8.111545 AGCCCATAATGCATCAATATCTTTAGA 58.888 33.333 0.00 0.00 0.00 2.10
3556 3818 6.379988 ACCAAACAACTCAACTCCAGTTATTT 59.620 34.615 0.00 0.00 31.98 1.40
3557 3819 7.558444 ACCAAACAACTCAACTCCAGTTATTTA 59.442 33.333 0.00 0.00 30.44 1.40
3604 3867 3.602104 CCAAATCTGGGTGCCTCAT 57.398 52.632 0.00 0.00 39.30 2.90
3606 3869 1.753073 CCAAATCTGGGTGCCTCATTC 59.247 52.381 0.00 0.00 39.30 2.67
4048 4420 4.459337 CCACTAAGAATGTCCCCTTGAAAC 59.541 45.833 0.00 0.00 0.00 2.78
4120 4492 4.523813 CGTTCCATTGTTGTGTTGTAGAC 58.476 43.478 0.00 0.00 0.00 2.59
4148 4520 4.499183 TGCCGTTCAGTTTCATTGTTTTT 58.501 34.783 0.00 0.00 0.00 1.94
4172 4544 2.935042 TCTTTCTCTCTCGTTCAAGCG 58.065 47.619 0.00 0.00 0.00 4.68
4174 4546 3.501062 TCTTTCTCTCTCGTTCAAGCGTA 59.499 43.478 0.00 0.00 0.00 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 112 3.916761 TGGCTTTTGCTAAAATCTGCAG 58.083 40.909 7.63 7.63 46.54 4.41
153 159 6.043411 GGTCAGATACATTTCTGTAGGTGAC 58.957 44.000 15.35 15.35 44.44 3.67
395 600 0.457851 ACTGATCTCCTACTGCGCAC 59.542 55.000 5.66 0.00 0.00 5.34
474 679 0.605589 CCCTCCCACCGTTCTGAAAC 60.606 60.000 0.00 0.00 0.00 2.78
488 693 2.190578 CCATCAGTTCGCCCCTCC 59.809 66.667 0.00 0.00 0.00 4.30
507 712 1.797211 CGGTAGGGCCTCGCTCTTAG 61.797 65.000 10.74 0.00 34.72 2.18
669 874 3.213402 GCTAGTCGCCGCCTCTCT 61.213 66.667 0.00 0.00 0.00 3.10
703 908 3.316573 CTGGAACCTCTCCCGTGCC 62.317 68.421 0.00 0.00 44.69 5.01
710 915 2.726351 CGCCTCCCTGGAACCTCTC 61.726 68.421 0.00 0.00 38.35 3.20
719 924 4.241555 CCCGATTCCGCCTCCCTG 62.242 72.222 0.00 0.00 0.00 4.45
874 1085 2.510238 CGGCTGAGAAAGGGCTCG 60.510 66.667 0.00 0.00 37.73 5.03
930 1141 0.465705 GATTCTGCGTCATCCCCTCA 59.534 55.000 0.00 0.00 0.00 3.86
969 1180 6.864165 GGCAGGTGATGTTTTCGTTTTATTTA 59.136 34.615 0.00 0.00 0.00 1.40
970 1181 5.694458 GGCAGGTGATGTTTTCGTTTTATTT 59.306 36.000 0.00 0.00 0.00 1.40
973 1184 3.304123 CGGCAGGTGATGTTTTCGTTTTA 60.304 43.478 0.00 0.00 0.00 1.52
975 1186 1.001815 CGGCAGGTGATGTTTTCGTTT 60.002 47.619 0.00 0.00 0.00 3.60
976 1187 0.591170 CGGCAGGTGATGTTTTCGTT 59.409 50.000 0.00 0.00 0.00 3.85
977 1188 1.852067 GCGGCAGGTGATGTTTTCGT 61.852 55.000 0.00 0.00 0.00 3.85
978 1189 1.154225 GCGGCAGGTGATGTTTTCG 60.154 57.895 0.00 0.00 0.00 3.46
979 1190 1.154225 CGCGGCAGGTGATGTTTTC 60.154 57.895 0.00 0.00 0.00 2.29
980 1191 2.953821 CGCGGCAGGTGATGTTTT 59.046 55.556 0.00 0.00 0.00 2.43
1041 1253 0.179070 GAAGAAGGTGGAGGCGGATC 60.179 60.000 0.00 0.00 0.00 3.36
1096 1309 1.375326 GCGGACCCAGGTTCTTTCT 59.625 57.895 0.00 0.00 0.00 2.52
1097 1310 1.674651 GGCGGACCCAGGTTCTTTC 60.675 63.158 0.00 0.00 0.00 2.62
1098 1311 2.434774 GGCGGACCCAGGTTCTTT 59.565 61.111 0.00 0.00 0.00 2.52
1099 1312 2.852075 TGGCGGACCCAGGTTCTT 60.852 61.111 0.00 0.00 39.18 2.52
1226 1439 2.217620 GCAACACAAAAACGAAATCGGG 59.782 45.455 7.81 0.00 44.95 5.14
1239 1452 1.234821 GTCATCGAAGGGCAACACAA 58.765 50.000 0.00 0.00 39.74 3.33
1255 1468 2.401699 CTGCTGCTTCACCTGGGTCA 62.402 60.000 0.00 0.00 0.00 4.02
1455 1668 4.821589 CGGGGGCTCGTCTTGCTC 62.822 72.222 0.00 0.00 0.00 4.26
1536 1752 0.035630 AGAGAATCAGCAAAGCCGCT 60.036 50.000 0.00 0.00 45.21 5.52
1555 1771 7.675161 TGAGAAGGATTAGTACCATCATCAA 57.325 36.000 5.29 0.00 0.00 2.57
1589 1838 4.402793 AGTGTACATTAGCAGATTCCGAGT 59.597 41.667 0.00 0.00 0.00 4.18
1593 1842 8.662781 TGATAAAGTGTACATTAGCAGATTCC 57.337 34.615 0.00 0.00 0.00 3.01
1621 1870 6.888088 GGAAGGCCTCTGTAAATTAAACCTTA 59.112 38.462 5.23 0.00 35.22 2.69
1661 1911 2.434702 CCAGTAGGCCCTACAGGTTTAG 59.565 54.545 22.58 0.00 38.34 1.85
1678 1928 3.087031 CAATTTCAGATCACAGCCCAGT 58.913 45.455 0.00 0.00 0.00 4.00
1762 2013 6.413783 TTGTACTAGGAACTTGTGACATGA 57.586 37.500 0.00 0.00 45.24 3.07
1766 2017 6.147328 GGTTCATTGTACTAGGAACTTGTGAC 59.853 42.308 25.85 11.00 45.24 3.67
1847 2098 7.760794 CCTGAATATAAAATGCAGCAACTCAAA 59.239 33.333 0.00 0.00 0.00 2.69
1850 2101 7.031226 TCCTGAATATAAAATGCAGCAACTC 57.969 36.000 0.00 0.00 0.00 3.01
1865 2116 3.321111 ACGCACGGTCTTATCCTGAATAT 59.679 43.478 0.00 0.00 0.00 1.28
1877 2128 0.815734 AAGCATACTACGCACGGTCT 59.184 50.000 0.00 0.00 0.00 3.85
1879 2130 0.179119 GGAAGCATACTACGCACGGT 60.179 55.000 0.00 0.00 0.00 4.83
1884 2135 3.245519 GCAACTTAGGAAGCATACTACGC 59.754 47.826 0.00 0.00 0.00 4.42
1964 2222 1.307097 GCAAACCCAAATGCTTTGCA 58.693 45.000 16.01 0.00 45.96 4.08
1970 2228 3.391506 AAGAGAAGCAAACCCAAATGC 57.608 42.857 0.00 0.00 42.87 3.56
2049 2307 8.150296 CACAGGTATGAATGTATGATTAGGTCA 58.850 37.037 0.00 0.00 42.06 4.02
2071 2329 1.069765 AACGGTCACAGCCTCACAG 59.930 57.895 0.00 0.00 0.00 3.66
2072 2330 1.227527 CAACGGTCACAGCCTCACA 60.228 57.895 0.00 0.00 0.00 3.58
2073 2331 1.227556 ACAACGGTCACAGCCTCAC 60.228 57.895 0.00 0.00 0.00 3.51
2074 2332 1.227527 CACAACGGTCACAGCCTCA 60.228 57.895 0.00 0.00 0.00 3.86
2075 2333 2.607892 GCACAACGGTCACAGCCTC 61.608 63.158 0.00 0.00 0.00 4.70
2076 2334 2.591715 GCACAACGGTCACAGCCT 60.592 61.111 0.00 0.00 0.00 4.58
2077 2335 3.660111 GGCACAACGGTCACAGCC 61.660 66.667 0.00 0.00 34.71 4.85
2078 2336 2.591715 AGGCACAACGGTCACAGC 60.592 61.111 0.00 0.00 0.00 4.40
2089 2347 2.360726 CATCAGCAGCCAGGCACA 60.361 61.111 15.80 0.00 35.83 4.57
2157 2415 4.460263 TGATCAAACCCATGCTACCATAC 58.540 43.478 0.00 0.00 0.00 2.39
2159 2417 3.668141 TGATCAAACCCATGCTACCAT 57.332 42.857 0.00 0.00 0.00 3.55
2324 2582 2.091166 TGCCTGGAAATGGGATGCTAAT 60.091 45.455 0.00 0.00 0.00 1.73
2353 2611 4.079844 TGGACTATGCATTGGAAATGAGGA 60.080 41.667 3.54 0.00 0.00 3.71
2435 2694 5.520288 CAGTTGTCACTTCAATCCCTATACG 59.480 44.000 0.00 0.00 0.00 3.06
2436 2695 6.640518 TCAGTTGTCACTTCAATCCCTATAC 58.359 40.000 0.00 0.00 0.00 1.47
2545 2804 2.959030 GGATAAAGAGGGGTTGATTGGC 59.041 50.000 0.00 0.00 0.00 4.52
2600 2859 0.590195 GTTGCAGAGCAGACAGTTGG 59.410 55.000 0.00 0.00 40.61 3.77
2641 2902 6.302269 AGAAAGTGTGATCAGGACTTTTCAT 58.698 36.000 23.97 15.20 39.46 2.57
2642 2903 5.684704 AGAAAGTGTGATCAGGACTTTTCA 58.315 37.500 23.97 4.69 39.46 2.69
2648 2909 4.691216 GGTGTAAGAAAGTGTGATCAGGAC 59.309 45.833 0.00 0.00 0.00 3.85
2704 2965 4.383850 TGTGCTGCACAAAACAATAACT 57.616 36.364 31.31 0.00 41.69 2.24
2787 3048 1.077212 CAGTCCAATGGAGCCCAGG 60.077 63.158 0.27 0.00 36.75 4.45
2908 3169 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
2909 3170 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
2910 3171 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2911 3172 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
2912 3173 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
2913 3174 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
2914 3175 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
2915 3176 7.491696 CCTAGAAAGACAAGTATTTAGGAACGG 59.508 40.741 4.01 0.00 26.70 4.44
2916 3177 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
2917 3178 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
2918 3179 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
2919 3180 7.490657 TGCCTAGAAAGACAAGTATTTAGGA 57.509 36.000 11.40 0.00 26.70 2.94
2920 3181 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
2922 3183 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
2923 3184 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
2924 3185 8.515414 GTTGAAATGCCTAGAAAGACAAGTATT 58.485 33.333 0.00 0.00 0.00 1.89
2925 3186 7.665559 TGTTGAAATGCCTAGAAAGACAAGTAT 59.334 33.333 0.00 0.00 0.00 2.12
2926 3187 6.995686 TGTTGAAATGCCTAGAAAGACAAGTA 59.004 34.615 0.00 0.00 0.00 2.24
2927 3188 5.827797 TGTTGAAATGCCTAGAAAGACAAGT 59.172 36.000 0.00 0.00 0.00 3.16
2928 3189 6.317789 TGTTGAAATGCCTAGAAAGACAAG 57.682 37.500 0.00 0.00 0.00 3.16
2929 3190 6.321181 ACTTGTTGAAATGCCTAGAAAGACAA 59.679 34.615 0.00 0.00 0.00 3.18
2930 3191 5.827797 ACTTGTTGAAATGCCTAGAAAGACA 59.172 36.000 0.00 0.00 0.00 3.41
2931 3192 6.017109 TCACTTGTTGAAATGCCTAGAAAGAC 60.017 38.462 0.00 0.00 0.00 3.01
2932 3193 6.017109 GTCACTTGTTGAAATGCCTAGAAAGA 60.017 38.462 0.00 0.00 35.39 2.52
2933 3194 6.016777 AGTCACTTGTTGAAATGCCTAGAAAG 60.017 38.462 0.00 0.00 35.39 2.62
2934 3195 5.827797 AGTCACTTGTTGAAATGCCTAGAAA 59.172 36.000 0.00 0.00 35.39 2.52
2935 3196 5.376625 AGTCACTTGTTGAAATGCCTAGAA 58.623 37.500 0.00 0.00 35.39 2.10
2936 3197 4.973168 AGTCACTTGTTGAAATGCCTAGA 58.027 39.130 0.00 0.00 35.39 2.43
2937 3198 5.700832 TGTAGTCACTTGTTGAAATGCCTAG 59.299 40.000 0.00 0.00 35.39 3.02
2938 3199 5.616270 TGTAGTCACTTGTTGAAATGCCTA 58.384 37.500 0.00 0.00 35.39 3.93
2939 3200 4.460263 TGTAGTCACTTGTTGAAATGCCT 58.540 39.130 0.00 0.00 35.39 4.75
2940 3201 4.829064 TGTAGTCACTTGTTGAAATGCC 57.171 40.909 0.00 0.00 35.39 4.40
2941 3202 6.015504 CGTATGTAGTCACTTGTTGAAATGC 58.984 40.000 0.00 0.00 35.39 3.56
2942 3203 6.367695 TCCGTATGTAGTCACTTGTTGAAATG 59.632 38.462 0.00 0.00 35.39 2.32
2943 3204 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
2944 3205 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2945 3206 5.010314 ACTCCGTATGTAGTCACTTGTTGAA 59.990 40.000 0.00 0.00 35.39 2.69
2946 3207 4.521639 ACTCCGTATGTAGTCACTTGTTGA 59.478 41.667 0.00 0.00 0.00 3.18
2947 3208 4.806330 ACTCCGTATGTAGTCACTTGTTG 58.194 43.478 0.00 0.00 0.00 3.33
2948 3209 6.579666 TTACTCCGTATGTAGTCACTTGTT 57.420 37.500 0.00 0.00 0.00 2.83
2949 3210 6.579666 TTTACTCCGTATGTAGTCACTTGT 57.420 37.500 0.00 0.00 0.00 3.16
2950 3211 7.758076 TCATTTTACTCCGTATGTAGTCACTTG 59.242 37.037 0.00 0.00 0.00 3.16
2951 3212 7.833786 TCATTTTACTCCGTATGTAGTCACTT 58.166 34.615 0.00 0.00 0.00 3.16
2952 3213 7.122353 ACTCATTTTACTCCGTATGTAGTCACT 59.878 37.037 0.00 0.00 0.00 3.41
2953 3214 7.220300 CACTCATTTTACTCCGTATGTAGTCAC 59.780 40.741 0.00 0.00 0.00 3.67
2954 3215 7.121611 TCACTCATTTTACTCCGTATGTAGTCA 59.878 37.037 0.00 0.00 0.00 3.41
2955 3216 7.478322 TCACTCATTTTACTCCGTATGTAGTC 58.522 38.462 0.00 0.00 0.00 2.59
2956 3217 7.400599 TCACTCATTTTACTCCGTATGTAGT 57.599 36.000 0.00 0.00 0.00 2.73
2957 3218 8.873215 ATTCACTCATTTTACTCCGTATGTAG 57.127 34.615 0.00 0.00 0.00 2.74
2958 3219 8.692710 AGATTCACTCATTTTACTCCGTATGTA 58.307 33.333 0.00 0.00 0.00 2.29
2959 3220 7.556844 AGATTCACTCATTTTACTCCGTATGT 58.443 34.615 0.00 0.00 0.00 2.29
2960 3221 8.969267 GTAGATTCACTCATTTTACTCCGTATG 58.031 37.037 0.00 0.00 0.00 2.39
2961 3222 8.692710 TGTAGATTCACTCATTTTACTCCGTAT 58.307 33.333 0.00 0.00 0.00 3.06
2962 3223 7.972277 GTGTAGATTCACTCATTTTACTCCGTA 59.028 37.037 0.00 0.00 35.68 4.02
2963 3224 6.812160 GTGTAGATTCACTCATTTTACTCCGT 59.188 38.462 0.00 0.00 35.68 4.69
2964 3225 7.036220 AGTGTAGATTCACTCATTTTACTCCG 58.964 38.462 0.00 0.00 44.07 4.63
3005 3266 8.585018 TCAAATGACTATCACATACGGATGTAT 58.415 33.333 14.23 10.02 44.82 2.29
3006 3267 7.947282 TCAAATGACTATCACATACGGATGTA 58.053 34.615 14.23 2.61 44.82 2.29
3008 3269 7.713764 TTCAAATGACTATCACATACGGATG 57.286 36.000 5.94 5.94 39.16 3.51
3009 3270 8.777413 CATTTCAAATGACTATCACATACGGAT 58.223 33.333 3.82 0.00 0.00 4.18
3010 3271 7.254761 GCATTTCAAATGACTATCACATACGGA 60.255 37.037 14.65 0.00 0.00 4.69
3011 3272 6.852853 GCATTTCAAATGACTATCACATACGG 59.147 38.462 14.65 0.00 0.00 4.02
3012 3273 6.852853 GGCATTTCAAATGACTATCACATACG 59.147 38.462 14.65 0.00 0.00 3.06
3013 3274 7.934457 AGGCATTTCAAATGACTATCACATAC 58.066 34.615 17.52 0.00 35.20 2.39
3014 3275 9.276590 CTAGGCATTTCAAATGACTATCACATA 57.723 33.333 23.50 4.36 38.80 2.29
3015 3276 7.994911 TCTAGGCATTTCAAATGACTATCACAT 59.005 33.333 23.50 1.77 38.80 3.21
3016 3277 7.337938 TCTAGGCATTTCAAATGACTATCACA 58.662 34.615 23.50 5.75 38.80 3.58
3017 3278 7.792374 TCTAGGCATTTCAAATGACTATCAC 57.208 36.000 23.50 0.15 38.80 3.06
3018 3279 8.806429 TTTCTAGGCATTTCAAATGACTATCA 57.194 30.769 23.50 12.23 38.80 2.15
3019 3280 9.113838 TCTTTCTAGGCATTTCAAATGACTATC 57.886 33.333 23.50 1.52 38.80 2.08
3020 3281 8.897752 GTCTTTCTAGGCATTTCAAATGACTAT 58.102 33.333 23.50 4.64 38.80 2.12
3021 3282 7.882791 TGTCTTTCTAGGCATTTCAAATGACTA 59.117 33.333 22.19 22.19 38.54 2.59
3022 3283 6.716628 TGTCTTTCTAGGCATTTCAAATGACT 59.283 34.615 22.35 22.35 41.04 3.41
3023 3284 6.913170 TGTCTTTCTAGGCATTTCAAATGAC 58.087 36.000 14.65 11.48 29.10 3.06
3024 3285 7.231317 ACTTGTCTTTCTAGGCATTTCAAATGA 59.769 33.333 14.65 0.00 35.56 2.57
3025 3286 7.373493 ACTTGTCTTTCTAGGCATTTCAAATG 58.627 34.615 5.68 5.68 35.56 2.32
3026 3287 7.530426 ACTTGTCTTTCTAGGCATTTCAAAT 57.470 32.000 0.00 0.00 35.56 2.32
3027 3288 6.959639 ACTTGTCTTTCTAGGCATTTCAAA 57.040 33.333 0.00 0.00 35.56 2.69
3028 3289 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
3029 3290 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
3031 3292 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
3032 3293 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
3033 3294 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
3034 3295 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
3035 3296 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
3036 3297 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
3037 3298 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
3038 3299 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
3039 3300 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
3040 3301 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
3041 3302 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
3042 3303 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
3043 3304 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
3044 3305 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
3045 3306 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
3046 3307 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
3047 3308 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
3048 3309 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
3049 3310 7.715266 ATATACTCCCTCCGTTCCTAAATAC 57.285 40.000 0.00 0.00 0.00 1.89
3051 3312 8.912614 AATATATACTCCCTCCGTTCCTAAAT 57.087 34.615 0.00 0.00 0.00 1.40
3052 3313 8.731591 AAATATATACTCCCTCCGTTCCTAAA 57.268 34.615 0.00 0.00 0.00 1.85
3053 3314 9.827198 TTAAATATATACTCCCTCCGTTCCTAA 57.173 33.333 0.00 0.00 0.00 2.69
3054 3315 9.827198 TTTAAATATATACTCCCTCCGTTCCTA 57.173 33.333 0.00 0.00 0.00 2.94
3055 3316 8.731591 TTTAAATATATACTCCCTCCGTTCCT 57.268 34.615 0.00 0.00 0.00 3.36
3056 3317 9.955102 ATTTTAAATATATACTCCCTCCGTTCC 57.045 33.333 0.00 0.00 0.00 3.62
3143 3404 7.060383 TCAAAAGCATTCCAAAAGTCCATAA 57.940 32.000 0.00 0.00 0.00 1.90
3162 3424 6.036735 CAGTACTCTTTTCGTCCAACTCAAAA 59.963 38.462 0.00 0.00 0.00 2.44
3199 3461 8.774890 TTGCGTAGAAAAATTAGTATGTACCA 57.225 30.769 0.00 0.00 0.00 3.25
3393 3655 1.867233 CATTATGGGCTCGTGCAGTAC 59.133 52.381 12.07 0.00 41.91 2.73
3632 3979 6.184580 GTCCTACGACTACCATATGATCAG 57.815 45.833 3.65 0.61 35.99 2.90
3863 4234 1.294659 GGCTCTGTCGCTCCAACAAG 61.295 60.000 0.00 0.00 0.00 3.16
3864 4235 1.301716 GGCTCTGTCGCTCCAACAA 60.302 57.895 0.00 0.00 0.00 2.83
3987 4358 7.383687 TGCTAACCGGATAGATTAGGTTATTG 58.616 38.462 21.93 0.00 39.66 1.90
4001 4372 1.084289 GTTTCGCTTGCTAACCGGAT 58.916 50.000 9.46 0.00 0.00 4.18
4004 4375 4.717917 CGTTTCGCTTGCTAACCG 57.282 55.556 0.00 0.00 0.00 4.44
4020 4391 1.737793 GGGACATTCTTAGTGGTTGCG 59.262 52.381 0.00 0.00 0.00 4.85
4025 4397 4.301072 TTCAAGGGGACATTCTTAGTGG 57.699 45.455 0.00 0.00 0.00 4.00
4048 4420 5.309323 TCATAAAATGCGAAGTTGGGAAG 57.691 39.130 0.00 0.00 0.00 3.46
4120 4492 1.879380 TGAAACTGAACGGCATCCTTG 59.121 47.619 0.00 0.00 0.00 3.61
4148 4520 5.276868 CGCTTGAACGAGAGAGAAAGAAAAA 60.277 40.000 0.00 0.00 34.06 1.94
4149 4521 4.209288 CGCTTGAACGAGAGAGAAAGAAAA 59.791 41.667 0.00 0.00 34.06 2.29
4150 4522 3.736252 CGCTTGAACGAGAGAGAAAGAAA 59.264 43.478 0.00 0.00 34.06 2.52
4151 4523 3.243434 ACGCTTGAACGAGAGAGAAAGAA 60.243 43.478 0.00 0.00 36.70 2.52


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

AutoCloner maintained by Alex Coulton.