Multiple sequence alignment - TraesCS5D01G205200

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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 TraesCS5D01G205200 chr5D 100.000 3558 0 0 2679 6236 311310742 311307185 0.000000e+00 6571
1 TraesCS5D01G205200 chr5D 100.000 2311 0 0 1 2311 311313420 311311110 0.000000e+00 4268
2 TraesCS5D01G205200 chr5D 80.080 497 91 6 4872 5363 310703469 310702976 4.590000e-96 363
3 TraesCS5D01G205200 chr5D 88.546 227 26 0 2679 2905 311310685 311310459 6.160000e-70 276
4 TraesCS5D01G205200 chr5D 88.546 227 26 0 2736 2962 311310742 311310516 6.160000e-70 276
5 TraesCS5D01G205200 chr5D 74.194 496 95 26 5323 5811 310702974 310702505 6.420000e-40 176
6 TraesCS5D01G205200 chr5D 86.331 139 13 3 2058 2196 311311243 311311111 5.040000e-31 147
7 TraesCS5D01G205200 chr5D 86.331 139 13 3 2178 2310 311311363 311311225 5.040000e-31 147
8 TraesCS5D01G205200 chr5A 96.013 3562 99 12 2684 6236 404314179 404310652 0.000000e+00 5751
9 TraesCS5D01G205200 chr5A 95.355 2110 57 21 166 2258 404316586 404314501 0.000000e+00 3315
10 TraesCS5D01G205200 chr5A 88.106 227 27 0 2679 2905 404314127 404313901 2.860000e-68 270
11 TraesCS5D01G205200 chr5A 86.937 222 29 0 2741 2962 404314179 404313958 3.730000e-62 250
12 TraesCS5D01G205200 chr5A 85.222 203 18 5 2115 2311 404314701 404314505 1.370000e-46 198
13 TraesCS5D01G205200 chr5A 87.952 166 17 3 1 164 404316703 404316539 6.380000e-45 193
14 TraesCS5D01G205200 chr5A 74.104 502 90 30 5323 5811 404232944 404232470 2.990000e-38 171
15 TraesCS5D01G205200 chr5A 87.770 139 11 3 2178 2310 404314701 404314563 2.330000e-34 158
16 TraesCS5D01G205200 chr5A 90.756 119 10 1 1501 1619 440988307 440988424 2.330000e-34 158
17 TraesCS5D01G205200 chr5A 86.713 143 15 3 1500 1641 476640515 476640376 8.370000e-34 156
18 TraesCS5D01G205200 chr5A 92.105 76 6 0 2058 2133 404314581 404314506 2.380000e-19 108
19 TraesCS5D01G205200 chr5B 95.573 2304 64 17 3941 6236 357105620 357103347 0.000000e+00 3655
20 TraesCS5D01G205200 chr5B 95.254 2128 56 12 168 2282 357109318 357107223 0.000000e+00 3328
21 TraesCS5D01G205200 chr5B 97.275 1211 31 2 2687 3895 357106827 357105617 0.000000e+00 2052
22 TraesCS5D01G205200 chr5B 77.841 528 93 16 4839 5363 356722009 356721503 7.850000e-79 305
23 TraesCS5D01G205200 chr5B 89.427 227 24 0 2679 2905 357106778 357106552 2.840000e-73 287
24 TraesCS5D01G205200 chr5B 75.050 501 88 27 5323 5811 356721501 356721026 1.370000e-46 198
25 TraesCS5D01G205200 chr5B 85.222 203 18 5 2115 2311 357107447 357107251 1.370000e-46 198
26 TraesCS5D01G205200 chr5B 85.143 175 13 6 2058 2226 357107390 357107223 3.870000e-37 167
27 TraesCS5D01G205200 chr5B 90.756 119 11 0 1500 1618 635560826 635560708 6.470000e-35 159
28 TraesCS5D01G205200 chr5B 87.050 139 12 3 2178 2310 357107447 357107309 1.080000e-32 152
29 TraesCS5D01G205200 chr5B 94.737 76 4 0 2235 2310 357107447 357107372 1.100000e-22 119
30 TraesCS5D01G205200 chr5B 88.372 86 10 0 2058 2143 357107327 357107242 3.070000e-18 104
31 TraesCS5D01G205200 chr1B 93.333 120 8 0 1500 1619 48266477 48266358 1.790000e-40 178
32 TraesCS5D01G205200 chrUn 90.678 118 11 0 1501 1618 61037037 61037154 2.330000e-34 158
33 TraesCS5D01G205200 chr7D 88.800 125 13 1 1493 1617 565705253 565705130 1.080000e-32 152
34 TraesCS5D01G205200 chr4B 85.816 141 17 3 1500 1638 136675858 136675719 5.040000e-31 147


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 TraesCS5D01G205200 chr5D 311307185 311313420 6235 True 1947.500 6571 91.625667 1 6236 6 chr5D.!!$R2 6235
1 TraesCS5D01G205200 chr5D 310702505 310703469 964 True 269.500 363 77.137000 4872 5811 2 chr5D.!!$R1 939
2 TraesCS5D01G205200 chr5A 404310652 404316703 6051 True 1280.375 5751 89.932500 1 6236 8 chr5A.!!$R3 6235
3 TraesCS5D01G205200 chr5B 357103347 357109318 5971 True 1118.000 3655 90.894778 168 6236 9 chr5B.!!$R3 6068
4 TraesCS5D01G205200 chr5B 356721026 356722009 983 True 251.500 305 76.445500 4839 5811 2 chr5B.!!$R2 972

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
164 165 0.102300 CACGAGGTATGACATGGCGA 59.898 55.0 0.00 0.00 0.0 5.54 F
1620 1631 0.104304 CCGGACGGAGGGAGTATTTG 59.896 60.0 4.40 0.00 37.5 2.32 F
2287 2305 0.251165 GCACTTGTTCCCCCAGCTAA 60.251 55.0 0.00 0.00 0.0 3.09 F
2707 2725 0.533032 GAGCTGTGACTAGACCACCC 59.467 60.0 14.24 7.94 33.8 4.61 F
4583 4605 0.463654 AAAGCTTCCGTCTGCACACA 60.464 50.0 0.00 0.00 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2122 2140 1.070786 GGTCTTGTCACGGCTCCAA 59.929 57.895 0.00 0.00 0.00 3.53 R
2678 2696 0.108585 GTCACAGCTCCAGGACCAAA 59.891 55.000 0.00 0.00 0.00 3.28 R
3949 3969 2.739943 CCATCTCTCCACTCACTGGTA 58.260 52.381 0.00 0.00 41.52 3.25 R
4589 4611 2.189521 CAAGATCGAACCCCGGGG 59.810 66.667 39.18 39.18 39.14 5.73 R
6104 6176 0.451783 GTCCGCCAATCGCTTTTGAT 59.548 50.000 0.00 0.00 36.73 2.57 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
82 83 4.770874 ACGAAATCGCGGTGGGGG 62.771 66.667 6.13 0.00 44.43 5.40
116 117 1.134220 GGGGGTTGTAGCATTCATCGA 60.134 52.381 0.00 0.00 0.00 3.59
117 118 2.487265 GGGGGTTGTAGCATTCATCGAT 60.487 50.000 0.00 0.00 0.00 3.59
118 119 2.549754 GGGGTTGTAGCATTCATCGATG 59.450 50.000 19.61 19.61 0.00 3.84
129 130 3.507103 TTCATCGATGCATTGGTTTGG 57.493 42.857 20.81 0.00 0.00 3.28
130 131 2.720915 TCATCGATGCATTGGTTTGGA 58.279 42.857 20.81 0.00 0.00 3.53
131 132 2.684374 TCATCGATGCATTGGTTTGGAG 59.316 45.455 20.81 0.00 0.00 3.86
132 133 1.462616 TCGATGCATTGGTTTGGAGG 58.537 50.000 14.12 0.00 0.00 4.30
133 134 0.457035 CGATGCATTGGTTTGGAGGG 59.543 55.000 5.98 0.00 0.00 4.30
134 135 0.826062 GATGCATTGGTTTGGAGGGG 59.174 55.000 0.00 0.00 0.00 4.79
135 136 0.413037 ATGCATTGGTTTGGAGGGGA 59.587 50.000 0.00 0.00 0.00 4.81
136 137 0.541764 TGCATTGGTTTGGAGGGGAC 60.542 55.000 0.00 0.00 0.00 4.46
137 138 1.595093 GCATTGGTTTGGAGGGGACG 61.595 60.000 0.00 0.00 0.00 4.79
138 139 0.965363 CATTGGTTTGGAGGGGACGG 60.965 60.000 0.00 0.00 0.00 4.79
139 140 2.781431 ATTGGTTTGGAGGGGACGGC 62.781 60.000 0.00 0.00 0.00 5.68
161 162 2.992089 GGCACGAGGTATGACATGG 58.008 57.895 0.00 0.00 0.00 3.66
162 163 1.160329 GGCACGAGGTATGACATGGC 61.160 60.000 0.00 0.00 0.00 4.40
163 164 1.490693 GCACGAGGTATGACATGGCG 61.491 60.000 0.00 0.00 0.00 5.69
164 165 0.102300 CACGAGGTATGACATGGCGA 59.898 55.000 0.00 0.00 0.00 5.54
176 177 2.098614 ACATGGCGATGCATTGGTTTA 58.901 42.857 15.85 0.00 32.14 2.01
233 243 1.602771 GGCGAAGAACCCTAAGGCT 59.397 57.895 0.00 0.00 36.11 4.58
298 308 3.986996 TTTAACCCTAAACCTCCCTCG 57.013 47.619 0.00 0.00 0.00 4.63
304 314 2.025898 CCTAAACCTCCCTCGAGAGTC 58.974 57.143 15.71 0.00 38.52 3.36
410 420 2.048023 CCGCCGTGGTACTGGTAGA 61.048 63.158 0.00 0.00 0.00 2.59
591 601 4.530857 CCGGCGCCCTTCTACCAG 62.531 72.222 23.46 2.52 0.00 4.00
1145 1155 9.587772 CTAACTGATTACATGCTGTAACTTACT 57.412 33.333 9.85 0.00 44.54 2.24
1214 1224 5.936956 ACTGTGGATTTTTGCAAACTTCAAA 59.063 32.000 12.39 3.33 0.00 2.69
1235 1245 7.270779 TCAAATGTGACATTTCCAAAATGTGA 58.729 30.769 19.77 9.55 40.62 3.58
1239 1249 5.534278 TGTGACATTTCCAAAATGTGAGCTA 59.466 36.000 19.60 2.41 40.62 3.32
1297 1307 4.406649 ACCATTTTAATGAGAGGCCATTGG 59.593 41.667 5.01 0.00 38.70 3.16
1521 1531 2.271777 ACTCCCTCCGTCCCAAATTAA 58.728 47.619 0.00 0.00 0.00 1.40
1620 1631 0.104304 CCGGACGGAGGGAGTATTTG 59.896 60.000 4.40 0.00 37.50 2.32
1901 1912 5.769662 TGTGTTTGGATTGCTGAAGTCTTAT 59.230 36.000 0.00 0.00 0.00 1.73
1915 1926 6.841601 TGAAGTCTTATTAATATGGCAGGCT 58.158 36.000 13.60 4.85 0.00 4.58
1922 1933 9.806448 TCTTATTAATATGGCAGGCTGATTTTA 57.194 29.630 20.86 6.82 0.00 1.52
2122 2140 4.082125 CCTCCAGCTAATGTTTTTGGTCT 58.918 43.478 0.00 0.00 0.00 3.85
2148 2166 3.606886 GTGACAAGACCACGACCAT 57.393 52.632 0.00 0.00 0.00 3.55
2159 2177 2.039216 ACCACGACCATTTATGACACCA 59.961 45.455 0.00 0.00 0.00 4.17
2282 2300 0.251916 CTATCGCACTTGTTCCCCCA 59.748 55.000 0.00 0.00 0.00 4.96
2283 2301 0.251916 TATCGCACTTGTTCCCCCAG 59.748 55.000 0.00 0.00 0.00 4.45
2284 2302 3.365265 CGCACTTGTTCCCCCAGC 61.365 66.667 0.00 0.00 0.00 4.85
2285 2303 2.116125 GCACTTGTTCCCCCAGCT 59.884 61.111 0.00 0.00 0.00 4.24
2286 2304 1.378762 GCACTTGTTCCCCCAGCTA 59.621 57.895 0.00 0.00 0.00 3.32
2287 2305 0.251165 GCACTTGTTCCCCCAGCTAA 60.251 55.000 0.00 0.00 0.00 3.09
2288 2306 1.616994 GCACTTGTTCCCCCAGCTAAT 60.617 52.381 0.00 0.00 0.00 1.73
2289 2307 2.094675 CACTTGTTCCCCCAGCTAATG 58.905 52.381 0.00 0.00 0.00 1.90
2290 2308 1.710809 ACTTGTTCCCCCAGCTAATGT 59.289 47.619 0.00 0.00 0.00 2.71
2291 2309 2.110011 ACTTGTTCCCCCAGCTAATGTT 59.890 45.455 0.00 0.00 0.00 2.71
2292 2310 2.990740 TGTTCCCCCAGCTAATGTTT 57.009 45.000 0.00 0.00 0.00 2.83
2293 2311 3.252554 TGTTCCCCCAGCTAATGTTTT 57.747 42.857 0.00 0.00 0.00 2.43
2294 2312 3.582164 TGTTCCCCCAGCTAATGTTTTT 58.418 40.909 0.00 0.00 0.00 1.94
2295 2313 3.323403 TGTTCCCCCAGCTAATGTTTTTG 59.677 43.478 0.00 0.00 0.00 2.44
2296 2314 2.534990 TCCCCCAGCTAATGTTTTTGG 58.465 47.619 0.00 0.00 0.00 3.28
2297 2315 2.158234 TCCCCCAGCTAATGTTTTTGGT 60.158 45.455 0.00 0.00 0.00 3.67
2298 2316 2.233676 CCCCCAGCTAATGTTTTTGGTC 59.766 50.000 0.00 0.00 0.00 4.02
2299 2317 2.233676 CCCCAGCTAATGTTTTTGGTCC 59.766 50.000 0.00 0.00 0.00 4.46
2300 2318 3.165071 CCCAGCTAATGTTTTTGGTCCT 58.835 45.455 0.00 0.00 0.00 3.85
2301 2319 3.056607 CCCAGCTAATGTTTTTGGTCCTG 60.057 47.826 0.00 0.00 0.00 3.86
2302 2320 3.056607 CCAGCTAATGTTTTTGGTCCTGG 60.057 47.826 0.00 0.00 0.00 4.45
2303 2321 3.826157 CAGCTAATGTTTTTGGTCCTGGA 59.174 43.478 0.00 0.00 0.00 3.86
2304 2322 4.082125 AGCTAATGTTTTTGGTCCTGGAG 58.918 43.478 0.00 0.00 0.00 3.86
2305 2323 3.367395 GCTAATGTTTTTGGTCCTGGAGC 60.367 47.826 18.72 18.72 0.00 4.70
2306 2324 1.632589 ATGTTTTTGGTCCTGGAGCC 58.367 50.000 22.16 14.49 0.00 4.70
2307 2325 0.821711 TGTTTTTGGTCCTGGAGCCG 60.822 55.000 22.16 0.00 0.00 5.52
2308 2326 0.822121 GTTTTTGGTCCTGGAGCCGT 60.822 55.000 22.16 0.00 0.00 5.68
2309 2327 0.821711 TTTTTGGTCCTGGAGCCGTG 60.822 55.000 22.16 0.00 0.00 4.94
2310 2328 2.690653 TTTTGGTCCTGGAGCCGTGG 62.691 60.000 22.16 0.00 0.00 4.94
2707 2725 0.533032 GAGCTGTGACTAGACCACCC 59.467 60.000 14.24 7.94 33.80 4.61
2768 2786 3.024547 GCTGTGACTAGACCACCTATCA 58.975 50.000 14.24 0.00 33.80 2.15
2832 2850 2.438434 ACCACCTATTGCGCCTGC 60.438 61.111 4.18 0.00 43.20 4.85
2950 2968 1.138859 CCTCATATCGCACCTGTTCCA 59.861 52.381 0.00 0.00 0.00 3.53
2968 2986 2.086869 CCACCAGTTAATGAGCCACAG 58.913 52.381 0.00 0.00 0.00 3.66
3140 3159 9.622004 CATATTAGATTCTGGCAAATCATGTTC 57.378 33.333 18.17 0.45 37.98 3.18
3308 3327 7.595819 TTGTAAAAAGTTGGAATCCAGTCAT 57.404 32.000 0.86 0.00 33.81 3.06
3388 3407 4.166011 GTCTTCGTGCATGGCGGC 62.166 66.667 5.98 0.00 0.00 6.53
3446 3465 2.213499 GGTATGTACTGGTCTGCATGC 58.787 52.381 11.82 11.82 0.00 4.06
3949 3969 2.858476 TGACAGGTGGGCCCATGT 60.858 61.111 31.45 29.27 34.66 3.21
4033 4053 2.669434 TCGCGCTAGTTGTTAAATGGAC 59.331 45.455 5.56 0.00 0.00 4.02
4124 4144 3.347958 TTTGCTTTGAAACTAGTGGCG 57.652 42.857 0.00 0.00 0.00 5.69
4507 4528 2.935238 GCGTAGGAGAACCTGCATTTGA 60.935 50.000 0.00 0.00 46.80 2.69
4583 4605 0.463654 AAAGCTTCCGTCTGCACACA 60.464 50.000 0.00 0.00 0.00 3.72
4584 4606 0.882042 AAGCTTCCGTCTGCACACAG 60.882 55.000 0.00 0.00 45.95 3.66
4585 4607 2.959357 GCTTCCGTCTGCACACAGC 61.959 63.158 0.00 0.00 44.10 4.40
4732 4754 4.670765 ACAGAAGAGAAGGCCAATGAAAT 58.329 39.130 5.01 0.00 0.00 2.17
4850 4872 3.996921 AGCATCAGTGATGAGAAAGGT 57.003 42.857 32.61 10.60 42.09 3.50
5089 5111 1.676014 GCGCAGGGAAAGTGAGTGTAT 60.676 52.381 0.30 0.00 0.00 2.29
5213 5242 3.281727 TGGTGAAGGGCATTGTATCTC 57.718 47.619 0.00 0.00 0.00 2.75
5271 5300 2.158460 CCCCAGGAGAAAAGGTGAGTTT 60.158 50.000 0.00 0.00 0.00 2.66
5545 5617 7.675161 TGAACTCCCATCTCATTCTTATACA 57.325 36.000 0.00 0.00 0.00 2.29
5548 5620 9.566432 GAACTCCCATCTCATTCTTATACAATT 57.434 33.333 0.00 0.00 0.00 2.32
5549 5621 8.915057 ACTCCCATCTCATTCTTATACAATTG 57.085 34.615 3.24 3.24 0.00 2.32
5722 5794 1.794714 TGGAGGCCCTTGTATCTCTC 58.205 55.000 0.00 0.00 0.00 3.20
5817 5889 5.677319 ACCGGATTAGAATGAAGACAGAA 57.323 39.130 9.46 0.00 0.00 3.02
6104 6176 3.093814 TGCTCAAGGTCGGTGAGTAATA 58.906 45.455 3.58 0.00 43.71 0.98
6112 6184 5.116882 AGGTCGGTGAGTAATATCAAAAGC 58.883 41.667 0.00 0.00 0.00 3.51
6171 6243 3.181493 GCTGCAGTTGTTGATATCTTGGG 60.181 47.826 16.64 0.00 0.00 4.12
6208 6281 0.952984 GCACTGTGTTCTCCTGGCTC 60.953 60.000 9.86 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.152830 TTCACTGGCCCCTTCCAAC 59.847 57.895 0.00 0.00 35.36 3.77
89 90 2.046314 CTACAACCCCCACGGCAG 60.046 66.667 0.00 0.00 33.26 4.85
90 91 4.338710 GCTACAACCCCCACGGCA 62.339 66.667 0.00 0.00 33.26 5.69
97 98 2.325583 TCGATGAATGCTACAACCCC 57.674 50.000 0.00 0.00 0.00 4.95
116 117 0.413037 TCCCCTCCAAACCAATGCAT 59.587 50.000 0.00 0.00 0.00 3.96
117 118 0.541764 GTCCCCTCCAAACCAATGCA 60.542 55.000 0.00 0.00 0.00 3.96
118 119 1.595093 CGTCCCCTCCAAACCAATGC 61.595 60.000 0.00 0.00 0.00 3.56
119 120 0.965363 CCGTCCCCTCCAAACCAATG 60.965 60.000 0.00 0.00 0.00 2.82
120 121 1.382629 CCGTCCCCTCCAAACCAAT 59.617 57.895 0.00 0.00 0.00 3.16
121 122 2.840576 CCGTCCCCTCCAAACCAA 59.159 61.111 0.00 0.00 0.00 3.67
122 123 3.961414 GCCGTCCCCTCCAAACCA 61.961 66.667 0.00 0.00 0.00 3.67
139 140 4.201679 TCATACCTCGTGCCGCCG 62.202 66.667 0.00 0.00 0.00 6.46
140 141 2.585247 GTCATACCTCGTGCCGCC 60.585 66.667 0.00 0.00 0.00 6.13
141 142 1.227263 ATGTCATACCTCGTGCCGC 60.227 57.895 0.00 0.00 0.00 6.53
142 143 0.875908 CCATGTCATACCTCGTGCCG 60.876 60.000 0.00 0.00 0.00 5.69
143 144 1.160329 GCCATGTCATACCTCGTGCC 61.160 60.000 0.00 0.00 0.00 5.01
144 145 1.490693 CGCCATGTCATACCTCGTGC 61.491 60.000 0.00 0.00 0.00 5.34
145 146 0.102300 TCGCCATGTCATACCTCGTG 59.898 55.000 0.00 0.00 0.00 4.35
146 147 1.040646 ATCGCCATGTCATACCTCGT 58.959 50.000 0.00 0.00 0.00 4.18
147 148 1.422388 CATCGCCATGTCATACCTCG 58.578 55.000 0.00 0.00 0.00 4.63
148 149 1.151668 GCATCGCCATGTCATACCTC 58.848 55.000 0.00 0.00 31.86 3.85
149 150 0.469494 TGCATCGCCATGTCATACCT 59.531 50.000 0.00 0.00 31.86 3.08
150 151 1.527034 ATGCATCGCCATGTCATACC 58.473 50.000 0.00 0.00 29.93 2.73
151 152 2.351060 CCAATGCATCGCCATGTCATAC 60.351 50.000 0.00 0.00 30.89 2.39
152 153 1.881324 CCAATGCATCGCCATGTCATA 59.119 47.619 0.00 0.00 30.89 2.15
153 154 0.671796 CCAATGCATCGCCATGTCAT 59.328 50.000 0.00 0.00 31.79 3.06
154 155 0.680601 ACCAATGCATCGCCATGTCA 60.681 50.000 0.00 0.00 31.86 3.58
155 156 0.457035 AACCAATGCATCGCCATGTC 59.543 50.000 0.00 0.00 31.86 3.06
156 157 0.896923 AAACCAATGCATCGCCATGT 59.103 45.000 0.00 0.00 31.86 3.21
157 158 2.358582 TCTAAACCAATGCATCGCCATG 59.641 45.455 0.00 0.00 0.00 3.66
158 159 2.620115 CTCTAAACCAATGCATCGCCAT 59.380 45.455 0.00 0.00 0.00 4.40
159 160 2.016318 CTCTAAACCAATGCATCGCCA 58.984 47.619 0.00 0.00 0.00 5.69
160 161 1.334869 CCTCTAAACCAATGCATCGCC 59.665 52.381 0.00 0.00 0.00 5.54
161 162 1.334869 CCCTCTAAACCAATGCATCGC 59.665 52.381 0.00 0.00 0.00 4.58
162 163 1.949525 CCCCTCTAAACCAATGCATCG 59.050 52.381 0.00 0.00 0.00 3.84
163 164 2.310538 CCCCCTCTAAACCAATGCATC 58.689 52.381 0.00 0.00 0.00 3.91
164 165 1.689258 GCCCCCTCTAAACCAATGCAT 60.689 52.381 0.00 0.00 0.00 3.96
191 196 1.441729 CCGCCATGTCATACCTCGT 59.558 57.895 0.00 0.00 0.00 4.18
194 199 1.383943 TCCCCGCCATGTCATACCT 60.384 57.895 0.00 0.00 0.00 3.08
198 203 3.492353 CCCTCCCCGCCATGTCAT 61.492 66.667 0.00 0.00 0.00 3.06
233 243 5.298777 GCACGGTATTCTCTTCTAGGTCTAA 59.701 44.000 0.00 0.00 0.00 2.10
304 314 1.065251 GCGTACGAGAACTAAGAGGGG 59.935 57.143 21.65 0.00 0.00 4.79
335 345 0.754957 AGGGCAGATCTGGACGAGAG 60.755 60.000 23.89 0.00 32.80 3.20
340 350 1.127343 AAGCTAGGGCAGATCTGGAC 58.873 55.000 23.89 8.26 41.70 4.02
458 468 3.611674 GTTGGTTGGGTTGGGCGG 61.612 66.667 0.00 0.00 0.00 6.13
459 469 3.611674 GGTTGGTTGGGTTGGGCG 61.612 66.667 0.00 0.00 0.00 6.13
460 470 3.611674 CGGTTGGTTGGGTTGGGC 61.612 66.667 0.00 0.00 0.00 5.36
461 471 1.228737 ATCGGTTGGTTGGGTTGGG 60.229 57.895 0.00 0.00 0.00 4.12
462 472 0.538516 TCATCGGTTGGTTGGGTTGG 60.539 55.000 0.00 0.00 0.00 3.77
463 473 1.000717 GTTCATCGGTTGGTTGGGTTG 60.001 52.381 0.00 0.00 0.00 3.77
464 474 1.324383 GTTCATCGGTTGGTTGGGTT 58.676 50.000 0.00 0.00 0.00 4.11
465 475 0.887387 CGTTCATCGGTTGGTTGGGT 60.887 55.000 0.00 0.00 35.71 4.51
466 476 1.873165 CGTTCATCGGTTGGTTGGG 59.127 57.895 0.00 0.00 35.71 4.12
467 477 1.209127 GCGTTCATCGGTTGGTTGG 59.791 57.895 0.00 0.00 40.26 3.77
468 478 4.838959 GCGTTCATCGGTTGGTTG 57.161 55.556 0.00 0.00 40.26 3.77
640 650 2.028631 GTATACGCGAGGCCCACC 59.971 66.667 15.93 0.00 0.00 4.61
1214 1224 5.011329 AGCTCACATTTTGGAAATGTCACAT 59.989 36.000 14.27 0.00 38.69 3.21
1297 1307 7.423314 CGAAATATTTACAAAATGCTTTGCTGC 59.577 33.333 0.00 0.00 44.96 5.25
1521 1531 9.868277 TCCATTTTTATTTATTTCTGCGACAAT 57.132 25.926 0.00 0.00 0.00 2.71
1660 1671 4.518249 TCAGAGAGATCGTACATGACTGT 58.482 43.478 0.00 0.00 39.49 3.55
2047 2065 2.089980 CAGGACCAAAAGCTCCATCAG 58.910 52.381 0.00 0.00 0.00 2.90
2122 2140 1.070786 GGTCTTGTCACGGCTCCAA 59.929 57.895 0.00 0.00 0.00 3.53
2148 2166 3.559171 GCTGGAGGAACTGGTGTCATAAA 60.559 47.826 0.00 0.00 41.55 1.40
2258 2276 1.338769 GGAACAAGTGCGATAGGTGGT 60.339 52.381 0.00 0.00 0.00 4.16
2282 2300 4.082125 CTCCAGGACCAAAAACATTAGCT 58.918 43.478 0.00 0.00 0.00 3.32
2283 2301 3.367395 GCTCCAGGACCAAAAACATTAGC 60.367 47.826 0.00 0.00 0.00 3.09
2284 2302 3.193479 GGCTCCAGGACCAAAAACATTAG 59.807 47.826 0.00 0.00 0.00 1.73
2285 2303 3.161866 GGCTCCAGGACCAAAAACATTA 58.838 45.455 0.00 0.00 0.00 1.90
2286 2304 1.970640 GGCTCCAGGACCAAAAACATT 59.029 47.619 0.00 0.00 0.00 2.71
2287 2305 1.632589 GGCTCCAGGACCAAAAACAT 58.367 50.000 0.00 0.00 0.00 2.71
2288 2306 0.821711 CGGCTCCAGGACCAAAAACA 60.822 55.000 8.35 0.00 0.00 2.83
2289 2307 0.822121 ACGGCTCCAGGACCAAAAAC 60.822 55.000 8.35 0.00 0.00 2.43
2290 2308 0.821711 CACGGCTCCAGGACCAAAAA 60.822 55.000 8.35 0.00 0.00 1.94
2291 2309 1.228124 CACGGCTCCAGGACCAAAA 60.228 57.895 8.35 0.00 0.00 2.44
2292 2310 2.429930 CACGGCTCCAGGACCAAA 59.570 61.111 8.35 0.00 0.00 3.28
2293 2311 3.636231 CCACGGCTCCAGGACCAA 61.636 66.667 8.35 0.00 0.00 3.67
2678 2696 0.108585 GTCACAGCTCCAGGACCAAA 59.891 55.000 0.00 0.00 0.00 3.28
2679 2697 0.764369 AGTCACAGCTCCAGGACCAA 60.764 55.000 0.00 0.00 0.00 3.67
2680 2698 0.114364 TAGTCACAGCTCCAGGACCA 59.886 55.000 0.00 0.00 0.00 4.02
2681 2699 0.820871 CTAGTCACAGCTCCAGGACC 59.179 60.000 0.00 0.00 0.00 4.46
2682 2700 1.474879 GTCTAGTCACAGCTCCAGGAC 59.525 57.143 0.00 0.00 0.00 3.85
2707 2725 1.699656 CTGAAGGAACAGGCGCGATG 61.700 60.000 12.10 10.70 34.64 3.84
2768 2786 1.192146 TTAGCTGGAGGAACAGGCGT 61.192 55.000 0.00 0.00 38.90 5.68
2832 2850 2.611518 CAAAGACGTTAGCTGGAGGAG 58.388 52.381 0.00 0.00 0.00 3.69
2950 2968 3.508845 AACTGTGGCTCATTAACTGGT 57.491 42.857 0.00 0.00 0.00 4.00
3112 3131 9.139734 ACATGATTTGCCAGAATCTAATATGTT 57.860 29.630 0.00 0.00 37.04 2.71
3115 3134 8.800332 GGAACATGATTTGCCAGAATCTAATAT 58.200 33.333 0.00 0.00 37.04 1.28
3163 3182 8.973182 CCTTTTATAAACCCCAATTAACTAGCA 58.027 33.333 0.00 0.00 0.00 3.49
3177 3196 7.116376 GCTTCACAGCTTTTCCTTTTATAAACC 59.884 37.037 0.00 0.00 43.51 3.27
3388 3407 6.805271 CCATCAATTCTTAGTTTGTTGAGCAG 59.195 38.462 8.90 0.00 32.93 4.24
3446 3465 4.126208 TGGATGTTGCAAGCATAAATGG 57.874 40.909 0.00 0.00 0.00 3.16
3505 3524 3.105283 TCTAACTAGGGCCAACTCCTTC 58.895 50.000 6.18 0.00 35.92 3.46
3949 3969 2.739943 CCATCTCTCCACTCACTGGTA 58.260 52.381 0.00 0.00 41.52 3.25
4124 4144 6.594284 AGTCTAACAAAACTTTACACCGAC 57.406 37.500 0.00 0.00 0.00 4.79
4212 4232 8.389603 CAAATGTTTTAAACAACACTGCAGAAT 58.610 29.630 23.35 4.45 45.86 2.40
4466 4487 7.855904 CCTACGCCATTAGCTTTATACAAAAAG 59.144 37.037 0.00 0.00 40.39 2.27
4588 4610 3.793888 AAGATCGAACCCCGGGGC 61.794 66.667 40.67 23.53 39.32 5.80
4589 4611 2.189521 CAAGATCGAACCCCGGGG 59.810 66.667 39.18 39.18 39.14 5.73
4600 4622 8.457261 AGAACAGAATAAGCATTTCACAAGATC 58.543 33.333 0.00 0.00 0.00 2.75
4732 4754 3.003585 CGTTTGCATAGCAGCCATATCAA 59.996 43.478 0.00 0.00 40.61 2.57
4850 4872 3.055167 CACCACTCCTTGTATGACCATCA 60.055 47.826 0.00 0.00 0.00 3.07
5122 5146 7.038941 AGTCAACTTCAAGGTAGCTACACTATT 60.039 37.037 24.75 10.91 32.15 1.73
5213 5242 5.278266 GCTTATCTGAGACTAGCACTGGTAG 60.278 48.000 12.79 12.79 39.25 3.18
5271 5300 4.523943 ACTTGGATGTAGCTTGCAATTCAA 59.476 37.500 0.00 0.00 0.00 2.69
5314 5343 0.592637 CAAGCAACTGTTCCGCATCA 59.407 50.000 5.76 0.00 0.00 3.07
5320 5349 4.641777 GCAGCAAGCAACTGTTCC 57.358 55.556 0.00 0.00 44.79 3.62
5466 5537 5.123227 TGACTGGTTCTCATTTCGAGTTTT 58.877 37.500 0.00 0.00 42.88 2.43
5722 5794 5.578005 ACTTTTCTGCAGAATCATCCATG 57.422 39.130 28.89 16.63 33.54 3.66
5817 5889 5.221925 ACAAACCTGACATAGTGACATTCCT 60.222 40.000 0.00 0.00 0.00 3.36
6040 6112 1.002201 TCTTTGTGATTACCCGCCGAA 59.998 47.619 0.00 0.00 0.00 4.30
6104 6176 0.451783 GTCCGCCAATCGCTTTTGAT 59.548 50.000 0.00 0.00 36.73 2.57
6112 6184 2.736682 GGTTGTCGTCCGCCAATCG 61.737 63.158 0.00 0.00 38.08 3.34
6208 6281 3.790091 TCATCAGCGAAAGATTCAGGAG 58.210 45.455 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.