Multiple sequence alignment - TraesCS5A01G280200

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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 TraesCS5A01G280200 chr5A 100.000 4252 0 0 1 4252 489671838 489676089 0.000000e+00 7853.0
1 TraesCS5A01G280200 chr5A 98.492 199 2 1 2093 2291 514195607 514195804 2.430000e-92 350.0
2 TraesCS5A01G280200 chr7B 98.953 2102 22 0 4 2105 674023874 674021773 0.000000e+00 3760.0
3 TraesCS5A01G280200 chr7B 99.147 1172 10 0 2289 3460 674021787 674020616 0.000000e+00 2109.0
4 TraesCS5A01G280200 chr7B 98.992 794 7 1 3460 4252 674015211 674014418 0.000000e+00 1421.0
5 TraesCS5A01G280200 chr7B 88.361 653 71 5 975 1624 643499314 643498664 0.000000e+00 780.0
6 TraesCS5A01G280200 chr7D 90.204 1225 89 17 1 1222 171750914 171749718 0.000000e+00 1568.0
7 TraesCS5A01G280200 chr7D 88.556 935 91 13 3325 4252 506890468 506889543 0.000000e+00 1120.0
8 TraesCS5A01G280200 chr7D 87.706 545 49 12 1433 1974 171749586 171749057 1.680000e-173 619.0
9 TraesCS5A01G280200 chr7D 84.857 350 26 12 3928 4252 171748555 171748208 1.140000e-85 327.0
10 TraesCS5A01G280200 chr7D 91.667 132 10 1 1251 1382 171749722 171749592 9.390000e-42 182.0
11 TraesCS5A01G280200 chr2A 91.644 742 56 5 2369 3107 716481654 716482392 0.000000e+00 1022.0
12 TraesCS5A01G280200 chr2A 87.335 908 95 16 3357 4252 716482409 716483308 0.000000e+00 1022.0
13 TraesCS5A01G280200 chr2A 87.299 685 68 13 1437 2105 716480903 716481584 0.000000e+00 765.0
14 TraesCS5A01G280200 chr2A 88.160 549 54 9 303 845 716480209 716480752 0.000000e+00 643.0
15 TraesCS5A01G280200 chr2A 91.209 273 20 4 1355 1624 756521763 756521492 6.720000e-98 368.0
16 TraesCS5A01G280200 chr2A 98.980 196 1 1 2105 2300 569281849 569281655 2.430000e-92 350.0
17 TraesCS5A01G280200 chr2A 82.005 389 41 15 11 377 716479669 716480050 1.920000e-78 303.0
18 TraesCS5A01G280200 chr2B 88.208 653 72 5 975 1624 744690556 744689906 0.000000e+00 774.0
19 TraesCS5A01G280200 chr2B 98.010 201 3 1 2096 2296 535506442 535506243 8.750000e-92 348.0
20 TraesCS5A01G280200 chr2B 88.889 54 5 1 250 303 595312 595364 9.870000e-07 65.8
21 TraesCS5A01G280200 chrUn 89.568 556 52 4 3325 3879 29552939 29553489 0.000000e+00 701.0
22 TraesCS5A01G280200 chr3D 88.946 389 43 0 3491 3879 553769290 553769678 8.270000e-132 481.0
23 TraesCS5A01G280200 chr3D 89.222 167 16 1 3325 3491 553764995 553765159 1.550000e-49 207.0
24 TraesCS5A01G280200 chr4B 98.492 199 1 2 2105 2302 545868021 545868218 2.430000e-92 350.0
25 TraesCS5A01G280200 chr7A 98.485 198 1 2 2100 2297 332425358 332425553 8.750000e-92 348.0
26 TraesCS5A01G280200 chr7A 97.970 197 4 0 2096 2292 291727867 291727671 4.070000e-90 342.0
27 TraesCS5A01G280200 chr1B 96.651 209 5 2 2094 2300 374010139 374010347 3.150000e-91 346.0
28 TraesCS5A01G280200 chr1B 98.000 200 2 2 2095 2294 567190758 567190955 3.150000e-91 346.0
29 TraesCS5A01G280200 chr1B 96.209 211 5 3 2105 2315 70235861 70235654 4.070000e-90 342.0
30 TraesCS5A01G280200 chr6B 78.659 164 32 3 3465 3626 37054879 37055041 5.810000e-19 106.0


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 TraesCS5A01G280200 chr5A 489671838 489676089 4251 False 7853.0 7853 100.0000 1 4252 1 chr5A.!!$F1 4251
1 TraesCS5A01G280200 chr7B 674020616 674023874 3258 True 2934.5 3760 99.0500 4 3460 2 chr7B.!!$R3 3456
2 TraesCS5A01G280200 chr7B 674014418 674015211 793 True 1421.0 1421 98.9920 3460 4252 1 chr7B.!!$R2 792
3 TraesCS5A01G280200 chr7B 643498664 643499314 650 True 780.0 780 88.3610 975 1624 1 chr7B.!!$R1 649
4 TraesCS5A01G280200 chr7D 506889543 506890468 925 True 1120.0 1120 88.5560 3325 4252 1 chr7D.!!$R1 927
5 TraesCS5A01G280200 chr7D 171748208 171750914 2706 True 674.0 1568 88.6085 1 4252 4 chr7D.!!$R2 4251
6 TraesCS5A01G280200 chr2A 716479669 716483308 3639 False 751.0 1022 87.2886 11 4252 5 chr2A.!!$F1 4241
7 TraesCS5A01G280200 chr2B 744689906 744690556 650 True 774.0 774 88.2080 975 1624 1 chr2B.!!$R2 649
8 TraesCS5A01G280200 chrUn 29552939 29553489 550 False 701.0 701 89.5680 3325 3879 1 chrUn.!!$F1 554

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
168 188 1.208776 GGATGGTACTAGGCCAACGTT 59.791 52.381 5.01 0.0 39.72 3.99 F
2132 2809 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.0 44.29 3.32 F
2257 2934 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.0 44.78 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 2830 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46 R
3176 3880 1.002430 GTGGATGTGCTTCTCCTGTGA 59.998 52.381 0.00 0.00 32.47 3.58 R
3513 4219 4.631377 CGCTCACATCAAGTTCTTTATCCA 59.369 41.667 0.00 0.00 0.00 3.41 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
96 99 1.406887 GGCGGCTGAGGTTTTCTATGA 60.407 52.381 0.00 0.00 0.00 2.15
162 182 2.741747 GGCGGATGGTACTAGGCC 59.258 66.667 0.00 0.00 0.00 5.19
168 188 1.208776 GGATGGTACTAGGCCAACGTT 59.791 52.381 5.01 0.00 39.72 3.99
368 392 1.375908 CTGTGTATGGCCGTGCAGT 60.376 57.895 16.86 0.00 0.00 4.40
369 393 1.638388 CTGTGTATGGCCGTGCAGTG 61.638 60.000 16.86 8.29 0.00 3.66
370 394 1.671054 GTGTATGGCCGTGCAGTGT 60.671 57.895 16.86 0.00 0.00 3.55
1679 2029 3.544698 TCCAGGGTGTTCTAGTCTCTT 57.455 47.619 0.00 0.00 0.00 2.85
2085 2762 3.197766 GTGTGACAGTGGATTAGATGGGA 59.802 47.826 0.00 0.00 0.00 4.37
2100 2777 2.488204 TGGGAGTCGCATCAAAATGA 57.512 45.000 5.66 0.00 34.61 2.57
2101 2778 3.003394 TGGGAGTCGCATCAAAATGAT 57.997 42.857 5.66 0.00 37.65 2.45
2129 2806 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
2130 2807 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
2131 2808 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
2132 2809 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
2133 2810 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
2139 2816 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2140 2817 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2141 2818 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2142 2819 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2145 2822 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2157 2834 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
2158 2835 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
2159 2836 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
2160 2837 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
2161 2838 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
2162 2839 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
2163 2840 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
2164 2841 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
2165 2842 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
2166 2843 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
2167 2844 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
2168 2845 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
2169 2846 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2170 2847 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2171 2848 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
2172 2849 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
2173 2850 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2174 2851 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2175 2852 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2185 2862 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
2186 2863 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
2187 2864 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
2188 2865 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
2189 2866 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
2190 2867 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
2191 2868 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
2192 2869 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
2193 2870 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
2194 2871 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
2195 2872 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
2196 2873 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
2197 2874 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
2198 2875 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
2199 2876 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
2200 2877 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
2201 2878 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2202 2879 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2203 2880 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
2204 2881 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2205 2882 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
2206 2883 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
2207 2884 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
2208 2885 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
2209 2886 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
2210 2887 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
2211 2888 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
2223 2900 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
2224 2901 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
2225 2902 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
2226 2903 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
2227 2904 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
2228 2905 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
2229 2906 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
2230 2907 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
2231 2908 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
2232 2909 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
2233 2910 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
2234 2911 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
2235 2912 1.566703 TGTTTCCAGGACTTGAACCCA 59.433 47.619 0.00 0.00 0.00 4.51
2236 2913 2.176798 TGTTTCCAGGACTTGAACCCAT 59.823 45.455 0.00 0.00 0.00 4.00
2237 2914 2.558359 GTTTCCAGGACTTGAACCCATG 59.442 50.000 0.00 0.00 0.00 3.66
2238 2915 1.741028 TCCAGGACTTGAACCCATGA 58.259 50.000 0.00 0.00 0.00 3.07
2239 2916 1.351017 TCCAGGACTTGAACCCATGAC 59.649 52.381 0.00 0.00 0.00 3.06
2240 2917 1.614317 CCAGGACTTGAACCCATGACC 60.614 57.143 0.00 0.00 34.29 4.02
2241 2918 1.352352 CAGGACTTGAACCCATGACCT 59.648 52.381 0.00 0.00 40.96 3.85
2242 2919 1.630878 AGGACTTGAACCCATGACCTC 59.369 52.381 0.00 0.00 37.82 3.85
2243 2920 1.351017 GGACTTGAACCCATGACCTCA 59.649 52.381 0.00 0.00 32.45 3.86
2244 2921 2.025887 GGACTTGAACCCATGACCTCAT 60.026 50.000 0.00 0.00 36.96 2.90
2256 2933 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
2257 2934 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
2258 2935 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
2259 2936 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
2260 2937 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
2261 2938 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
2262 2939 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
2263 2940 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
2264 2941 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
2265 2942 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
2266 2943 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
2267 2944 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
2268 2945 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
2269 2946 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
2270 2947 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
2271 2948 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
2275 2952 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
2276 2953 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
2277 2954 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
2278 2955 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
2279 2956 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
2280 2957 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
2281 2958 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
2282 2959 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
2801 3498 7.014134 TGACTGCATTTGAGAAAATTGTAAGGA 59.986 33.333 0.00 0.00 0.00 3.36
3110 3814 2.249139 GTGGAGAACACTAGGTCCTGT 58.751 52.381 0.00 0.00 46.72 4.00
3176 3880 4.832248 ACAATGAGTGGTACATCGTTCAT 58.168 39.130 0.00 0.00 44.52 2.57
3513 4219 0.538287 GCAGGCAGACAAAGAGGGTT 60.538 55.000 0.00 0.00 0.00 4.11
4054 4781 3.348554 TAGTGCTAGGCCCGACGGA 62.349 63.158 17.49 0.00 0.00 4.69
4127 4859 1.169577 TTTGTGTTGCACTCGTTGGT 58.830 45.000 0.00 0.00 35.11 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 99 0.911769 TGGATCTGTGGCGGAGAAAT 59.088 50.000 0.00 0.00 0.00 2.17
162 182 2.025441 CCACCCGCACAAACGTTG 59.975 61.111 0.00 0.00 0.00 4.10
368 392 3.856521 CGCAAACAATTCAGTCAACAACA 59.143 39.130 0.00 0.00 0.00 3.33
369 393 3.242712 CCGCAAACAATTCAGTCAACAAC 59.757 43.478 0.00 0.00 0.00 3.32
370 394 3.443037 CCGCAAACAATTCAGTCAACAA 58.557 40.909 0.00 0.00 0.00 2.83
981 1324 1.358152 TCTTCCCGGTGGACAATTCT 58.642 50.000 0.00 0.00 41.57 2.40
1067 1410 0.966875 TGCTCCATGCCAGCGAAAAT 60.967 50.000 9.60 0.00 40.01 1.82
1391 1735 9.438291 CAGCCATCAAATTACTAATAAACTTCG 57.562 33.333 0.00 0.00 0.00 3.79
1917 2277 3.403038 CCATGGACATTTCCGATACCTC 58.597 50.000 5.56 0.00 46.37 3.85
2046 2723 4.074259 TCACACTCTGCTTGCAATTGTAT 58.926 39.130 7.40 0.00 0.00 2.29
2106 2783 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
2107 2784 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
2108 2785 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
2109 2786 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
2110 2787 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
2111 2788 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
2112 2789 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
2113 2790 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
2114 2791 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
2115 2792 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
2140 2817 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
2141 2818 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
2142 2819 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
2143 2820 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
2144 2821 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
2145 2822 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
2146 2823 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
2147 2824 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
2148 2825 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
2149 2826 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
2150 2827 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
2151 2828 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
2152 2829 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
2153 2830 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
2154 2831 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2155 2832 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2156 2833 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2157 2834 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
2158 2835 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2159 2836 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2164 2841 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
2165 2842 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
2166 2843 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
2167 2844 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
2168 2845 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
2169 2846 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
2170 2847 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
2171 2848 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
2172 2849 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
2173 2850 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
2174 2851 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
2175 2852 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
2176 2853 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
2177 2854 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
2178 2855 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
2179 2856 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
2180 2857 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
2181 2858 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
2182 2859 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
2183 2860 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2184 2861 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2185 2862 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2186 2863 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
2187 2864 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
2188 2865 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
2189 2866 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
2190 2867 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
2191 2868 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
2192 2869 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
2193 2870 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
2194 2871 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
2195 2872 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
2196 2873 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
2197 2874 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
2198 2875 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
2199 2876 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
2200 2877 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
2201 2878 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
2215 2892 1.566703 TGGGTTCAAGTCCTGGAAACA 59.433 47.619 0.00 0.00 32.36 2.83
2216 2893 2.358322 TGGGTTCAAGTCCTGGAAAC 57.642 50.000 0.00 0.00 0.00 2.78
2217 2894 2.445145 TCATGGGTTCAAGTCCTGGAAA 59.555 45.455 0.00 0.00 0.00 3.13
2218 2895 2.061848 TCATGGGTTCAAGTCCTGGAA 58.938 47.619 0.00 0.00 0.00 3.53
2219 2896 1.351017 GTCATGGGTTCAAGTCCTGGA 59.649 52.381 0.00 0.00 0.00 3.86
2220 2897 1.614317 GGTCATGGGTTCAAGTCCTGG 60.614 57.143 0.00 0.00 0.00 4.45
2221 2898 1.352352 AGGTCATGGGTTCAAGTCCTG 59.648 52.381 0.00 0.00 0.00 3.86
2222 2899 1.630878 GAGGTCATGGGTTCAAGTCCT 59.369 52.381 0.00 0.00 0.00 3.85
2223 2900 1.351017 TGAGGTCATGGGTTCAAGTCC 59.649 52.381 0.00 0.00 0.00 3.85
2224 2901 2.859165 TGAGGTCATGGGTTCAAGTC 57.141 50.000 0.00 0.00 0.00 3.01
2239 2916 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
2240 2917 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
2241 2918 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
2242 2919 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
2243 2920 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
2244 2921 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
2245 2922 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
2246 2923 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
2247 2924 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
2248 2925 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
2249 2926 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
2250 2927 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
2251 2928 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
2252 2929 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
2253 2930 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
2258 2935 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
2259 2936 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
2260 2937 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
2261 2938 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
2262 2939 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
2263 2940 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
2264 2941 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
2272 2949 3.350031 ATGAAGGGGAGCCTTGGCG 62.350 63.158 5.95 0.00 0.00 5.69
2273 2950 1.454663 GATGAAGGGGAGCCTTGGC 60.455 63.158 2.97 2.97 0.00 4.52
2274 2951 0.332632 TTGATGAAGGGGAGCCTTGG 59.667 55.000 0.00 0.00 0.00 3.61
2275 2952 2.220653 TTTGATGAAGGGGAGCCTTG 57.779 50.000 0.00 0.00 0.00 3.61
2276 2953 2.999185 TTTTGATGAAGGGGAGCCTT 57.001 45.000 0.00 0.00 0.00 4.35
2277 2954 2.312741 TCATTTTGATGAAGGGGAGCCT 59.687 45.455 0.00 0.00 0.00 4.58
2278 2955 2.738743 TCATTTTGATGAAGGGGAGCC 58.261 47.619 0.00 0.00 0.00 4.70
2318 2995 6.998074 CACATTATAACCATTGAGAGGCCTAA 59.002 38.462 4.42 0.00 0.00 2.69
2801 3498 2.503356 CAGAAGGGTTCTCTGCATACCT 59.497 50.000 0.00 0.00 38.11 3.08
3110 3814 1.372872 CGCATGACACTCACACCGA 60.373 57.895 0.00 0.00 0.00 4.69
3176 3880 1.002430 GTGGATGTGCTTCTCCTGTGA 59.998 52.381 0.00 0.00 32.47 3.58
3513 4219 4.631377 CGCTCACATCAAGTTCTTTATCCA 59.369 41.667 0.00 0.00 0.00 3.41
4077 4804 9.995003 AAAATAATCCACAACACAACATAACAT 57.005 25.926 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.