Multiple sequence alignment - TraesCS2A01G148100

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 TraesCS2A01G148100 chr2A 100.000 2868 0 0 1 2868 94274745 94277612 0.000000e+00 5297.0
1 TraesCS2A01G148100 chr2A 88.396 1241 76 29 672 1849 94205386 94204151 0.000000e+00 1432.0
2 TraesCS2A01G148100 chr2A 93.192 661 45 0 2208 2868 57826128 57825468 0.000000e+00 972.0
3 TraesCS2A01G148100 chr2A 82.810 605 98 6 1248 1849 94162156 94161555 1.170000e-148 536.0
4 TraesCS2A01G148100 chr2D 93.937 1534 65 11 333 1849 95666679 95668201 0.000000e+00 2292.0
5 TraesCS2A01G148100 chr2D 89.422 1229 68 31 672 1849 95655503 95654286 0.000000e+00 1493.0
6 TraesCS2A01G148100 chr2D 85.061 1071 70 36 672 1661 95683755 95684816 0.000000e+00 1009.0
7 TraesCS2A01G148100 chr2D 93.703 667 39 1 2205 2868 469107807 469108473 0.000000e+00 996.0
8 TraesCS2A01G148100 chr2D 82.781 604 100 4 1248 1849 95649043 95648442 1.170000e-148 536.0
9 TraesCS2A01G148100 chr2D 92.705 329 10 3 9 336 95666317 95666632 2.010000e-126 462.0
10 TraesCS2A01G148100 chr2D 87.375 301 29 6 1902 2200 95686877 95687170 1.270000e-88 337.0
11 TraesCS2A01G148100 chr2D 95.980 199 8 0 1653 1851 95685840 95686038 9.910000e-85 324.0
12 TraesCS2A01G148100 chr2D 87.654 243 15 4 9 251 95683138 95683365 4.710000e-68 268.0
13 TraesCS2A01G148100 chr2D 92.727 55 4 0 1982 2036 17451887 17451833 2.370000e-11 80.5
14 TraesCS2A01G148100 chr2B 89.365 1213 72 27 531 1716 147409103 147407921 0.000000e+00 1472.0
15 TraesCS2A01G148100 chr2B 86.969 1343 90 44 565 1849 147286557 147285242 0.000000e+00 1432.0
16 TraesCS2A01G148100 chr2B 81.983 605 103 6 1248 1849 146996625 146996024 2.550000e-140 508.0
17 TraesCS2A01G148100 chr2B 88.581 289 29 3 1902 2189 147435359 147435644 5.880000e-92 348.0
18 TraesCS2A01G148100 chr2B 96.094 128 5 0 333 460 147302082 147302209 2.900000e-50 209.0
19 TraesCS2A01G148100 chr2B 95.652 92 4 0 245 336 147301941 147302032 6.400000e-32 148.0
20 TraesCS2A01G148100 chr2B 90.000 90 5 1 13 102 147289994 147290079 2.340000e-21 113.0
21 TraesCS2A01G148100 chrUn 93.514 663 41 1 2208 2868 96553200 96552538 0.000000e+00 985.0
22 TraesCS2A01G148100 chr1A 93.083 665 45 1 2205 2868 461966661 461967325 0.000000e+00 972.0
23 TraesCS2A01G148100 chr1A 92.481 665 49 1 2205 2868 35563876 35564540 0.000000e+00 950.0
24 TraesCS2A01G148100 chr7A 93.041 661 46 0 2208 2868 48781428 48780768 0.000000e+00 966.0
25 TraesCS2A01G148100 chr5A 92.890 661 47 0 2208 2868 570488520 570487860 0.000000e+00 961.0
26 TraesCS2A01G148100 chr5A 92.319 664 51 0 2205 2868 564352251 564352914 0.000000e+00 944.0
27 TraesCS2A01G148100 chr5A 75.100 249 57 5 1946 2191 567269873 567270119 8.400000e-21 111.0
28 TraesCS2A01G148100 chr4D 92.900 662 46 1 2208 2868 459191467 459190806 0.000000e+00 961.0
29 TraesCS2A01G148100 chr4A 89.583 96 8 2 101 195 501573235 501573329 1.400000e-23 121.0


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 TraesCS2A01G148100 chr2A 94274745 94277612 2867 False 5297.0 5297 100.0000 1 2868 1 chr2A.!!$F1 2867
1 TraesCS2A01G148100 chr2A 94204151 94205386 1235 True 1432.0 1432 88.3960 672 1849 1 chr2A.!!$R3 1177
2 TraesCS2A01G148100 chr2A 57825468 57826128 660 True 972.0 972 93.1920 2208 2868 1 chr2A.!!$R1 660
3 TraesCS2A01G148100 chr2A 94161555 94162156 601 True 536.0 536 82.8100 1248 1849 1 chr2A.!!$R2 601
4 TraesCS2A01G148100 chr2D 95654286 95655503 1217 True 1493.0 1493 89.4220 672 1849 1 chr2D.!!$R3 1177
5 TraesCS2A01G148100 chr2D 95666317 95668201 1884 False 1377.0 2292 93.3210 9 1849 2 chr2D.!!$F2 1840
6 TraesCS2A01G148100 chr2D 469107807 469108473 666 False 996.0 996 93.7030 2205 2868 1 chr2D.!!$F1 663
7 TraesCS2A01G148100 chr2D 95648442 95649043 601 True 536.0 536 82.7810 1248 1849 1 chr2D.!!$R2 601
8 TraesCS2A01G148100 chr2D 95683138 95687170 4032 False 484.5 1009 89.0175 9 2200 4 chr2D.!!$F3 2191
9 TraesCS2A01G148100 chr2B 147407921 147409103 1182 True 1472.0 1472 89.3650 531 1716 1 chr2B.!!$R3 1185
10 TraesCS2A01G148100 chr2B 147285242 147286557 1315 True 1432.0 1432 86.9690 565 1849 1 chr2B.!!$R2 1284
11 TraesCS2A01G148100 chr2B 146996024 146996625 601 True 508.0 508 81.9830 1248 1849 1 chr2B.!!$R1 601
12 TraesCS2A01G148100 chrUn 96552538 96553200 662 True 985.0 985 93.5140 2208 2868 1 chrUn.!!$R1 660
13 TraesCS2A01G148100 chr1A 461966661 461967325 664 False 972.0 972 93.0830 2205 2868 1 chr1A.!!$F2 663
14 TraesCS2A01G148100 chr1A 35563876 35564540 664 False 950.0 950 92.4810 2205 2868 1 chr1A.!!$F1 663
15 TraesCS2A01G148100 chr7A 48780768 48781428 660 True 966.0 966 93.0410 2208 2868 1 chr7A.!!$R1 660
16 TraesCS2A01G148100 chr5A 570487860 570488520 660 True 961.0 961 92.8900 2208 2868 1 chr5A.!!$R1 660
17 TraesCS2A01G148100 chr5A 564352251 564352914 663 False 944.0 944 92.3190 2205 2868 1 chr5A.!!$F1 663
18 TraesCS2A01G148100 chr4D 459190806 459191467 661 True 961.0 961 92.9000 2208 2868 1 chr4D.!!$R1 660

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
653 819 0.323178 ATGGAGCTGCAGAAACCCAG 60.323 55.0 20.43 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 3183 0.032952 AAGTACGTTCCGCTTGAGCA 59.967 50.0 0.0 0.0 42.21 4.26 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
52 53 5.536161 AGCCCATCGACAATTTAAGCATTAT 59.464 36.000 0.00 0.00 0.00 1.28
53 54 6.714810 AGCCCATCGACAATTTAAGCATTATA 59.285 34.615 0.00 0.00 0.00 0.98
54 55 7.394359 AGCCCATCGACAATTTAAGCATTATAT 59.606 33.333 0.00 0.00 0.00 0.86
55 56 8.673711 GCCCATCGACAATTTAAGCATTATATA 58.326 33.333 0.00 0.00 0.00 0.86
197 198 9.926158 ACAACAAATATACATCATGCAAAAGAA 57.074 25.926 0.00 0.00 0.00 2.52
337 484 5.970317 TTGTTCAGTCAGACGAGGTATAA 57.030 39.130 0.00 0.00 0.00 0.98
436 583 5.598416 TGATCGAGATGTCTTTACCATGT 57.402 39.130 0.00 0.00 0.00 3.21
488 642 5.558307 CGAAGAGTAAACACGTACTAGAGG 58.442 45.833 0.00 0.00 34.40 3.69
514 668 1.826720 TGATGTACCGGAGTTACCACC 59.173 52.381 9.46 0.00 38.90 4.61
558 716 3.363378 GGAGCGACATGAATTATTGCTCG 60.363 47.826 13.50 4.77 46.17 5.03
576 736 2.614057 CTCGGAATGGAATGTGCTAACC 59.386 50.000 0.00 0.00 0.00 2.85
588 748 3.236047 TGTGCTAACCTAACCTCAGTCA 58.764 45.455 0.00 0.00 0.00 3.41
653 819 0.323178 ATGGAGCTGCAGAAACCCAG 60.323 55.000 20.43 0.00 0.00 4.45
665 831 4.954118 ACCCAGTCGTCCCAGCCA 62.954 66.667 0.00 0.00 0.00 4.75
666 832 4.087892 CCCAGTCGTCCCAGCCAG 62.088 72.222 0.00 0.00 0.00 4.85
667 833 2.997315 CCAGTCGTCCCAGCCAGA 60.997 66.667 0.00 0.00 0.00 3.86
668 834 2.362369 CCAGTCGTCCCAGCCAGAT 61.362 63.158 0.00 0.00 0.00 2.90
701 870 2.368439 TGCCTACATCACCATTCAAGC 58.632 47.619 0.00 0.00 0.00 4.01
925 1150 1.079543 CACTTCCAGTCTCCTGCCG 60.080 63.158 0.00 0.00 37.38 5.69
939 1167 4.927782 GCCGCCCACACACACTCA 62.928 66.667 0.00 0.00 0.00 3.41
944 1195 1.291877 GCCCACACACACTCATCGTC 61.292 60.000 0.00 0.00 0.00 4.20
1215 1470 4.726416 CTTGCTTTTTCATGCACGTAGAT 58.274 39.130 0.00 0.00 39.05 1.98
1330 1600 3.966543 CCGCCCAACTTCCCCAGT 61.967 66.667 0.00 0.00 37.30 4.00
1651 2954 2.653702 GTGTCGCACTGCTCCTCT 59.346 61.111 0.00 0.00 0.00 3.69
1801 3104 3.278574 CAACCGGATGGACAACATGTAT 58.721 45.455 9.46 0.00 40.72 2.29
1860 3163 4.845580 CGCGGCCTGCCAGAAGAT 62.846 66.667 9.17 0.00 42.08 2.40
1862 3165 3.207669 CGGCCTGCCAGAAGATGC 61.208 66.667 9.17 0.00 35.37 3.91
1863 3166 2.832201 GGCCTGCCAGAAGATGCC 60.832 66.667 2.58 0.00 35.81 4.40
1864 3167 2.044650 GCCTGCCAGAAGATGCCA 60.045 61.111 0.00 0.00 0.00 4.92
1865 3168 1.455217 GCCTGCCAGAAGATGCCAT 60.455 57.895 0.00 0.00 0.00 4.40
1868 3171 1.236628 CTGCCAGAAGATGCCATAGC 58.763 55.000 0.00 0.00 40.48 2.97
1869 3172 0.533531 TGCCAGAAGATGCCATAGCG 60.534 55.000 0.00 0.00 44.31 4.26
1870 3173 0.533755 GCCAGAAGATGCCATAGCGT 60.534 55.000 0.00 0.00 44.31 5.07
1873 3176 0.533755 AGAAGATGCCATAGCGTGCC 60.534 55.000 0.00 0.00 44.31 5.01
1874 3177 0.815213 GAAGATGCCATAGCGTGCCA 60.815 55.000 0.00 0.00 44.31 4.92
1876 3179 0.686789 AGATGCCATAGCGTGCCATA 59.313 50.000 0.00 0.00 44.31 2.74
1877 3180 1.081892 GATGCCATAGCGTGCCATAG 58.918 55.000 0.00 0.00 44.31 2.23
1878 3181 0.957395 ATGCCATAGCGTGCCATAGC 60.957 55.000 0.00 0.00 44.31 2.97
1880 3183 1.300931 CCATAGCGTGCCATAGCGT 60.301 57.895 0.00 0.00 44.31 5.07
1881 3184 1.560004 CCATAGCGTGCCATAGCGTG 61.560 60.000 0.00 0.00 44.31 5.34
1882 3185 1.956170 ATAGCGTGCCATAGCGTGC 60.956 57.895 0.00 0.00 44.31 5.34
1883 3186 4.457496 AGCGTGCCATAGCGTGCT 62.457 61.111 0.00 0.00 44.45 4.40
1884 3187 2.954020 TAGCGTGCCATAGCGTGCTC 62.954 60.000 5.27 0.00 45.68 4.26
1885 3188 2.509111 CGTGCCATAGCGTGCTCA 60.509 61.111 0.00 0.00 44.31 4.26
1886 3189 2.100031 CGTGCCATAGCGTGCTCAA 61.100 57.895 0.00 0.00 44.31 3.02
1887 3190 1.717937 GTGCCATAGCGTGCTCAAG 59.282 57.895 0.00 0.00 44.31 3.02
1888 3191 2.108514 TGCCATAGCGTGCTCAAGC 61.109 57.895 0.00 0.13 44.31 4.01
1889 3192 3.009140 CCATAGCGTGCTCAAGCG 58.991 61.111 0.00 0.00 45.83 4.68
1890 3193 2.528743 CCATAGCGTGCTCAAGCGG 61.529 63.158 0.00 0.00 45.83 5.52
1891 3194 1.519234 CATAGCGTGCTCAAGCGGA 60.519 57.895 0.00 0.00 45.83 5.54
1892 3195 1.083806 CATAGCGTGCTCAAGCGGAA 61.084 55.000 0.00 0.00 45.83 4.30
1922 4014 4.347292 TGAGGGAGATTGGATCAGAAGATG 59.653 45.833 0.00 0.00 33.72 2.90
1945 4037 4.205587 CCATAGCTCAAGGAAAGATGCTT 58.794 43.478 0.00 0.00 37.77 3.91
1956 4049 4.289672 AGGAAAGATGCTTTAGGAGGTGAA 59.710 41.667 0.00 0.00 0.00 3.18
1958 4051 3.922171 AGATGCTTTAGGAGGTGAAGG 57.078 47.619 0.00 0.00 0.00 3.46
1959 4052 3.454858 AGATGCTTTAGGAGGTGAAGGA 58.545 45.455 0.00 0.00 0.00 3.36
2006 4099 0.533531 TCAATCATGCCGCCTAGCTG 60.534 55.000 0.00 0.00 0.00 4.24
2055 4148 0.176910 GACAGTCCTGCTAGAAGGCC 59.823 60.000 12.63 0.00 37.24 5.19
2060 4153 1.279271 GTCCTGCTAGAAGGCCAGAAA 59.721 52.381 12.63 0.00 37.24 2.52
2062 4155 1.280421 CCTGCTAGAAGGCCAGAAACT 59.720 52.381 2.98 0.00 0.00 2.66
2063 4156 2.290577 CCTGCTAGAAGGCCAGAAACTT 60.291 50.000 2.98 0.00 0.00 2.66
2065 4158 4.565652 CCTGCTAGAAGGCCAGAAACTTAA 60.566 45.833 2.98 0.00 0.00 1.85
2066 4159 4.579869 TGCTAGAAGGCCAGAAACTTAAG 58.420 43.478 5.01 0.00 0.00 1.85
2067 4160 3.375610 GCTAGAAGGCCAGAAACTTAAGC 59.624 47.826 5.01 0.00 32.33 3.09
2068 4161 3.508845 AGAAGGCCAGAAACTTAAGCA 57.491 42.857 5.01 0.00 0.00 3.91
2069 4162 3.149981 AGAAGGCCAGAAACTTAAGCAC 58.850 45.455 5.01 0.00 0.00 4.40
2070 4163 1.523758 AGGCCAGAAACTTAAGCACG 58.476 50.000 5.01 0.00 0.00 5.34
2072 4165 1.519408 GCCAGAAACTTAAGCACGGA 58.481 50.000 1.29 0.00 0.00 4.69
2073 4166 1.464997 GCCAGAAACTTAAGCACGGAG 59.535 52.381 1.29 0.00 0.00 4.63
2075 4168 2.737252 CCAGAAACTTAAGCACGGAGTC 59.263 50.000 1.29 0.00 41.61 3.36
2076 4169 3.390135 CAGAAACTTAAGCACGGAGTCA 58.610 45.455 1.29 0.00 41.61 3.41
2077 4170 3.184581 CAGAAACTTAAGCACGGAGTCAC 59.815 47.826 1.29 0.00 41.61 3.67
2084 4177 1.218047 GCACGGAGTCACAGGCATA 59.782 57.895 0.00 0.00 41.61 3.14
2098 4191 1.557832 AGGCATACCGCAAAAGACCTA 59.442 47.619 0.00 0.00 45.17 3.08
2114 4207 5.579753 AGACCTACTCGATAACCATCCTA 57.420 43.478 0.00 0.00 0.00 2.94
2119 4212 6.373774 ACCTACTCGATAACCATCCTATTACG 59.626 42.308 0.00 0.00 0.00 3.18
2120 4213 5.056894 ACTCGATAACCATCCTATTACGC 57.943 43.478 0.00 0.00 0.00 4.42
2121 4214 4.521639 ACTCGATAACCATCCTATTACGCA 59.478 41.667 0.00 0.00 0.00 5.24
2129 4222 3.307691 CCATCCTATTACGCATGGTCCAT 60.308 47.826 0.00 0.00 32.49 3.41
2136 4229 1.204146 ACGCATGGTCCATAAGGTCT 58.796 50.000 3.38 0.00 35.89 3.85
2137 4230 2.394632 ACGCATGGTCCATAAGGTCTA 58.605 47.619 3.38 0.00 35.89 2.59
2146 4239 4.039366 GGTCCATAAGGTCTAGGTCATCAC 59.961 50.000 0.00 0.00 35.89 3.06
2147 4240 4.039366 GTCCATAAGGTCTAGGTCATCACC 59.961 50.000 0.00 0.00 38.49 4.02
2148 4241 4.078571 TCCATAAGGTCTAGGTCATCACCT 60.079 45.833 0.00 0.00 45.48 4.00
2186 4279 1.443322 GGCGTCTCTCCTACCGGTAC 61.443 65.000 11.16 0.00 0.00 3.34
2270 4363 3.456644 TGTCAACTTGGACTGGGAAAGTA 59.543 43.478 0.00 0.00 40.07 2.24
2399 4492 6.320164 CCTTATCATTTTGGACCGGATTGTTA 59.680 38.462 9.46 0.00 0.00 2.41
2404 4497 1.153309 GGACCGGATTGTTACCCCG 60.153 63.158 9.46 0.00 42.64 5.73
2432 4525 3.462169 TGGTACCTCACACCACGG 58.538 61.111 14.36 0.00 41.17 4.94
2489 4582 4.499357 CCGGCATCAACTAGGTAGTACTTC 60.499 50.000 0.00 0.00 34.99 3.01
2548 4644 7.012421 GGTTTCTTAAGGCAGTAACATATGGAG 59.988 40.741 7.80 0.00 0.00 3.86
2570 4666 8.502738 TGGAGAATTTATATCTAGGGCAACTTT 58.497 33.333 0.00 0.00 0.00 2.66
2576 4672 8.756486 TTTATATCTAGGGCAACTTTTTACCC 57.244 34.615 0.00 0.00 43.17 3.69
2605 4701 2.491675 TGTAAGCCTCTCTCACGAGA 57.508 50.000 0.00 0.00 43.82 4.04
2616 4712 5.508657 CCTCTCTCACGAGATAATGCATCAA 60.509 44.000 0.00 0.00 44.86 2.57
2627 4723 7.391148 AGATAATGCATCAACTAAAACGGTT 57.609 32.000 0.00 0.00 35.96 4.44
2693 4789 2.280628 CGGAGGTCAAAATCTACTGCC 58.719 52.381 0.00 0.00 0.00 4.85
2715 4811 3.378112 CGCCATCACATTTTGAGTGGTAT 59.622 43.478 0.00 0.00 37.77 2.73
2739 4835 3.344515 GCCTTCCTACCACGAAAAGAAT 58.655 45.455 0.00 0.00 0.00 2.40
2747 4843 1.135972 CCACGAAAAGAATGCTCCACG 60.136 52.381 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.353607 GCTACACCTCGATCGCCG 60.354 66.667 11.09 4.90 40.25 6.46
1 2 1.589196 GTGCTACACCTCGATCGCC 60.589 63.158 11.09 0.00 0.00 5.54
11 12 1.069358 GGCTAGATCTGGGTGCTACAC 59.931 57.143 5.18 0.00 0.00 2.90
52 53 5.861787 CGTGCACCAACTCGAATGATATATA 59.138 40.000 12.15 0.00 0.00 0.86
53 54 4.686091 CGTGCACCAACTCGAATGATATAT 59.314 41.667 12.15 0.00 0.00 0.86
54 55 4.048504 CGTGCACCAACTCGAATGATATA 58.951 43.478 12.15 0.00 0.00 0.86
55 56 2.866156 CGTGCACCAACTCGAATGATAT 59.134 45.455 12.15 0.00 0.00 1.63
201 202 7.480760 AGAGTATGCATTTGTATGGGTTTTT 57.519 32.000 3.54 0.00 32.15 1.94
202 203 7.178274 TCAAGAGTATGCATTTGTATGGGTTTT 59.822 33.333 3.54 0.00 32.15 2.43
203 204 6.663093 TCAAGAGTATGCATTTGTATGGGTTT 59.337 34.615 3.54 0.00 32.15 3.27
309 351 4.092529 CCTCGTCTGACTGAACAAATCATG 59.907 45.833 6.21 0.00 37.44 3.07
337 484 4.503741 ACGCAATGACAAAAATACTGCT 57.496 36.364 0.00 0.00 0.00 4.24
415 562 4.210120 GCACATGGTAAAGACATCTCGATC 59.790 45.833 0.00 0.00 0.00 3.69
488 642 2.094762 ACTCCGGTACATCAACTTGC 57.905 50.000 0.00 0.00 0.00 4.01
514 668 7.329717 GCTCCTGTATTATTCTTAACCTGATCG 59.670 40.741 0.00 0.00 0.00 3.69
524 678 6.161855 TCATGTCGCTCCTGTATTATTCTT 57.838 37.500 0.00 0.00 0.00 2.52
526 680 7.426929 AATTCATGTCGCTCCTGTATTATTC 57.573 36.000 0.00 0.00 0.00 1.75
558 716 4.338400 GGTTAGGTTAGCACATTCCATTCC 59.662 45.833 0.00 0.00 0.00 3.01
576 736 5.180304 GCTTTTCTTTCCTGACTGAGGTTAG 59.820 44.000 0.00 0.00 43.37 2.34
588 748 3.956848 GCATGGATAGGCTTTTCTTTCCT 59.043 43.478 0.00 0.00 36.34 3.36
644 809 2.058675 CTGGGACGACTGGGTTTCT 58.941 57.895 0.00 0.00 0.00 2.52
645 810 1.671379 GCTGGGACGACTGGGTTTC 60.671 63.158 0.00 0.00 0.00 2.78
653 819 1.142748 CTGATCTGGCTGGGACGAC 59.857 63.158 0.00 0.00 0.00 4.34
665 831 1.769465 AGGCATGTGCAGATCTGATCT 59.231 47.619 27.04 14.31 44.36 2.75
666 832 2.257691 AGGCATGTGCAGATCTGATC 57.742 50.000 27.04 17.05 44.36 2.92
667 833 2.436911 TGTAGGCATGTGCAGATCTGAT 59.563 45.455 27.04 8.25 44.36 2.90
668 834 1.832998 TGTAGGCATGTGCAGATCTGA 59.167 47.619 27.04 5.94 44.36 3.27
747 929 4.576053 GCACAACTCAGCATACATCCAATA 59.424 41.667 0.00 0.00 0.00 1.90
925 1150 1.291877 GACGATGAGTGTGTGTGGGC 61.292 60.000 0.00 0.00 0.00 5.36
939 1167 1.424638 CCTACCCATCCTTGGACGAT 58.575 55.000 0.00 0.00 46.92 3.73
944 1195 0.395724 GCAACCCTACCCATCCTTGG 60.396 60.000 0.00 0.00 43.23 3.61
996 1249 2.615465 CCCTTCCCCTGGCATGTCA 61.615 63.158 0.00 0.00 0.00 3.58
1379 1649 1.477923 GGAGACGACTCTAGGGCAGAT 60.478 57.143 14.36 0.00 42.28 2.90
1545 1816 3.114616 CGAGCTGCGTGAGGTTGG 61.115 66.667 0.00 0.00 34.64 3.77
1681 2984 2.610859 AGGCCGGGGTTCATGTCT 60.611 61.111 2.18 0.00 0.00 3.41
1761 3064 2.509336 GGGTGACGATGTCCTGCG 60.509 66.667 0.00 0.00 0.00 5.18
1801 3104 1.604604 GCTTGAGCAGGTTGGTGTAA 58.395 50.000 0.00 0.00 41.59 2.41
1852 3155 1.224075 CACGCTATGGCATCTTCTGG 58.776 55.000 1.65 0.00 38.60 3.86
1854 3157 2.997899 GCACGCTATGGCATCTTCT 58.002 52.632 1.65 0.00 38.60 2.85
1862 3165 1.300931 ACGCTATGGCACGCTATGG 60.301 57.895 0.74 0.00 38.60 2.74
1863 3166 1.855338 CACGCTATGGCACGCTATG 59.145 57.895 0.74 3.92 38.60 2.23
1864 3167 1.956170 GCACGCTATGGCACGCTAT 60.956 57.895 0.74 0.00 38.60 2.97
1865 3168 2.584970 GCACGCTATGGCACGCTA 60.585 61.111 0.74 0.00 38.60 4.26
1868 3171 2.028766 CTTGAGCACGCTATGGCACG 62.029 60.000 0.74 0.00 38.60 5.34
1869 3172 1.717937 CTTGAGCACGCTATGGCAC 59.282 57.895 0.74 0.00 38.60 5.01
1870 3173 2.108514 GCTTGAGCACGCTATGGCA 61.109 57.895 0.74 0.00 41.59 4.92
1873 3176 1.083806 TTCCGCTTGAGCACGCTATG 61.084 55.000 3.65 0.00 42.21 2.23
1874 3177 1.084370 GTTCCGCTTGAGCACGCTAT 61.084 55.000 3.65 0.00 42.21 2.97
1876 3179 3.044305 GTTCCGCTTGAGCACGCT 61.044 61.111 3.65 0.00 42.21 5.07
1877 3180 4.430423 CGTTCCGCTTGAGCACGC 62.430 66.667 3.65 0.00 42.21 5.34
1878 3181 1.731613 TACGTTCCGCTTGAGCACG 60.732 57.895 11.31 11.31 41.66 5.34
1880 3183 0.032952 AAGTACGTTCCGCTTGAGCA 59.967 50.000 0.00 0.00 42.21 4.26
1881 3184 0.438830 CAAGTACGTTCCGCTTGAGC 59.561 55.000 13.09 0.00 41.31 4.26
1882 3185 2.060326 TCAAGTACGTTCCGCTTGAG 57.940 50.000 15.53 0.00 42.24 3.02
1883 3186 1.336517 CCTCAAGTACGTTCCGCTTGA 60.337 52.381 17.30 17.30 44.08 3.02
1884 3187 1.068474 CCTCAAGTACGTTCCGCTTG 58.932 55.000 0.00 4.47 40.47 4.01
1885 3188 0.037605 CCCTCAAGTACGTTCCGCTT 60.038 55.000 0.00 0.00 0.00 4.68
1886 3189 0.896940 TCCCTCAAGTACGTTCCGCT 60.897 55.000 0.00 0.00 0.00 5.52
1887 3190 0.458025 CTCCCTCAAGTACGTTCCGC 60.458 60.000 0.00 0.00 0.00 5.54
1888 3191 1.171308 TCTCCCTCAAGTACGTTCCG 58.829 55.000 0.00 0.00 0.00 4.30
1889 3192 3.522553 CAATCTCCCTCAAGTACGTTCC 58.477 50.000 0.00 0.00 0.00 3.62
1890 3193 3.194968 TCCAATCTCCCTCAAGTACGTTC 59.805 47.826 0.00 0.00 0.00 3.95
1891 3194 3.170717 TCCAATCTCCCTCAAGTACGTT 58.829 45.455 0.00 0.00 0.00 3.99
1892 3195 2.816411 TCCAATCTCCCTCAAGTACGT 58.184 47.619 0.00 0.00 0.00 3.57
1894 3197 4.651503 TCTGATCCAATCTCCCTCAAGTAC 59.348 45.833 0.00 0.00 0.00 2.73
1922 4014 2.292845 GCATCTTTCCTTGAGCTATGGC 59.707 50.000 0.00 0.00 39.06 4.40
1945 4037 2.176889 CGGTCTTCCTTCACCTCCTAA 58.823 52.381 0.00 0.00 0.00 2.69
1980 4073 1.199327 GGCGGCATGATTGATGATCTG 59.801 52.381 3.07 0.00 35.69 2.90
1982 4075 1.531423 AGGCGGCATGATTGATGATC 58.469 50.000 13.08 0.00 33.31 2.92
2006 4099 0.323629 TGGACAACGGGACAAGGATC 59.676 55.000 0.00 0.00 0.00 3.36
2037 4130 0.545309 TGGCCTTCTAGCAGGACTGT 60.545 55.000 15.86 0.00 43.50 3.55
2040 4133 0.905357 TTCTGGCCTTCTAGCAGGAC 59.095 55.000 13.15 10.37 43.39 3.85
2055 4148 3.184581 GTGACTCCGTGCTTAAGTTTCTG 59.815 47.826 4.02 0.00 0.00 3.02
2060 4153 1.000955 CCTGTGACTCCGTGCTTAAGT 59.999 52.381 4.02 0.00 0.00 2.24
2062 4155 0.320421 GCCTGTGACTCCGTGCTTAA 60.320 55.000 0.00 0.00 0.00 1.85
2063 4156 1.292223 GCCTGTGACTCCGTGCTTA 59.708 57.895 0.00 0.00 0.00 3.09
2065 4158 1.257750 TATGCCTGTGACTCCGTGCT 61.258 55.000 0.00 0.00 0.00 4.40
2066 4159 1.084370 GTATGCCTGTGACTCCGTGC 61.084 60.000 0.00 0.00 0.00 5.34
2067 4160 0.460284 GGTATGCCTGTGACTCCGTG 60.460 60.000 0.00 0.00 0.00 4.94
2068 4161 1.898154 GGTATGCCTGTGACTCCGT 59.102 57.895 0.00 0.00 0.00 4.69
2069 4162 1.226974 CGGTATGCCTGTGACTCCG 60.227 63.158 0.00 0.00 0.00 4.63
2070 4163 1.521681 GCGGTATGCCTGTGACTCC 60.522 63.158 0.00 0.00 37.76 3.85
2072 4165 0.036164 TTTGCGGTATGCCTGTGACT 59.964 50.000 0.00 0.00 45.60 3.41
2073 4166 0.878416 TTTTGCGGTATGCCTGTGAC 59.122 50.000 0.00 0.00 45.60 3.67
2074 4167 1.164411 CTTTTGCGGTATGCCTGTGA 58.836 50.000 0.00 0.00 45.60 3.58
2075 4168 1.135689 GTCTTTTGCGGTATGCCTGTG 60.136 52.381 0.00 0.00 45.60 3.66
2076 4169 1.165270 GTCTTTTGCGGTATGCCTGT 58.835 50.000 0.00 0.00 45.60 4.00
2077 4170 0.451783 GGTCTTTTGCGGTATGCCTG 59.548 55.000 0.00 0.00 45.60 4.85
2084 4177 0.963962 TCGAGTAGGTCTTTTGCGGT 59.036 50.000 0.00 0.00 0.00 5.68
2098 4191 4.521639 TGCGTAATAGGATGGTTATCGAGT 59.478 41.667 0.00 0.00 33.98 4.18
2114 4207 3.391296 AGACCTTATGGACCATGCGTAAT 59.609 43.478 17.73 0.00 37.04 1.89
2119 4212 2.706190 ACCTAGACCTTATGGACCATGC 59.294 50.000 17.73 1.61 37.04 4.06
2120 4213 3.967326 TGACCTAGACCTTATGGACCATG 59.033 47.826 17.73 2.89 37.04 3.66
2121 4214 4.280789 TGACCTAGACCTTATGGACCAT 57.719 45.455 12.67 12.67 37.04 3.55
2146 4239 4.775236 CCTCTTCTGGTTAGGATTTGAGG 58.225 47.826 0.00 0.00 33.68 3.86
2147 4240 4.195416 GCCTCTTCTGGTTAGGATTTGAG 58.805 47.826 0.00 0.00 31.64 3.02
2148 4241 3.369471 CGCCTCTTCTGGTTAGGATTTGA 60.369 47.826 0.00 0.00 31.64 2.69
2189 4282 7.710907 GCACTATCATAATTATGCTCGGGATAA 59.289 37.037 18.89 1.00 33.76 1.75
2227 4320 7.711846 TGACATTGTTATAGCTTGTTGTGTTT 58.288 30.769 0.00 0.00 0.00 2.83
2270 4363 6.855763 TTAGATGATGCCAAACCATTCTTT 57.144 33.333 0.00 0.00 0.00 2.52
2399 4492 0.039618 ACCATTTGAATGAGCGGGGT 59.960 50.000 5.32 0.00 38.70 4.95
2404 4497 4.009675 TGTGAGGTACCATTTGAATGAGC 58.990 43.478 15.94 0.00 38.70 4.26
2500 4596 7.216973 ACCGCTGTAACCAATATTTGTTTTA 57.783 32.000 9.92 0.62 0.00 1.52
2520 4616 2.809696 TGTTACTGCCTTAAGAAACCGC 59.190 45.455 3.36 0.00 0.00 5.68
2563 4659 3.877874 CCACCGGGTAAAAAGTTGC 57.122 52.632 6.32 0.00 0.00 4.17
2576 4672 1.549170 AGAGGCTTACAAGTACCACCG 59.451 52.381 0.00 0.00 0.00 4.94
2605 4701 5.804979 GCAACCGTTTTAGTTGATGCATTAT 59.195 36.000 0.00 0.00 46.03 1.28
2693 4789 1.541147 ACCACTCAAAATGTGATGGCG 59.459 47.619 0.00 0.00 37.94 5.69
2715 4811 1.941377 TTTCGTGGTAGGAAGGCCTA 58.059 50.000 5.16 0.00 44.74 3.93
2739 4835 1.139256 TGTTACCAAAGACGTGGAGCA 59.861 47.619 0.00 0.00 41.65 4.26
2747 4843 1.244816 GGGCAGGTGTTACCAAAGAC 58.755 55.000 0.28 0.00 41.95 3.01
2808 4904 7.878547 TGACATGCCATTTAATACTGATCAA 57.121 32.000 0.00 0.00 0.00 2.57
2812 4908 9.166173 GCTATATGACATGCCATTTAATACTGA 57.834 33.333 0.00 0.00 0.00 3.41
2829 4925 8.754991 TTCCTTAGCTATCTAGGCTATATGAC 57.245 38.462 5.22 0.00 41.16 3.06


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

AutoCloner maintained by Alex Coulton.