Multiple sequence alignment - TraesCS5A01G464100

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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 TraesCS5A01G464100 chr5A 100.000 2384 0 0 1 2384 643865991 643863608 0.000000e+00 4403
1 TraesCS5A01G464100 chr5A 87.945 730 86 2 1 729 6005834 6005106 0.000000e+00 859
2 TraesCS5A01G464100 chr5D 88.152 1131 65 28 727 1841 515642320 515641243 0.000000e+00 1282
3 TraesCS5A01G464100 chr5D 89.026 729 79 1 1 729 309877424 309878151 0.000000e+00 902
4 TraesCS5A01G464100 chr1A 96.571 729 25 0 1 729 361952057 361952785 0.000000e+00 1208
5 TraesCS5A01G464100 chr5B 89.044 1004 66 24 727 1710 648279059 648278080 0.000000e+00 1205
6 TraesCS5A01G464100 chr5B 90.326 889 54 15 728 1611 648338159 648339020 0.000000e+00 1136
7 TraesCS5A01G464100 chr5B 90.214 889 55 15 728 1611 648317036 648316175 0.000000e+00 1131
8 TraesCS5A01G464100 chr5B 89.347 291 30 1 2069 2359 337833365 337833654 4.840000e-97 364
9 TraesCS5A01G464100 chr5B 87.619 315 28 2 2070 2384 493633622 493633319 2.910000e-94 355
10 TraesCS5A01G464100 chr5B 89.076 238 18 7 1633 1864 648313248 648313013 3.000000e-74 289
11 TraesCS5A01G464100 chr5B 88.655 238 19 7 1633 1864 648341948 648342183 1.390000e-72 283
12 TraesCS5A01G464100 chr5B 91.558 154 9 4 1921 2070 648312775 648312622 2.400000e-50 209
13 TraesCS5A01G464100 chr5B 91.558 154 9 4 1921 2070 648342421 648342574 2.400000e-50 209
14 TraesCS5A01G464100 chr5B 90.506 158 6 3 1715 1865 648277950 648277795 1.450000e-47 200
15 TraesCS5A01G464100 chr2A 94.766 726 32 1 1 726 731245240 731244521 0.000000e+00 1125
16 TraesCS5A01G464100 chr1B 92.181 729 56 1 1 729 590993636 590992909 0.000000e+00 1029
17 TraesCS5A01G464100 chr1B 89.589 730 74 2 1 729 141762964 141763692 0.000000e+00 926
18 TraesCS5A01G464100 chr3D 91.084 729 64 1 1 729 114221408 114222135 0.000000e+00 985
19 TraesCS5A01G464100 chr4A 88.996 727 78 2 1 726 631905858 631906583 0.000000e+00 898
20 TraesCS5A01G464100 chr7A 88.219 730 84 2 1 729 126558602 126557874 0.000000e+00 870
21 TraesCS5A01G464100 chr4D 89.969 319 28 3 2068 2384 437248076 437247760 2.210000e-110 409
22 TraesCS5A01G464100 chr3B 84.255 235 34 3 2073 2307 78567200 78566969 2.380000e-55 226
23 TraesCS5A01G464100 chr3B 83.691 233 35 3 2075 2307 78566585 78566356 1.430000e-52 217
24 TraesCS5A01G464100 chr3B 82.979 235 37 3 2073 2307 78552601 78552370 2.400000e-50 209
25 TraesCS5A01G464100 chr7B 80.228 263 40 11 2069 2323 72314945 72315203 1.130000e-43 187
26 TraesCS5A01G464100 chrUn 83.590 195 31 1 2068 2261 26237960 26238154 5.230000e-42 182
27 TraesCS5A01G464100 chr1D 83.420 193 32 0 2069 2261 195998389 195998581 1.880000e-41 180


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 TraesCS5A01G464100 chr5A 643863608 643865991 2383 True 4403.000000 4403 100.000000 1 2384 1 chr5A.!!$R2 2383
1 TraesCS5A01G464100 chr5A 6005106 6005834 728 True 859.000000 859 87.945000 1 729 1 chr5A.!!$R1 728
2 TraesCS5A01G464100 chr5D 515641243 515642320 1077 True 1282.000000 1282 88.152000 727 1841 1 chr5D.!!$R1 1114
3 TraesCS5A01G464100 chr5D 309877424 309878151 727 False 902.000000 902 89.026000 1 729 1 chr5D.!!$F1 728
4 TraesCS5A01G464100 chr1A 361952057 361952785 728 False 1208.000000 1208 96.571000 1 729 1 chr1A.!!$F1 728
5 TraesCS5A01G464100 chr5B 648277795 648279059 1264 True 702.500000 1205 89.775000 727 1865 2 chr5B.!!$R2 1138
6 TraesCS5A01G464100 chr5B 648312622 648317036 4414 True 543.000000 1131 90.282667 728 2070 3 chr5B.!!$R3 1342
7 TraesCS5A01G464100 chr5B 648338159 648342574 4415 False 542.666667 1136 90.179667 728 2070 3 chr5B.!!$F2 1342
8 TraesCS5A01G464100 chr2A 731244521 731245240 719 True 1125.000000 1125 94.766000 1 726 1 chr2A.!!$R1 725
9 TraesCS5A01G464100 chr1B 590992909 590993636 727 True 1029.000000 1029 92.181000 1 729 1 chr1B.!!$R1 728
10 TraesCS5A01G464100 chr1B 141762964 141763692 728 False 926.000000 926 89.589000 1 729 1 chr1B.!!$F1 728
11 TraesCS5A01G464100 chr3D 114221408 114222135 727 False 985.000000 985 91.084000 1 729 1 chr3D.!!$F1 728
12 TraesCS5A01G464100 chr4A 631905858 631906583 725 False 898.000000 898 88.996000 1 726 1 chr4A.!!$F1 725
13 TraesCS5A01G464100 chr7A 126557874 126558602 728 True 870.000000 870 88.219000 1 729 1 chr7A.!!$R1 728
14 TraesCS5A01G464100 chr3B 78566356 78567200 844 True 221.500000 226 83.973000 2073 2307 2 chr3B.!!$R2 234

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
459 460 0.179059 TGTGCACTCAAAGAAGCGGA 60.179 50.0 19.41 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1867 4940 0.027194 GCGCTCATGCACATGTACAG 59.973 55.0 10.27 2.53 39.72 2.74 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
164 165 3.000727 GGTATGAAAACCTGTCTGACCG 58.999 50.000 5.17 0.00 36.53 4.79
264 265 1.451927 GCCGCATCAGTCCATTCCA 60.452 57.895 0.00 0.00 0.00 3.53
417 418 2.171840 GTCTAGGACAGAGCCTTGTGA 58.828 52.381 0.00 0.00 39.50 3.58
456 457 4.614946 AGAATTTGTGCACTCAAAGAAGC 58.385 39.130 19.41 2.85 40.00 3.86
459 460 0.179059 TGTGCACTCAAAGAAGCGGA 60.179 50.000 19.41 0.00 0.00 5.54
513 514 4.518211 CAGAAGTGCCAAGTTGAAGATCTT 59.482 41.667 7.95 7.95 0.00 2.40
521 522 5.649831 GCCAAGTTGAAGATCTTAATGTCCT 59.350 40.000 8.25 0.00 0.00 3.85
537 538 2.131023 GTCCTGGAATCCCAATCCTCT 58.869 52.381 0.00 0.00 42.98 3.69
573 574 3.733337 GAGTCATCAAATCCCACGCTAT 58.267 45.455 0.00 0.00 0.00 2.97
582 583 1.199615 TCCCACGCTATCCAACATGA 58.800 50.000 0.00 0.00 0.00 3.07
673 674 2.303022 TCTCGGAAGCCTGAAACAAGAT 59.697 45.455 0.00 0.00 0.00 2.40
771 772 2.240500 GCGGCGCTCATTGAGTAGG 61.241 63.158 26.86 6.39 31.39 3.18
772 773 2.240500 CGGCGCTCATTGAGTAGGC 61.241 63.158 19.92 19.92 34.16 3.93
773 774 1.889573 GGCGCTCATTGAGTAGGCC 60.890 63.158 21.36 21.36 36.29 5.19
774 775 2.240500 GCGCTCATTGAGTAGGCCG 61.241 63.158 14.90 10.23 31.39 6.13
775 776 1.592669 CGCTCATTGAGTAGGCCGG 60.593 63.158 14.90 0.00 31.39 6.13
776 777 1.889573 GCTCATTGAGTAGGCCGGC 60.890 63.158 21.18 21.18 31.39 6.13
931 932 2.521286 TCTGACCTCCTCCCCCTATAA 58.479 52.381 0.00 0.00 0.00 0.98
941 942 6.384305 CCTCCTCCCCCTATAAATATGTGTAG 59.616 46.154 0.00 0.00 0.00 2.74
945 946 5.421056 TCCCCCTATAAATATGTGTAGAGCG 59.579 44.000 0.00 0.00 0.00 5.03
946 947 5.109903 CCCCTATAAATATGTGTAGAGCGC 58.890 45.833 0.00 0.00 0.00 5.92
947 948 5.109903 CCCTATAAATATGTGTAGAGCGCC 58.890 45.833 2.29 0.00 0.00 6.53
948 949 5.109903 CCTATAAATATGTGTAGAGCGCCC 58.890 45.833 2.29 0.00 0.00 6.13
949 950 1.865865 AAATATGTGTAGAGCGCCCG 58.134 50.000 2.29 0.00 0.00 6.13
950 951 0.600255 AATATGTGTAGAGCGCCCGC 60.600 55.000 2.29 4.20 42.33 6.13
976 977 4.373116 AGCCCACGCATCGTTCGT 62.373 61.111 0.00 0.00 38.32 3.85
978 979 2.474266 CCCACGCATCGTTCGTTG 59.526 61.111 0.00 0.00 38.32 4.10
991 992 0.809385 TTCGTTGGAGAGCGTAGAGG 59.191 55.000 0.00 0.00 0.00 3.69
995 996 1.751924 GTTGGAGAGCGTAGAGGACAT 59.248 52.381 0.00 0.00 0.00 3.06
998 999 1.606668 GGAGAGCGTAGAGGACATCAG 59.393 57.143 0.00 0.00 0.00 2.90
1010 1011 0.322975 GACATCAGGATGGCGCCTAT 59.677 55.000 29.70 19.23 42.91 2.57
1356 1357 2.111878 GGCATCTCCATCCCCGTG 59.888 66.667 0.00 0.00 34.01 4.94
1394 1395 1.270094 CGACAAGTAAGCCCTCACACA 60.270 52.381 0.00 0.00 0.00 3.72
1395 1396 2.143925 GACAAGTAAGCCCTCACACAC 58.856 52.381 0.00 0.00 0.00 3.82
1429 1438 0.609662 ACCAGGGATTTTGCATGCAC 59.390 50.000 22.58 8.87 0.00 4.57
1430 1439 0.899720 CCAGGGATTTTGCATGCACT 59.100 50.000 22.58 10.39 0.00 4.40
1434 1443 2.028748 AGGGATTTTGCATGCACTGAAC 60.029 45.455 22.58 11.00 0.00 3.18
1440 1449 0.038067 TGCATGCACTGAACAATGCC 60.038 50.000 18.46 0.00 41.33 4.40
1451 1464 0.593128 AACAATGCCAGCTCGTCAAC 59.407 50.000 0.00 0.00 0.00 3.18
1537 1556 2.976903 GGGCGAGCTGATGATGGC 60.977 66.667 0.00 0.00 32.57 4.40
1601 1623 2.159179 TCGATGGAGGAGTTCATGGA 57.841 50.000 0.00 0.00 0.00 3.41
1671 4609 4.770531 TGCTACTACTGTAGTCATGGTTGT 59.229 41.667 22.79 0.16 45.84 3.32
1691 4632 9.772973 TGGTTGTATAATAATGGTGTCAGTATC 57.227 33.333 0.00 0.00 33.62 2.24
1692 4633 9.998106 GGTTGTATAATAATGGTGTCAGTATCT 57.002 33.333 0.00 0.00 33.62 1.98
1728 4794 4.553938 CGTACCACTTAACTGGTTTGCAAG 60.554 45.833 11.45 0.00 42.29 4.01
1751 4817 4.038162 GCACTATCCACGTATCTCTCCTTT 59.962 45.833 0.00 0.00 0.00 3.11
1834 4907 0.729116 CAGGCGACACATCACATTCC 59.271 55.000 0.00 0.00 0.00 3.01
1865 4938 2.069430 GGAGGCTGAGAGAAGGGGG 61.069 68.421 0.00 0.00 0.00 5.40
1866 4939 2.690510 AGGCTGAGAGAAGGGGGC 60.691 66.667 0.00 0.00 0.00 5.80
1867 4940 3.803162 GGCTGAGAGAAGGGGGCC 61.803 72.222 0.00 0.00 0.00 5.80
1868 4941 2.690510 GCTGAGAGAAGGGGGCCT 60.691 66.667 0.84 0.00 33.87 5.19
1870 4943 1.614824 CTGAGAGAAGGGGGCCTGT 60.615 63.158 0.84 0.00 32.13 4.00
1871 4944 0.325671 CTGAGAGAAGGGGGCCTGTA 60.326 60.000 0.84 0.00 32.13 2.74
1872 4945 0.617820 TGAGAGAAGGGGGCCTGTAC 60.618 60.000 0.84 0.00 32.13 2.90
1876 4949 0.550147 AGAAGGGGGCCTGTACATGT 60.550 55.000 0.84 2.69 32.13 3.21
1877 4950 0.394352 GAAGGGGGCCTGTACATGTG 60.394 60.000 9.11 0.00 32.13 3.21
1878 4951 2.440247 GGGGGCCTGTACATGTGC 60.440 66.667 9.11 8.01 0.00 4.57
1879 4952 2.354729 GGGGCCTGTACATGTGCA 59.645 61.111 16.13 16.13 0.00 4.57
1880 4953 1.076777 GGGGCCTGTACATGTGCAT 60.077 57.895 17.33 0.00 0.00 3.96
1881 4954 1.386525 GGGGCCTGTACATGTGCATG 61.387 60.000 17.33 15.22 44.15 4.06
1882 4955 0.394216 GGGCCTGTACATGTGCATGA 60.394 55.000 20.25 0.00 41.20 3.07
1885 4958 0.654160 CCTGTACATGTGCATGAGCG 59.346 55.000 17.33 5.19 46.23 5.03
1910 5154 2.178521 CGACCGGTTCGTCTCTGG 59.821 66.667 9.42 0.00 43.24 3.86
1912 5156 2.203596 ACCGGTTCGTCTCTGGGT 60.204 61.111 0.00 0.00 35.79 4.51
1913 5157 2.210341 GACCGGTTCGTCTCTGGGTC 62.210 65.000 9.42 0.00 37.40 4.46
1915 5159 1.507174 CGGTTCGTCTCTGGGTCTC 59.493 63.158 0.00 0.00 0.00 3.36
1916 5160 1.891616 GGTTCGTCTCTGGGTCTCC 59.108 63.158 0.00 0.00 0.00 3.71
1917 5161 1.605971 GGTTCGTCTCTGGGTCTCCC 61.606 65.000 0.00 0.00 45.71 4.30
1918 5162 0.612453 GTTCGTCTCTGGGTCTCCCT 60.612 60.000 6.38 0.00 45.70 4.20
1919 5163 0.114560 TTCGTCTCTGGGTCTCCCTT 59.885 55.000 6.38 0.00 45.70 3.95
1954 5208 3.945434 CGCGCAGGGTGATCATGC 61.945 66.667 8.75 9.32 36.60 4.06
1957 5211 2.124570 GCAGGGTGATCATGCGGT 60.125 61.111 0.00 0.00 0.00 5.68
2036 5291 1.439693 CTTGCCGTTTGCGTTACCG 60.440 57.895 0.00 0.00 45.60 4.02
2054 5309 2.193536 GGCAGCCGAACCAAACACT 61.194 57.895 0.00 0.00 0.00 3.55
2084 5342 7.068962 TGTTCCATATAGAGTCAATTACACCGA 59.931 37.037 0.00 0.00 0.00 4.69
2103 5361 2.423577 GATGGTGTTAGAACTTGGCGT 58.576 47.619 0.00 0.00 0.00 5.68
2109 5367 3.490526 GTGTTAGAACTTGGCGTAAACGA 59.509 43.478 6.71 0.00 43.02 3.85
2140 5398 3.372206 GTGCTAGAACTTGTGGCATACAG 59.628 47.826 0.15 0.00 41.10 2.74
2143 5401 3.769739 AGAACTTGTGGCATACAGTGA 57.230 42.857 0.00 0.00 41.10 3.41
2165 5423 6.428771 GTGAACTGGTGTAATAACTTGGCTTA 59.571 38.462 0.00 0.00 0.00 3.09
2166 5424 6.999272 TGAACTGGTGTAATAACTTGGCTTAA 59.001 34.615 0.00 0.00 0.00 1.85
2167 5425 7.502895 TGAACTGGTGTAATAACTTGGCTTAAA 59.497 33.333 0.00 0.00 0.00 1.52
2194 5452 3.465122 AATACGGTGCAAATCACGTTC 57.535 42.857 6.90 0.00 46.56 3.95
2195 5453 1.867166 TACGGTGCAAATCACGTTCA 58.133 45.000 6.90 0.00 46.56 3.18
2196 5454 0.586319 ACGGTGCAAATCACGTTCAG 59.414 50.000 0.00 0.00 46.56 3.02
2197 5455 0.865111 CGGTGCAAATCACGTTCAGA 59.135 50.000 0.00 0.00 46.56 3.27
2198 5456 1.464608 CGGTGCAAATCACGTTCAGAT 59.535 47.619 0.00 0.00 46.56 2.90
2199 5457 2.670905 CGGTGCAAATCACGTTCAGATA 59.329 45.455 0.00 0.00 46.56 1.98
2200 5458 3.309682 CGGTGCAAATCACGTTCAGATAT 59.690 43.478 0.00 0.00 46.56 1.63
2203 5461 6.192360 GGTGCAAATCACGTTCAGATATAAC 58.808 40.000 0.00 0.00 46.56 1.89
2205 5463 7.409697 GTGCAAATCACGTTCAGATATAACAT 58.590 34.615 0.00 0.00 35.76 2.71
2206 5464 7.584123 GTGCAAATCACGTTCAGATATAACATC 59.416 37.037 0.00 0.00 35.76 3.06
2207 5465 6.787515 GCAAATCACGTTCAGATATAACATCG 59.212 38.462 0.00 0.00 0.00 3.84
2208 5466 7.306574 GCAAATCACGTTCAGATATAACATCGA 60.307 37.037 0.00 0.00 0.00 3.59
2209 5467 7.624706 AATCACGTTCAGATATAACATCGAC 57.375 36.000 0.00 0.00 0.00 4.20
2210 5468 5.202640 TCACGTTCAGATATAACATCGACG 58.797 41.667 0.00 0.00 33.47 5.12
2211 5469 3.973135 ACGTTCAGATATAACATCGACGC 59.027 43.478 0.00 0.00 31.86 5.19
2216 5474 4.515567 TCAGATATAACATCGACGCTGACT 59.484 41.667 5.58 0.00 0.00 3.41
2238 5496 4.881440 GCGCCAGGATGCCATGGA 62.881 66.667 18.40 0.31 39.02 3.41
2243 5501 2.697263 AGGATGCCATGGAGCCCA 60.697 61.111 18.40 3.68 38.19 5.36
2251 5509 2.284625 ATGGAGCCCACCGTCAGA 60.285 61.111 0.00 0.00 35.80 3.27
2255 5513 1.979693 GAGCCCACCGTCAGAGACT 60.980 63.158 0.00 0.00 0.00 3.24
2256 5514 0.680280 GAGCCCACCGTCAGAGACTA 60.680 60.000 0.00 0.00 0.00 2.59
2263 5521 1.004979 ACCGTCAGAGACTAGAAGGCT 59.995 52.381 0.00 0.00 35.22 4.58
2271 5529 3.117888 AGAGACTAGAAGGCTGAGAGGAG 60.118 52.174 0.00 0.00 30.20 3.69
2311 5578 1.616374 GCGAAAACCCCCTTGATTTCA 59.384 47.619 0.00 0.00 32.64 2.69
2314 5581 3.068873 CGAAAACCCCCTTGATTTCACAA 59.931 43.478 0.00 0.00 32.64 3.33
2335 5602 2.094762 AAAGCCCATGTCTACGTGTC 57.905 50.000 0.00 0.00 0.00 3.67
2336 5603 1.267121 AAGCCCATGTCTACGTGTCT 58.733 50.000 0.00 0.00 0.00 3.41
2338 5605 0.246635 GCCCATGTCTACGTGTCTGT 59.753 55.000 0.00 0.00 0.00 3.41
2339 5606 1.337823 GCCCATGTCTACGTGTCTGTT 60.338 52.381 0.00 0.00 0.00 3.16
2340 5607 2.607187 CCCATGTCTACGTGTCTGTTC 58.393 52.381 0.00 0.00 0.00 3.18
2341 5608 2.231478 CCCATGTCTACGTGTCTGTTCT 59.769 50.000 0.00 0.00 0.00 3.01
2342 5609 3.306088 CCCATGTCTACGTGTCTGTTCTT 60.306 47.826 0.00 0.00 0.00 2.52
2346 5614 6.422701 CCATGTCTACGTGTCTGTTCTTTTTA 59.577 38.462 0.00 0.00 0.00 1.52
2347 5615 7.117812 CCATGTCTACGTGTCTGTTCTTTTTAT 59.882 37.037 0.00 0.00 0.00 1.40
2351 5619 9.712359 GTCTACGTGTCTGTTCTTTTTATTTTT 57.288 29.630 0.00 0.00 0.00 1.94
2373 5641 1.762370 TCGCATCTATGACACATGGGT 59.238 47.619 0.00 0.00 33.40 4.51
2374 5642 2.170397 TCGCATCTATGACACATGGGTT 59.830 45.455 0.00 0.00 33.40 4.11
2378 5646 3.627395 TCTATGACACATGGGTTCCAC 57.373 47.619 0.00 0.00 35.80 4.02
2382 5650 1.228552 ACACATGGGTTCCACCTGC 60.229 57.895 0.00 0.00 38.64 4.85
2383 5651 1.228521 CACATGGGTTCCACCTGCA 60.229 57.895 0.00 0.00 38.64 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 4.824479 TTCATACCACTTGATGCTGAGA 57.176 40.909 0.00 0.00 0.00 3.27
456 457 5.235186 GTGTGGAGACTATTGAATGATTCCG 59.765 44.000 2.26 0.00 0.00 4.30
459 460 7.170965 ACAAGTGTGGAGACTATTGAATGATT 58.829 34.615 0.00 0.00 0.00 2.57
513 514 4.054369 AGGATTGGGATTCCAGGACATTA 58.946 43.478 4.80 0.00 45.04 1.90
521 522 3.593328 AGTTTGAGAGGATTGGGATTCCA 59.407 43.478 4.80 0.00 42.25 3.53
537 538 6.859420 TGATGACTCGATCAAAAAGTTTGA 57.141 33.333 5.92 5.92 41.93 2.69
573 574 3.511146 GGGCAAGAGAAAATCATGTTGGA 59.489 43.478 0.00 0.00 0.00 3.53
582 583 2.174360 GCAAGAGGGGCAAGAGAAAAT 58.826 47.619 0.00 0.00 0.00 1.82
800 801 3.370209 GCTTATTAAACCGGAGACCCTGT 60.370 47.826 9.46 0.00 0.00 4.00
931 932 0.600255 GCGGGCGCTCTACACATATT 60.600 55.000 5.36 0.00 38.26 1.28
976 977 2.025155 GATGTCCTCTACGCTCTCCAA 58.975 52.381 0.00 0.00 0.00 3.53
978 979 1.606668 CTGATGTCCTCTACGCTCTCC 59.393 57.143 0.00 0.00 0.00 3.71
991 992 0.322975 ATAGGCGCCATCCTGATGTC 59.677 55.000 31.54 0.00 37.01 3.06
995 996 0.760567 AGTGATAGGCGCCATCCTGA 60.761 55.000 31.54 10.75 37.01 3.86
998 999 1.373497 CGAGTGATAGGCGCCATCC 60.373 63.158 31.54 19.97 0.00 3.51
1010 1011 1.220749 GCATTGGCCCTACGAGTGA 59.779 57.895 0.00 0.00 0.00 3.41
1356 1357 4.394712 CAGTCGGTGTGGGGGCTC 62.395 72.222 0.00 0.00 0.00 4.70
1394 1395 2.591715 GTGTGCTCCGCAAGTGGT 60.592 61.111 0.00 0.00 41.47 4.16
1395 1396 3.357079 GGTGTGCTCCGCAAGTGG 61.357 66.667 0.00 0.00 41.47 4.00
1407 1408 1.673626 GCATGCAAAATCCCTGGTGTG 60.674 52.381 14.21 0.00 0.00 3.82
1412 1421 1.546923 TCAGTGCATGCAAAATCCCTG 59.453 47.619 24.58 22.70 0.00 4.45
1429 1438 0.445436 GACGAGCTGGCATTGTTCAG 59.555 55.000 0.00 5.25 0.00 3.02
1430 1439 0.250252 TGACGAGCTGGCATTGTTCA 60.250 50.000 0.00 0.00 0.00 3.18
1434 1443 0.957395 AGGTTGACGAGCTGGCATTG 60.957 55.000 0.00 0.00 34.08 2.82
1440 1449 0.318699 TCAACGAGGTTGACGAGCTG 60.319 55.000 7.07 0.00 45.88 4.24
1525 1543 2.507944 GTCGGGCCATCATCAGCT 59.492 61.111 4.39 0.00 0.00 4.24
1528 1546 4.889856 CGCGTCGGGCCATCATCA 62.890 66.667 4.39 0.00 38.94 3.07
1529 1547 4.891727 ACGCGTCGGGCCATCATC 62.892 66.667 5.58 0.00 38.94 2.92
1554 1573 3.027170 GCCATCACTTCACGCCACG 62.027 63.158 0.00 0.00 0.00 4.94
1579 1601 2.196749 CATGAACTCCTCCATCGAACG 58.803 52.381 0.00 0.00 0.00 3.95
1625 1947 4.131596 GGGCAGGCGAAATACATTTAGTA 58.868 43.478 0.00 0.00 37.06 1.82
1627 1949 3.003689 CAGGGCAGGCGAAATACATTTAG 59.996 47.826 0.00 0.00 0.00 1.85
1628 1950 2.948979 CAGGGCAGGCGAAATACATTTA 59.051 45.455 0.00 0.00 0.00 1.40
1629 1951 1.750778 CAGGGCAGGCGAAATACATTT 59.249 47.619 0.00 0.00 0.00 2.32
1631 1953 1.103398 GCAGGGCAGGCGAAATACAT 61.103 55.000 0.00 0.00 0.00 2.29
1691 4632 4.360563 AGTGGTACGAATGCGAAAGATAG 58.639 43.478 0.00 0.00 41.64 2.08
1692 4633 4.380841 AGTGGTACGAATGCGAAAGATA 57.619 40.909 0.00 0.00 41.64 1.98
1728 4794 3.150767 AGGAGAGATACGTGGATAGTGC 58.849 50.000 0.00 0.00 0.00 4.40
1751 4817 0.406361 ATTCCTTGGGTGCGGGTTTA 59.594 50.000 0.00 0.00 0.00 2.01
1834 4907 2.002586 CAGCCTCCACGACACAAATAG 58.997 52.381 0.00 0.00 0.00 1.73
1865 4938 0.379669 GCTCATGCACATGTACAGGC 59.620 55.000 7.57 8.62 39.72 4.85
1866 4939 0.654160 CGCTCATGCACATGTACAGG 59.346 55.000 5.87 5.87 39.72 4.00
1867 4940 0.027194 GCGCTCATGCACATGTACAG 59.973 55.000 10.27 2.53 39.72 2.74
1868 4941 0.673022 TGCGCTCATGCACATGTACA 60.673 50.000 9.73 0.15 40.62 2.90
1870 4943 4.613929 TGCGCTCATGCACATGTA 57.386 50.000 9.73 0.00 40.62 2.29
1912 5156 0.902531 GTTCGATCACCCAAGGGAGA 59.097 55.000 13.15 10.23 39.10 3.71
1913 5157 0.460284 CGTTCGATCACCCAAGGGAG 60.460 60.000 13.15 3.82 38.96 4.30
1915 5159 1.449601 CCGTTCGATCACCCAAGGG 60.450 63.158 2.91 2.91 42.03 3.95
1916 5160 2.106683 GCCGTTCGATCACCCAAGG 61.107 63.158 0.00 0.00 0.00 3.61
1917 5161 1.079127 AGCCGTTCGATCACCCAAG 60.079 57.895 0.00 0.00 0.00 3.61
1918 5162 1.375396 CAGCCGTTCGATCACCCAA 60.375 57.895 0.00 0.00 0.00 4.12
1919 5163 2.264480 CAGCCGTTCGATCACCCA 59.736 61.111 0.00 0.00 0.00 4.51
1983 5237 2.584970 GCGTCGGCCAATCGATCA 60.585 61.111 13.94 0.00 41.40 2.92
2006 5260 2.266055 GGCAAGGACGACTCTGGG 59.734 66.667 0.00 0.00 0.00 4.45
2009 5263 0.600255 CAAACGGCAAGGACGACTCT 60.600 55.000 0.00 0.00 35.20 3.24
2010 5264 1.860078 CAAACGGCAAGGACGACTC 59.140 57.895 0.00 0.00 35.20 3.36
2011 5265 2.251642 GCAAACGGCAAGGACGACT 61.252 57.895 0.00 0.00 43.97 4.18
2012 5266 2.251371 GCAAACGGCAAGGACGAC 59.749 61.111 0.00 0.00 43.97 4.34
2036 5291 1.734388 AAGTGTTTGGTTCGGCTGCC 61.734 55.000 9.11 9.11 0.00 4.85
2084 5342 2.561478 ACGCCAAGTTCTAACACCAT 57.439 45.000 0.00 0.00 0.00 3.55
2090 5348 4.386652 GTGATCGTTTACGCCAAGTTCTAA 59.613 41.667 0.00 0.00 39.60 2.10
2140 5398 4.760204 AGCCAAGTTATTACACCAGTTCAC 59.240 41.667 0.00 0.00 0.00 3.18
2143 5401 7.520937 CGTTTAAGCCAAGTTATTACACCAGTT 60.521 37.037 0.00 0.00 0.00 3.16
2151 5409 5.943706 TGCACGTTTAAGCCAAGTTATTA 57.056 34.783 0.00 0.00 0.00 0.98
2165 5423 0.663688 TGCACCGTATTTGCACGTTT 59.336 45.000 0.00 0.00 45.06 3.60
2166 5424 2.322212 TGCACCGTATTTGCACGTT 58.678 47.368 0.00 0.00 45.06 3.99
2167 5425 4.050955 TGCACCGTATTTGCACGT 57.949 50.000 0.00 0.00 45.06 4.49
2194 5452 4.788690 AGTCAGCGTCGATGTTATATCTG 58.211 43.478 10.70 4.09 0.00 2.90
2195 5453 5.215903 CAAGTCAGCGTCGATGTTATATCT 58.784 41.667 10.70 0.00 0.00 1.98
2196 5454 4.383052 CCAAGTCAGCGTCGATGTTATATC 59.617 45.833 10.70 0.00 0.00 1.63
2197 5455 4.299155 CCAAGTCAGCGTCGATGTTATAT 58.701 43.478 10.70 0.00 0.00 0.86
2198 5456 3.702330 CCAAGTCAGCGTCGATGTTATA 58.298 45.455 10.70 0.00 0.00 0.98
2199 5457 2.540515 CCAAGTCAGCGTCGATGTTAT 58.459 47.619 10.70 0.00 0.00 1.89
2200 5458 1.990799 CCAAGTCAGCGTCGATGTTA 58.009 50.000 10.70 0.00 0.00 2.41
2203 5461 3.084579 GCCAAGTCAGCGTCGATG 58.915 61.111 3.58 3.58 0.00 3.84
2228 5486 2.520260 GGTGGGCTCCATGGCATC 60.520 66.667 6.96 0.00 43.83 3.91
2229 5487 4.511246 CGGTGGGCTCCATGGCAT 62.511 66.667 6.96 0.00 43.83 4.40
2232 5490 3.687321 CTGACGGTGGGCTCCATGG 62.687 68.421 4.97 4.97 35.28 3.66
2238 5496 0.681564 CTAGTCTCTGACGGTGGGCT 60.682 60.000 0.00 0.00 37.67 5.19
2243 5501 1.004979 AGCCTTCTAGTCTCTGACGGT 59.995 52.381 0.00 0.00 37.67 4.83
2251 5509 2.686715 GCTCCTCTCAGCCTTCTAGTCT 60.687 54.545 0.00 0.00 32.76 3.24
2255 5513 1.388065 GCGCTCCTCTCAGCCTTCTA 61.388 60.000 0.00 0.00 35.84 2.10
2256 5514 2.720134 GCGCTCCTCTCAGCCTTCT 61.720 63.158 0.00 0.00 35.84 2.85
2263 5521 4.056125 CCACACGCGCTCCTCTCA 62.056 66.667 5.73 0.00 0.00 3.27
2271 5529 1.211709 AAAAATAGGCCACACGCGC 59.788 52.632 5.73 0.00 38.94 6.86
2290 5548 1.616374 GAAATCAAGGGGGTTTTCGCA 59.384 47.619 0.00 0.00 34.25 5.10
2291 5549 1.616374 TGAAATCAAGGGGGTTTTCGC 59.384 47.619 0.00 0.00 32.13 4.70
2292 5550 2.625790 TGTGAAATCAAGGGGGTTTTCG 59.374 45.455 0.00 0.00 32.13 3.46
2293 5551 4.681074 TTGTGAAATCAAGGGGGTTTTC 57.319 40.909 0.00 0.00 0.00 2.29
2294 5552 5.443230 TTTTGTGAAATCAAGGGGGTTTT 57.557 34.783 0.00 0.00 0.00 2.43
2314 5581 2.812011 GACACGTAGACATGGGCTTTTT 59.188 45.455 0.00 0.00 0.00 1.94
2351 5619 3.205338 CCCATGTGTCATAGATGCGAAA 58.795 45.455 0.00 0.00 0.00 3.46
2353 5621 1.762370 ACCCATGTGTCATAGATGCGA 59.238 47.619 0.00 0.00 0.00 5.10
2357 5625 4.156455 GTGGAACCCATGTGTCATAGAT 57.844 45.455 0.00 0.00 35.28 1.98


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

AutoCloner maintained by Alex Coulton.