Multiple sequence alignment - TraesCS7D01G075300

Loading Multiple Alignment...

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 TraesCS7D01G075300 chr7D 100.000 3128 0 0 1 3128 44657291 44654164 0.000000e+00 5777.0
1 TraesCS7D01G075300 chr7D 99.884 2578 2 1 429 3006 44708485 44711061 0.000000e+00 4743.0
2 TraesCS7D01G075300 chr7D 74.975 991 185 42 985 1948 44538281 44539235 6.290000e-107 398.0
3 TraesCS7D01G075300 chr7D 74.724 997 187 43 983 1948 43169432 43168470 4.890000e-103 385.0
4 TraesCS7D01G075300 chr7D 86.806 288 36 2 1662 1948 44560966 44561252 1.400000e-83 320.0
5 TraesCS7D01G075300 chr7D 83.857 223 29 2 1947 2164 44561728 44561948 4.090000e-49 206.0
6 TraesCS7D01G075300 chr7D 82.609 230 35 4 2823 3049 44562559 44562786 6.840000e-47 198.0
7 TraesCS7D01G075300 chr7D 93.496 123 8 0 256 378 44705180 44705302 1.920000e-42 183.0
8 TraesCS7D01G075300 chr7D 81.443 194 26 7 2498 2682 44701964 44702156 1.940000e-32 150.0
9 TraesCS7D01G075300 chr7D 98.551 69 1 0 365 433 44707270 44707338 4.240000e-24 122.0
10 TraesCS7D01G075300 chr7D 85.714 84 12 0 2541 2624 44547630 44547713 4.300000e-14 89.8
11 TraesCS7D01G075300 chr7D 93.182 44 2 1 2465 2507 618263012 618263055 2.600000e-06 63.9
12 TraesCS7D01G075300 chr7A 89.354 1578 94 19 405 1948 47256956 47255419 0.000000e+00 1916.0
13 TraesCS7D01G075300 chr7A 93.192 426 24 1 2053 2473 47226148 47225723 3.430000e-174 621.0
14 TraesCS7D01G075300 chr7A 88.235 255 28 2 9 262 201966917 201966664 1.410000e-78 303.0
15 TraesCS7D01G075300 chr7A 83.056 301 23 10 2512 2808 47225728 47225452 6.700000e-62 248.0
16 TraesCS7D01G075300 chr7A 84.581 227 21 4 2859 3084 47012326 47012539 2.440000e-51 213.0
17 TraesCS7D01G075300 chr7A 84.112 214 30 4 1020 1231 47033975 47033764 1.470000e-48 204.0
18 TraesCS7D01G075300 chr7A 94.030 134 7 1 269 401 47257276 47257143 5.290000e-48 202.0
19 TraesCS7D01G075300 chr7A 88.961 154 14 3 2898 3049 47021292 47021444 1.480000e-43 187.0
20 TraesCS7D01G075300 chr7A 73.896 498 93 20 1310 1781 47225011 47224525 6.940000e-37 165.0
21 TraesCS7D01G075300 chr7A 86.822 129 13 3 2924 3049 47501876 47501749 1.170000e-29 141.0
22 TraesCS7D01G075300 chr7A 81.203 133 22 2 2296 2425 47284575 47284707 1.530000e-18 104.0
23 TraesCS7D01G075300 chrUn 90.059 1177 71 14 793 1948 48987662 48986511 0.000000e+00 1483.0
24 TraesCS7D01G075300 chrUn 92.087 1011 60 8 1947 2937 48986147 48985137 0.000000e+00 1406.0
25 TraesCS7D01G075300 chrUn 84.314 255 10 9 550 789 48988334 48988095 4.060000e-54 222.0
26 TraesCS7D01G075300 chr3D 92.066 731 40 12 2376 3093 510332033 510332758 0.000000e+00 1013.0
27 TraesCS7D01G075300 chr3D 73.378 740 139 32 1022 1735 9199567 9200274 4.060000e-54 222.0
28 TraesCS7D01G075300 chr3D 86.607 112 10 1 2040 2146 510331919 510332030 5.480000e-23 119.0
29 TraesCS7D01G075300 chr3D 87.013 77 8 1 2264 2340 510331947 510332021 5.560000e-13 86.1
30 TraesCS7D01G075300 chr4A 82.864 782 96 17 1120 1887 656556861 656556104 0.000000e+00 667.0
31 TraesCS7D01G075300 chr4A 77.262 431 75 16 1537 1948 656472944 656473370 6.750000e-57 231.0
32 TraesCS7D01G075300 chr4A 76.798 431 77 16 1537 1948 656030523 656030949 1.460000e-53 220.0
33 TraesCS7D01G075300 chr4A 87.931 174 20 1 2300 2472 656554942 656554769 1.470000e-48 204.0
34 TraesCS7D01G075300 chr4A 84.112 214 27 6 2838 3049 656554148 656553940 1.900000e-47 200.0
35 TraesCS7D01G075300 chr4A 86.047 129 12 6 2924 3049 656853706 656853581 1.960000e-27 134.0
36 TraesCS7D01G075300 chr4A 86.047 129 12 6 2924 3049 656854156 656854031 1.960000e-27 134.0
37 TraesCS7D01G075300 chr4A 87.069 116 14 1 1947 2061 656555135 656555020 2.530000e-26 130.0
38 TraesCS7D01G075300 chr5D 92.748 262 16 2 2 262 319427671 319427930 2.950000e-100 375.0
39 TraesCS7D01G075300 chr3A 90.566 265 21 3 1 263 140012576 140012838 6.420000e-92 348.0
40 TraesCS7D01G075300 chr3A 88.213 263 27 3 1 260 93079724 93079463 8.420000e-81 311.0
41 TraesCS7D01G075300 chr3A 87.218 266 29 3 1 263 428799959 428799696 6.560000e-77 298.0
42 TraesCS7D01G075300 chr2D 90.421 261 22 3 1 260 166104955 166105213 1.070000e-89 340.0
43 TraesCS7D01G075300 chr2D 89.695 262 21 5 1 260 144389213 144389470 2.330000e-86 329.0
44 TraesCS7D01G075300 chr2D 95.238 42 0 1 2466 2507 10963880 10963841 7.240000e-07 65.8
45 TraesCS7D01G075300 chr6A 89.453 256 22 5 9 260 426609610 426609864 5.030000e-83 318.0
46 TraesCS7D01G075300 chr6D 86.692 263 22 7 1 262 141278663 141278413 2.380000e-71 279.0
47 TraesCS7D01G075300 chr3B 72.952 891 177 45 1030 1903 11511055 11511898 5.180000e-63 252.0
48 TraesCS7D01G075300 chr3B 93.182 44 1 1 2464 2507 10759916 10759875 2.600000e-06 63.9
49 TraesCS7D01G075300 chr5B 93.750 48 0 2 2460 2507 704985388 704985432 5.600000e-08 69.4
50 TraesCS7D01G075300 chr2B 95.238 42 0 1 2466 2507 778286879 778286918 7.240000e-07 65.8
51 TraesCS7D01G075300 chr6B 100.000 33 0 0 2475 2507 18869 18837 9.370000e-06 62.1


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 TraesCS7D01G075300 chr7D 44654164 44657291 3127 True 5777.000000 5777 100.000000 1 3128 1 chr7D.!!$R2 3127
1 TraesCS7D01G075300 chr7D 44701964 44711061 9097 False 1299.500000 4743 93.343500 256 3006 4 chr7D.!!$F5 2750
2 TraesCS7D01G075300 chr7D 44538281 44539235 954 False 398.000000 398 74.975000 985 1948 1 chr7D.!!$F1 963
3 TraesCS7D01G075300 chr7D 43168470 43169432 962 True 385.000000 385 74.724000 983 1948 1 chr7D.!!$R1 965
4 TraesCS7D01G075300 chr7D 44560966 44562786 1820 False 241.333333 320 84.424000 1662 3049 3 chr7D.!!$F4 1387
5 TraesCS7D01G075300 chr7A 47255419 47257276 1857 True 1059.000000 1916 91.692000 269 1948 2 chr7A.!!$R5 1679
6 TraesCS7D01G075300 chr7A 47224525 47226148 1623 True 344.666667 621 83.381333 1310 2808 3 chr7A.!!$R4 1498
7 TraesCS7D01G075300 chrUn 48985137 48988334 3197 True 1037.000000 1483 88.820000 550 2937 3 chrUn.!!$R1 2387
8 TraesCS7D01G075300 chr3D 510331919 510332758 839 False 406.033333 1013 88.562000 2040 3093 3 chr3D.!!$F2 1053
9 TraesCS7D01G075300 chr3D 9199567 9200274 707 False 222.000000 222 73.378000 1022 1735 1 chr3D.!!$F1 713
10 TraesCS7D01G075300 chr4A 656553940 656556861 2921 True 300.250000 667 85.494000 1120 3049 4 chr4A.!!$R1 1929
11 TraesCS7D01G075300 chr3B 11511055 11511898 843 False 252.000000 252 72.952000 1030 1903 1 chr3B.!!$F1 873

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
232 233 0.165511 GCAGAGAAAAGCGCTGTCTG 59.834 55.0 24.32 24.38 45.05 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2886 11482 6.267496 TCTTTGGCTAAAATAGAAGCAACC 57.733 37.5 0.0 0.0 40.61 3.77 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
20 21 1.980844 CTGCGCGTCGTCTAGTTTTTA 59.019 47.619 8.43 0.00 0.00 1.52
22 23 1.981533 GCGCGTCGTCTAGTTTTTAGT 59.018 47.619 8.43 0.00 0.00 2.24
27 28 6.571588 CGCGTCGTCTAGTTTTTAGTTTTTA 58.428 36.000 0.00 0.00 0.00 1.52
30 31 8.824779 GCGTCGTCTAGTTTTTAGTTTTTAATG 58.175 33.333 0.00 0.00 0.00 1.90
31 32 8.824779 CGTCGTCTAGTTTTTAGTTTTTAATGC 58.175 33.333 0.00 0.00 0.00 3.56
55 56 8.394877 TGCTAATTAATGTAATGTGGACTTTCG 58.605 33.333 0.00 0.00 0.00 3.46
56 57 7.376072 GCTAATTAATGTAATGTGGACTTTCGC 59.624 37.037 0.00 0.00 0.00 4.70
58 59 1.434555 TGTAATGTGGACTTTCGCCG 58.565 50.000 0.00 0.00 0.00 6.46
60 61 1.022451 TAATGTGGACTTTCGCCGGC 61.022 55.000 19.07 19.07 0.00 6.13
63 64 3.948719 TGGACTTTCGCCGGCCTT 61.949 61.111 23.46 0.00 0.00 4.35
64 65 3.125573 GGACTTTCGCCGGCCTTC 61.126 66.667 23.46 9.81 0.00 3.46
65 66 3.488090 GACTTTCGCCGGCCTTCG 61.488 66.667 23.46 6.82 38.88 3.79
67 68 3.788766 CTTTCGCCGGCCTTCGTG 61.789 66.667 23.46 5.48 37.11 4.35
78 79 1.673009 CCTTCGTGGCCGGCTTTTA 60.673 57.895 28.56 7.23 33.95 1.52
79 80 1.029947 CCTTCGTGGCCGGCTTTTAT 61.030 55.000 28.56 0.00 33.95 1.40
82 83 0.606944 TCGTGGCCGGCTTTTATGTT 60.607 50.000 28.56 0.00 33.95 2.71
84 85 1.469308 CGTGGCCGGCTTTTATGTTTA 59.531 47.619 28.56 0.00 0.00 2.01
88 89 5.652518 GTGGCCGGCTTTTATGTTTAATTA 58.347 37.500 28.56 0.00 0.00 1.40
89 90 6.100668 GTGGCCGGCTTTTATGTTTAATTAA 58.899 36.000 28.56 0.00 0.00 1.40
93 94 7.123190 GCCGGCTTTTATGTTTAATTAAATGC 58.877 34.615 22.15 6.26 37.56 3.56
94 95 7.201565 GCCGGCTTTTATGTTTAATTAAATGCA 60.202 33.333 22.15 8.51 38.87 3.96
116 117 7.680062 TGCATATTAAACTTTTATTTTGGCGC 58.320 30.769 0.00 0.00 0.00 6.53
117 118 6.838806 GCATATTAAACTTTTATTTTGGCGCG 59.161 34.615 0.00 0.00 0.00 6.86
118 119 4.632740 TTAAACTTTTATTTTGGCGCGC 57.367 36.364 25.94 25.94 0.00 6.86
119 120 1.424403 AACTTTTATTTTGGCGCGCC 58.576 45.000 42.35 42.35 0.00 6.53
120 121 0.731174 ACTTTTATTTTGGCGCGCCG 60.731 50.000 41.73 27.11 39.42 6.46
122 123 0.729816 TTTTATTTTGGCGCGCCGAC 60.730 50.000 41.73 21.88 39.42 4.79
128 129 4.397090 TGGCGCGCCGACAAAATG 62.397 61.111 41.73 0.00 44.01 2.32
132 133 2.178273 GCGCCGACAAAATGGGTC 59.822 61.111 0.00 0.00 0.00 4.46
138 139 3.332706 GACAAAATGGGTCGGACCA 57.667 52.632 27.32 14.49 46.24 4.02
140 141 0.893727 ACAAAATGGGTCGGACCAGC 60.894 55.000 27.32 12.47 45.20 4.85
141 142 1.674322 AAAATGGGTCGGACCAGCG 60.674 57.895 27.32 0.00 45.20 5.18
168 169 4.025401 GCGCCGACCCAAACACAG 62.025 66.667 0.00 0.00 0.00 3.66
170 171 4.025401 GCCGACCCAAACACAGCG 62.025 66.667 0.00 0.00 0.00 5.18
171 172 4.025401 CCGACCCAAACACAGCGC 62.025 66.667 0.00 0.00 0.00 5.92
176 177 4.025401 CCAAACACAGCGCCGGAC 62.025 66.667 5.05 0.00 0.00 4.79
181 182 4.368808 CACAGCGCCGGACGTTTG 62.369 66.667 5.05 13.47 46.11 2.93
185 186 4.364409 GCGCCGGACGTTTGTGTC 62.364 66.667 5.05 0.00 46.11 3.67
191 192 3.708734 GACGTTTGTGTCCGCCGG 61.709 66.667 0.00 0.00 32.61 6.13
213 214 2.113910 CGACCCAAACGGACAAAAAG 57.886 50.000 0.00 0.00 34.64 2.27
214 215 1.847818 GACCCAAACGGACAAAAAGC 58.152 50.000 0.00 0.00 34.64 3.51
215 216 1.135333 GACCCAAACGGACAAAAAGCA 59.865 47.619 0.00 0.00 34.64 3.91
216 217 1.136110 ACCCAAACGGACAAAAAGCAG 59.864 47.619 0.00 0.00 34.64 4.24
217 218 1.407258 CCCAAACGGACAAAAAGCAGA 59.593 47.619 0.00 0.00 0.00 4.26
218 219 2.543653 CCCAAACGGACAAAAAGCAGAG 60.544 50.000 0.00 0.00 0.00 3.35
220 221 3.181491 CCAAACGGACAAAAAGCAGAGAA 60.181 43.478 0.00 0.00 0.00 2.87
221 222 4.420168 CAAACGGACAAAAAGCAGAGAAA 58.580 39.130 0.00 0.00 0.00 2.52
223 224 4.292977 ACGGACAAAAAGCAGAGAAAAG 57.707 40.909 0.00 0.00 0.00 2.27
224 225 3.045688 CGGACAAAAAGCAGAGAAAAGC 58.954 45.455 0.00 0.00 0.00 3.51
225 226 3.045688 GGACAAAAAGCAGAGAAAAGCG 58.954 45.455 0.00 0.00 35.48 4.68
227 228 2.099756 ACAAAAAGCAGAGAAAAGCGCT 59.900 40.909 2.64 2.64 35.90 5.92
229 230 1.312815 AAAGCAGAGAAAAGCGCTGT 58.687 45.000 12.58 0.14 45.05 4.40
232 233 0.165511 GCAGAGAAAAGCGCTGTCTG 59.834 55.000 24.32 24.38 45.05 3.51
235 236 2.289002 CAGAGAAAAGCGCTGTCTGTTT 59.711 45.455 24.32 15.09 39.29 2.83
237 238 1.334869 AGAAAAGCGCTGTCTGTTTGG 59.665 47.619 20.02 0.00 0.00 3.28
238 239 0.385390 AAAAGCGCTGTCTGTTTGGG 59.615 50.000 12.58 0.00 0.00 4.12
240 241 1.166531 AAGCGCTGTCTGTTTGGGTC 61.167 55.000 12.58 0.00 0.00 4.46
242 243 2.317609 CGCTGTCTGTTTGGGTCGG 61.318 63.158 0.00 0.00 0.00 4.79
244 245 1.966451 CTGTCTGTTTGGGTCGGCC 60.966 63.158 0.00 0.00 0.00 6.13
259 260 4.021925 GCCCGTTGGAGTGGCTCT 62.022 66.667 0.00 0.00 42.01 4.09
385 5328 4.620589 AATATGGAGAGATGCACTGGAG 57.379 45.455 0.00 0.00 0.00 3.86
2886 11482 1.134788 GTCATAGTGGACCCTGGTTCG 60.135 57.143 0.00 0.00 0.00 3.95
3006 11604 6.493115 ACAGTTTCACCATGATGTTTCCATTA 59.507 34.615 0.00 0.00 0.00 1.90
3007 11605 7.178983 ACAGTTTCACCATGATGTTTCCATTAT 59.821 33.333 0.00 0.00 0.00 1.28
3069 11671 9.003658 CAGATGTAGGACTTGAACTTACAAAAT 57.996 33.333 0.00 0.00 34.54 1.82
3070 11672 9.574516 AGATGTAGGACTTGAACTTACAAAATT 57.425 29.630 0.00 0.00 34.54 1.82
3115 11717 4.423231 GGAACCAAAGAGCCTGGG 57.577 61.111 0.00 0.00 38.36 4.45
3116 11718 1.767692 GGAACCAAAGAGCCTGGGA 59.232 57.895 0.00 0.00 38.36 4.37
3117 11719 0.112412 GGAACCAAAGAGCCTGGGAA 59.888 55.000 0.00 0.00 38.36 3.97
3118 11720 1.539157 GAACCAAAGAGCCTGGGAAG 58.461 55.000 0.00 0.00 38.36 3.46
3119 11721 0.540597 AACCAAAGAGCCTGGGAAGC 60.541 55.000 0.00 0.00 38.36 3.86
3120 11722 1.075482 CCAAAGAGCCTGGGAAGCA 59.925 57.895 0.00 0.00 0.00 3.91
3121 11723 1.246737 CCAAAGAGCCTGGGAAGCAC 61.247 60.000 0.00 0.00 0.00 4.40
3122 11724 0.251077 CAAAGAGCCTGGGAAGCACT 60.251 55.000 0.00 0.00 32.18 4.40
3123 11725 0.480252 AAAGAGCCTGGGAAGCACTT 59.520 50.000 0.00 0.00 41.95 3.16
3124 11726 0.480252 AAGAGCCTGGGAAGCACTTT 59.520 50.000 0.00 0.00 37.82 2.66
3125 11727 1.362224 AGAGCCTGGGAAGCACTTTA 58.638 50.000 0.00 0.00 0.00 1.85
3126 11728 1.918957 AGAGCCTGGGAAGCACTTTAT 59.081 47.619 0.00 0.00 0.00 1.40
3127 11729 2.019984 GAGCCTGGGAAGCACTTTATG 58.980 52.381 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.782384 AAAAACTAGACGACGCGCAG 59.218 50.000 5.73 2.10 0.00 5.18
1 2 1.980844 CTAAAAACTAGACGACGCGCA 59.019 47.619 5.73 0.00 0.00 6.09
2 3 1.981533 ACTAAAAACTAGACGACGCGC 59.018 47.619 5.73 0.00 0.00 6.86
6 7 9.874215 AGCATTAAAAACTAAAAACTAGACGAC 57.126 29.630 0.00 0.00 0.00 4.34
30 31 7.376072 GCGAAAGTCCACATTACATTAATTAGC 59.624 37.037 0.00 0.00 0.00 3.09
31 32 7.855904 GGCGAAAGTCCACATTACATTAATTAG 59.144 37.037 0.00 0.00 0.00 1.73
33 34 6.560711 GGCGAAAGTCCACATTACATTAATT 58.439 36.000 0.00 0.00 0.00 1.40
36 37 3.619483 CGGCGAAAGTCCACATTACATTA 59.381 43.478 0.00 0.00 0.00 1.90
38 39 2.006888 CGGCGAAAGTCCACATTACAT 58.993 47.619 0.00 0.00 0.00 2.29
41 42 1.022451 GCCGGCGAAAGTCCACATTA 61.022 55.000 12.58 0.00 0.00 1.90
42 43 2.332654 GCCGGCGAAAGTCCACATT 61.333 57.895 12.58 0.00 0.00 2.71
48 49 3.488090 CGAAGGCCGGCGAAAGTC 61.488 66.667 22.54 11.59 33.91 3.01
50 51 3.788766 CACGAAGGCCGGCGAAAG 61.789 66.667 22.54 14.55 43.93 2.62
60 61 1.029947 ATAAAAGCCGGCCACGAAGG 61.030 55.000 26.15 0.00 44.60 3.46
61 62 0.098728 CATAAAAGCCGGCCACGAAG 59.901 55.000 26.15 5.89 44.60 3.79
63 64 0.606944 AACATAAAAGCCGGCCACGA 60.607 50.000 26.15 7.05 44.60 4.35
64 65 0.242555 AAACATAAAAGCCGGCCACG 59.757 50.000 26.15 8.66 40.55 4.94
65 66 3.579335 TTAAACATAAAAGCCGGCCAC 57.421 42.857 26.15 0.00 0.00 5.01
67 68 7.626446 CATTTAATTAAACATAAAAGCCGGCC 58.374 34.615 26.15 5.07 0.00 6.13
93 94 6.838806 GCGCGCCAAAATAAAAGTTTAATATG 59.161 34.615 23.24 0.00 0.00 1.78
94 95 6.019398 GGCGCGCCAAAATAAAAGTTTAATAT 60.019 34.615 43.55 0.00 35.81 1.28
96 97 4.092237 GGCGCGCCAAAATAAAAGTTTAAT 59.908 37.500 43.55 0.00 35.81 1.40
99 100 1.795872 GGCGCGCCAAAATAAAAGTTT 59.204 42.857 43.55 0.00 35.81 2.66
101 102 0.731174 CGGCGCGCCAAAATAAAAGT 60.731 50.000 45.26 0.00 35.37 2.66
102 103 0.455295 TCGGCGCGCCAAAATAAAAG 60.455 50.000 45.26 27.49 35.37 2.27
104 105 1.154188 GTCGGCGCGCCAAAATAAA 60.154 52.632 45.26 20.64 35.37 1.40
107 108 2.685387 TTTTGTCGGCGCGCCAAAAT 62.685 50.000 45.26 0.00 35.37 1.82
108 109 2.685387 ATTTTGTCGGCGCGCCAAAA 62.685 50.000 45.26 39.18 35.37 2.44
109 110 3.200887 ATTTTGTCGGCGCGCCAAA 62.201 52.632 45.26 36.25 35.37 3.28
115 116 2.178273 GACCCATTTTGTCGGCGC 59.822 61.111 0.00 0.00 0.00 6.53
120 121 1.165270 CTGGTCCGACCCATTTTGTC 58.835 55.000 15.24 0.00 37.50 3.18
122 123 1.883021 GCTGGTCCGACCCATTTTG 59.117 57.895 15.24 0.20 37.50 2.44
124 125 2.046314 CGCTGGTCCGACCCATTT 60.046 61.111 15.24 0.00 37.50 2.32
126 127 3.319198 AACGCTGGTCCGACCCAT 61.319 61.111 15.24 0.00 37.50 4.00
151 152 4.025401 CTGTGTTTGGGTCGGCGC 62.025 66.667 0.00 0.00 0.00 6.53
152 153 4.025401 GCTGTGTTTGGGTCGGCG 62.025 66.667 0.00 0.00 0.00 6.46
153 154 4.025401 CGCTGTGTTTGGGTCGGC 62.025 66.667 0.00 0.00 0.00 5.54
154 155 4.025401 GCGCTGTGTTTGGGTCGG 62.025 66.667 0.00 0.00 0.00 4.79
156 157 4.025401 CGGCGCTGTGTTTGGGTC 62.025 66.667 8.45 0.00 0.00 4.46
159 160 4.025401 GTCCGGCGCTGTGTTTGG 62.025 66.667 16.49 0.00 0.00 3.28
160 161 4.368808 CGTCCGGCGCTGTGTTTG 62.369 66.667 16.49 0.00 0.00 2.93
161 162 4.903010 ACGTCCGGCGCTGTGTTT 62.903 61.111 16.49 0.00 46.11 2.83
164 165 4.368808 CAAACGTCCGGCGCTGTG 62.369 66.667 16.49 6.93 46.11 3.66
167 168 4.903010 ACACAAACGTCCGGCGCT 62.903 61.111 16.48 3.50 46.11 5.92
168 169 4.364409 GACACAAACGTCCGGCGC 62.364 66.667 16.48 0.00 46.11 6.53
192 193 1.102222 TTTTGTCCGTTTGGGTCGGG 61.102 55.000 4.58 0.00 46.82 5.14
194 195 1.862411 GCTTTTTGTCCGTTTGGGTCG 60.862 52.381 0.00 0.00 37.00 4.79
195 196 1.135333 TGCTTTTTGTCCGTTTGGGTC 59.865 47.619 0.00 0.00 37.00 4.46
198 199 2.357637 TCTCTGCTTTTTGTCCGTTTGG 59.642 45.455 0.00 0.00 0.00 3.28
201 202 4.672409 CTTTTCTCTGCTTTTTGTCCGTT 58.328 39.130 0.00 0.00 0.00 4.44
202 203 3.489229 GCTTTTCTCTGCTTTTTGTCCGT 60.489 43.478 0.00 0.00 0.00 4.69
203 204 3.045688 GCTTTTCTCTGCTTTTTGTCCG 58.954 45.455 0.00 0.00 0.00 4.79
204 205 3.045688 CGCTTTTCTCTGCTTTTTGTCC 58.954 45.455 0.00 0.00 0.00 4.02
205 206 2.469147 GCGCTTTTCTCTGCTTTTTGTC 59.531 45.455 0.00 0.00 0.00 3.18
206 207 2.099756 AGCGCTTTTCTCTGCTTTTTGT 59.900 40.909 2.64 0.00 32.89 2.83
209 210 1.678101 ACAGCGCTTTTCTCTGCTTTT 59.322 42.857 7.50 0.00 34.99 2.27
210 211 1.265365 GACAGCGCTTTTCTCTGCTTT 59.735 47.619 7.50 0.00 34.99 3.51
211 212 0.871057 GACAGCGCTTTTCTCTGCTT 59.129 50.000 7.50 0.00 34.99 3.91
213 214 0.165511 CAGACAGCGCTTTTCTCTGC 59.834 55.000 7.50 0.00 30.83 4.26
214 215 1.506493 ACAGACAGCGCTTTTCTCTG 58.494 50.000 21.30 21.30 35.48 3.35
215 216 2.246719 AACAGACAGCGCTTTTCTCT 57.753 45.000 7.50 2.08 0.00 3.10
216 217 2.603173 CCAAACAGACAGCGCTTTTCTC 60.603 50.000 7.50 0.00 0.00 2.87
217 218 1.334869 CCAAACAGACAGCGCTTTTCT 59.665 47.619 7.50 10.23 0.00 2.52
218 219 1.600413 CCCAAACAGACAGCGCTTTTC 60.600 52.381 7.50 7.55 0.00 2.29
220 221 0.751643 ACCCAAACAGACAGCGCTTT 60.752 50.000 7.50 0.00 0.00 3.51
221 222 1.152963 ACCCAAACAGACAGCGCTT 60.153 52.632 7.50 0.00 0.00 4.68
223 224 2.946762 GACCCAAACAGACAGCGC 59.053 61.111 0.00 0.00 0.00 5.92
224 225 2.317609 CCGACCCAAACAGACAGCG 61.318 63.158 0.00 0.00 0.00 5.18
225 226 2.617274 GCCGACCCAAACAGACAGC 61.617 63.158 0.00 0.00 0.00 4.40
227 228 2.112297 GGCCGACCCAAACAGACA 59.888 61.111 0.00 0.00 0.00 3.41
244 245 1.002087 AGTTTAGAGCCACTCCAACGG 59.998 52.381 0.00 0.00 32.60 4.44
245 246 2.457366 AGTTTAGAGCCACTCCAACG 57.543 50.000 0.00 0.00 32.60 4.10
247 248 5.562298 AAGTTAGTTTAGAGCCACTCCAA 57.438 39.130 0.00 0.00 0.00 3.53
248 249 5.071250 TGAAAGTTAGTTTAGAGCCACTCCA 59.929 40.000 0.00 0.00 0.00 3.86
249 250 5.408909 GTGAAAGTTAGTTTAGAGCCACTCC 59.591 44.000 0.00 0.00 0.00 3.85
251 252 5.163237 TGGTGAAAGTTAGTTTAGAGCCACT 60.163 40.000 0.00 0.00 0.00 4.00
252 253 5.049612 GTGGTGAAAGTTAGTTTAGAGCCAC 60.050 44.000 0.00 0.00 32.92 5.01
253 254 5.061179 GTGGTGAAAGTTAGTTTAGAGCCA 58.939 41.667 0.00 0.00 0.00 4.75
254 255 4.151867 CGTGGTGAAAGTTAGTTTAGAGCC 59.848 45.833 0.00 0.00 0.00 4.70
256 257 5.404667 GGTCGTGGTGAAAGTTAGTTTAGAG 59.595 44.000 0.00 0.00 0.00 2.43
259 260 5.021033 TGGTCGTGGTGAAAGTTAGTTTA 57.979 39.130 0.00 0.00 0.00 2.01
337 3299 1.750778 CCACATTGCTTGATGTACCCC 59.249 52.381 0.00 0.00 38.15 4.95
2886 11482 6.267496 TCTTTGGCTAAAATAGAAGCAACC 57.733 37.500 0.00 0.00 40.61 3.77
3081 11683 6.078456 TGGTTCCCACATATTCTTCTCAAT 57.922 37.500 0.00 0.00 0.00 2.57
3084 11686 6.180472 TCTTTGGTTCCCACATATTCTTCTC 58.820 40.000 0.00 0.00 30.78 2.87
3089 11691 3.381590 GGCTCTTTGGTTCCCACATATTC 59.618 47.826 0.00 0.00 30.78 1.75
3093 11695 0.779997 AGGCTCTTTGGTTCCCACAT 59.220 50.000 0.00 0.00 30.78 3.21
3094 11696 0.178992 CAGGCTCTTTGGTTCCCACA 60.179 55.000 0.00 0.00 30.78 4.17
3095 11697 0.895559 CCAGGCTCTTTGGTTCCCAC 60.896 60.000 0.00 0.00 30.78 4.61
3096 11698 1.460255 CCAGGCTCTTTGGTTCCCA 59.540 57.895 0.00 0.00 0.00 4.37
3097 11699 1.304464 CCCAGGCTCTTTGGTTCCC 60.304 63.158 0.00 0.00 33.73 3.97
3098 11700 0.112412 TTCCCAGGCTCTTTGGTTCC 59.888 55.000 0.00 0.00 33.73 3.62
3099 11701 1.539157 CTTCCCAGGCTCTTTGGTTC 58.461 55.000 0.00 0.00 33.73 3.62
3100 11702 0.540597 GCTTCCCAGGCTCTTTGGTT 60.541 55.000 0.00 0.00 33.73 3.67
3101 11703 1.075659 GCTTCCCAGGCTCTTTGGT 59.924 57.895 0.00 0.00 33.73 3.67
3102 11704 1.075482 TGCTTCCCAGGCTCTTTGG 59.925 57.895 0.00 0.00 35.41 3.28
3103 11705 0.251077 AGTGCTTCCCAGGCTCTTTG 60.251 55.000 0.00 0.00 30.77 2.77
3104 11706 0.480252 AAGTGCTTCCCAGGCTCTTT 59.520 50.000 0.00 0.00 39.46 2.52
3105 11707 0.480252 AAAGTGCTTCCCAGGCTCTT 59.520 50.000 0.00 0.00 42.67 2.85
3106 11708 1.362224 TAAAGTGCTTCCCAGGCTCT 58.638 50.000 0.00 0.00 35.45 4.09
3107 11709 2.019984 CATAAAGTGCTTCCCAGGCTC 58.980 52.381 0.00 0.00 0.00 4.70
3108 11710 2.134789 CATAAAGTGCTTCCCAGGCT 57.865 50.000 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.