Multiple sequence alignment - TraesCS2D01G091300

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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 TraesCS2D01G091300 chr2D 100.000 2294 0 0 1 2294 43296096 43293803 0.000000e+00 4237.0
1 TraesCS2D01G091300 chr2D 93.556 807 28 9 507 1293 43301219 43300417 0.000000e+00 1181.0
2 TraesCS2D01G091300 chr2D 79.295 227 37 9 126 344 417557982 417557758 1.420000e-32 150.0
3 TraesCS2D01G091300 chr2B 88.455 1871 102 44 1 1800 68202604 68200777 0.000000e+00 2154.0
4 TraesCS2D01G091300 chr2B 93.605 516 21 1 790 1293 68207195 68206680 0.000000e+00 760.0
5 TraesCS2D01G091300 chr2B 80.769 442 41 17 1883 2294 68200708 68200281 2.860000e-79 305.0
6 TraesCS2D01G091300 chr2B 83.117 231 31 7 161 386 614246108 614246335 1.070000e-48 204.0
7 TraesCS2D01G091300 chr2B 78.491 265 45 8 128 386 19081508 19081766 1.820000e-36 163.0
8 TraesCS2D01G091300 chr2B 80.952 210 32 6 139 344 19099211 19099416 2.360000e-35 159.0
9 TraesCS2D01G091300 chr2B 82.979 188 20 10 611 790 68207480 68207297 2.360000e-35 159.0
10 TraesCS2D01G091300 chr2B 100.000 29 0 0 762 790 68207282 68207254 1.000000e-03 54.7
11 TraesCS2D01G091300 chr2A 87.189 1366 64 38 507 1815 45086122 45084811 0.000000e+00 1450.0
12 TraesCS2D01G091300 chr2A 88.647 828 57 19 497 1293 45096593 45095772 0.000000e+00 974.0
13 TraesCS2D01G091300 chr2A 88.535 157 10 6 2143 2294 45084457 45084304 1.400000e-42 183.0
14 TraesCS2D01G091300 chr2A 81.500 200 10 6 1925 2104 45084756 45084564 3.070000e-29 139.0
15 TraesCS2D01G091300 chr1A 87.179 312 25 3 725 1021 133999207 133999518 7.850000e-90 340.0
16 TraesCS2D01G091300 chr1A 100.000 28 0 0 1893 1920 6324854 6324881 4.000000e-03 52.8
17 TraesCS2D01G091300 chr4A 83.243 370 46 11 863 1224 140756008 140755647 2.200000e-85 326.0
18 TraesCS2D01G091300 chr4D 82.825 361 49 8 863 1212 329311082 329311440 6.150000e-81 311.0
19 TraesCS2D01G091300 chr4B 81.301 369 54 10 869 1225 409339248 409339613 3.730000e-73 285.0
20 TraesCS2D01G091300 chr4B 80.000 95 8 2 1829 1920 416642621 416642535 2.460000e-05 60.2
21 TraesCS2D01G091300 chr1B 78.439 269 45 11 125 386 578098799 578099061 1.820000e-36 163.0
22 TraesCS2D01G091300 chr3D 77.444 266 49 8 124 386 608540160 608540417 5.110000e-32 148.0
23 TraesCS2D01G091300 chr1D 78.972 214 40 5 135 344 1235921 1235709 8.540000e-30 141.0
24 TraesCS2D01G091300 chr1D 100.000 28 0 0 1893 1920 4838466 4838493 4.000000e-03 52.8
25 TraesCS2D01G091300 chrUn 82.911 158 20 5 192 344 24450952 24450797 3.980000e-28 135.0
26 TraesCS2D01G091300 chr5A 81.818 88 5 4 1836 1920 430490791 430490870 1.900000e-06 63.9
27 TraesCS2D01G091300 chr7D 96.970 33 1 0 1889 1921 596063036 596063004 3.180000e-04 56.5


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 TraesCS2D01G091300 chr2D 43293803 43296096 2293 True 4237.000000 4237 100.000000 1 2294 1 chr2D.!!$R1 2293
1 TraesCS2D01G091300 chr2D 43300417 43301219 802 True 1181.000000 1181 93.556000 507 1293 1 chr2D.!!$R2 786
2 TraesCS2D01G091300 chr2B 68200281 68202604 2323 True 1229.500000 2154 84.612000 1 2294 2 chr2B.!!$R1 2293
3 TraesCS2D01G091300 chr2B 68206680 68207480 800 True 324.566667 760 92.194667 611 1293 3 chr2B.!!$R2 682
4 TraesCS2D01G091300 chr2A 45095772 45096593 821 True 974.000000 974 88.647000 497 1293 1 chr2A.!!$R1 796
5 TraesCS2D01G091300 chr2A 45084304 45086122 1818 True 590.666667 1450 85.741333 507 2294 3 chr2A.!!$R2 1787

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
724 755 0.325296 TATCCCGTTGCCTCTCACCT 60.325 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 2419 0.320421 TCTTCCTCGCTTGGGTTTCG 60.32 55.0 0.0 0.0 0.0 3.46 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
41 42 1.443702 CATGGCGTCGTCGACTTCA 60.444 57.895 22.18 18.77 46.49 3.02
53 54 4.083431 TCGTCGACTTCAACTCTTTCCTAG 60.083 45.833 14.70 0.00 0.00 3.02
55 56 4.918583 GTCGACTTCAACTCTTTCCTAGTG 59.081 45.833 8.70 0.00 0.00 2.74
56 57 4.825634 TCGACTTCAACTCTTTCCTAGTGA 59.174 41.667 0.00 0.00 0.00 3.41
64 65 3.584848 ACTCTTTCCTAGTGAGCCATTGT 59.415 43.478 0.00 0.00 0.00 2.71
72 73 1.021390 GTGAGCCATTGTCAGGGACG 61.021 60.000 0.00 0.00 34.95 4.79
75 76 2.819595 CCATTGTCAGGGACGCCG 60.820 66.667 0.00 0.00 34.95 6.46
82 83 2.892425 CAGGGACGCCGCAATCTC 60.892 66.667 0.00 0.00 0.00 2.75
90 91 2.107141 CCGCAATCTCCCCGTCTC 59.893 66.667 0.00 0.00 0.00 3.36
119 120 8.352942 ACATGAGTGAGGTTAGAATTTGTTTTC 58.647 33.333 0.00 0.00 0.00 2.29
247 249 9.573133 TCTACAATGTCACGCATATATCATTAG 57.427 33.333 0.00 0.00 36.67 1.73
252 254 8.654230 ATGTCACGCATATATCATTAGATTCC 57.346 34.615 0.00 0.00 35.74 3.01
381 383 5.516996 CGCACTACGTTATGAAATAGAGGA 58.483 41.667 0.00 0.00 36.87 3.71
398 400 9.528489 AAATAGAGGAAGTACCAAATAGCAAAA 57.472 29.630 0.00 0.00 42.04 2.44
401 403 5.076873 AGGAAGTACCAAATAGCAAAAGCA 58.923 37.500 0.00 0.00 42.04 3.91
407 409 5.382618 ACCAAATAGCAAAAGCAGAAGAG 57.617 39.130 0.00 0.00 0.00 2.85
452 454 9.535878 AAAAATTTGACGCAAATAGACCTTAAA 57.464 25.926 15.06 0.00 42.32 1.52
556 577 0.879400 CATCATCCGACTCAGCAGCC 60.879 60.000 0.00 0.00 0.00 4.85
618 640 4.430765 ACGCACGGTCCCATCGAC 62.431 66.667 0.00 0.00 41.15 4.20
629 653 1.069596 CCATCGACCCATCATCGCA 59.930 57.895 0.00 0.00 39.46 5.10
686 710 1.469940 CCGAACAGTCCAATCTCTCGG 60.470 57.143 0.00 0.00 35.28 4.63
709 739 1.144057 CTCTGCACCCACCGTATCC 59.856 63.158 0.00 0.00 0.00 2.59
724 755 0.325296 TATCCCGTTGCCTCTCACCT 60.325 55.000 0.00 0.00 0.00 4.00
1337 1541 4.063967 CACCACTGCTCGGGCGTA 62.064 66.667 1.14 0.00 42.25 4.42
1399 1611 1.228552 GCTTTCCCTGGCCTGTTGA 60.229 57.895 3.32 0.00 0.00 3.18
1547 1759 3.696051 GGTTGCTGTCATGGTGTGATAAT 59.304 43.478 0.00 0.00 39.48 1.28
1548 1760 4.881273 GGTTGCTGTCATGGTGTGATAATA 59.119 41.667 0.00 0.00 39.48 0.98
1549 1761 5.356751 GGTTGCTGTCATGGTGTGATAATAA 59.643 40.000 0.00 0.00 39.48 1.40
1550 1762 6.039717 GGTTGCTGTCATGGTGTGATAATAAT 59.960 38.462 0.00 0.00 39.48 1.28
1551 1763 7.228507 GGTTGCTGTCATGGTGTGATAATAATA 59.771 37.037 0.00 0.00 39.48 0.98
1552 1764 8.620416 GTTGCTGTCATGGTGTGATAATAATAA 58.380 33.333 0.00 0.00 39.48 1.40
1553 1765 8.922931 TGCTGTCATGGTGTGATAATAATAAT 57.077 30.769 0.00 0.00 39.48 1.28
1655 1867 2.143122 TGGTCGCTCTGTTGATTTGTC 58.857 47.619 0.00 0.00 0.00 3.18
1661 1873 3.063997 CGCTCTGTTGATTTGTCCATACC 59.936 47.826 0.00 0.00 0.00 2.73
1694 1906 6.155691 CCAATTGGTGATTTTGAACGATTG 57.844 37.500 16.90 0.00 0.00 2.67
1695 1907 5.925397 CCAATTGGTGATTTTGAACGATTGA 59.075 36.000 16.90 0.00 0.00 2.57
1703 1915 6.801377 GTGATTTTGAACGATTGATTGCTGTA 59.199 34.615 0.00 0.00 0.00 2.74
1706 1918 5.784750 TTGAACGATTGATTGCTGTAGAG 57.215 39.130 0.00 0.00 0.00 2.43
1709 1921 5.750547 TGAACGATTGATTGCTGTAGAGATC 59.249 40.000 0.00 0.00 0.00 2.75
1710 1922 4.294232 ACGATTGATTGCTGTAGAGATCG 58.706 43.478 5.26 5.26 40.47 3.69
1747 1959 0.250252 TCATCTTTGACCTGCGTGCA 60.250 50.000 0.00 0.00 0.00 4.57
1748 1960 0.167470 CATCTTTGACCTGCGTGCAG 59.833 55.000 14.82 14.82 43.26 4.41
1749 1961 0.250467 ATCTTTGACCTGCGTGCAGT 60.250 50.000 19.58 8.60 42.15 4.40
1750 1962 0.463654 TCTTTGACCTGCGTGCAGTT 60.464 50.000 19.58 6.34 42.15 3.16
1751 1963 0.317269 CTTTGACCTGCGTGCAGTTG 60.317 55.000 19.58 8.59 42.15 3.16
1752 1964 1.029408 TTTGACCTGCGTGCAGTTGT 61.029 50.000 19.58 11.65 42.15 3.32
1753 1965 1.436195 TTGACCTGCGTGCAGTTGTC 61.436 55.000 19.58 18.95 42.15 3.18
1755 1967 1.835483 GACCTGCGTGCAGTTGTCAG 61.835 60.000 19.58 6.55 42.15 3.51
1756 1968 2.610694 CCTGCGTGCAGTTGTCAGG 61.611 63.158 19.58 0.54 42.15 3.86
1757 1969 3.245948 CTGCGTGCAGTTGTCAGGC 62.246 63.158 13.62 11.51 43.32 4.85
1758 1970 3.279116 GCGTGCAGTTGTCAGGCA 61.279 61.111 12.74 0.00 42.76 4.75
1767 1981 2.227388 CAGTTGTCAGGCAGGCTTTAAG 59.773 50.000 0.00 0.00 0.00 1.85
1851 2097 9.905713 AGCAGAATATTATTACCTCTGTTTCAA 57.094 29.630 0.00 0.00 36.67 2.69
1865 2111 8.079809 ACCTCTGTTTCAAAATATACGTTTTGG 58.920 33.333 9.83 0.00 44.94 3.28
1866 2112 8.079809 CCTCTGTTTCAAAATATACGTTTTGGT 58.920 33.333 9.83 0.00 44.94 3.67
1869 2115 9.337091 CTGTTTCAAAATATACGTTTTGGTAGG 57.663 33.333 9.83 0.00 44.94 3.18
1870 2116 9.064706 TGTTTCAAAATATACGTTTTGGTAGGA 57.935 29.630 9.83 0.00 44.94 2.94
1871 2117 9.333497 GTTTCAAAATATACGTTTTGGTAGGAC 57.667 33.333 9.83 1.08 44.94 3.85
1872 2118 8.618702 TTCAAAATATACGTTTTGGTAGGACA 57.381 30.769 9.83 0.00 44.94 4.02
1873 2119 8.795842 TCAAAATATACGTTTTGGTAGGACAT 57.204 30.769 9.83 0.00 44.94 3.06
1874 2120 9.233649 TCAAAATATACGTTTTGGTAGGACATT 57.766 29.630 9.83 0.00 44.94 2.71
1875 2121 9.849166 CAAAATATACGTTTTGGTAGGACATTT 57.151 29.630 0.00 0.00 42.51 2.32
1879 2125 5.366829 ACGTTTTGGTAGGACATTTTAGC 57.633 39.130 0.00 0.00 0.00 3.09
1880 2126 4.216902 ACGTTTTGGTAGGACATTTTAGCC 59.783 41.667 0.00 0.00 0.00 3.93
1881 2127 4.457949 CGTTTTGGTAGGACATTTTAGCCT 59.542 41.667 0.00 0.00 35.82 4.58
1920 2166 5.531287 ACGTCTTATATTTTGGAATGGAGGC 59.469 40.000 0.00 0.00 0.00 4.70
1921 2167 5.334105 CGTCTTATATTTTGGAATGGAGGCG 60.334 44.000 0.00 0.00 0.00 5.52
1922 2168 4.518970 TCTTATATTTTGGAATGGAGGCGC 59.481 41.667 0.00 0.00 0.00 6.53
1935 2181 6.351117 GGAATGGAGGCGCTAGTATATTACTT 60.351 42.308 7.64 0.00 40.14 2.24
1951 2197 2.580661 CTTGTGCAAACAAGGCGTG 58.419 52.632 10.14 0.00 42.34 5.34
1969 2217 2.930040 CGTGCACCGATAAAGTTCAGAT 59.070 45.455 12.15 0.00 39.56 2.90
1970 2218 3.370978 CGTGCACCGATAAAGTTCAGATT 59.629 43.478 12.15 0.00 39.56 2.40
1971 2219 4.565166 CGTGCACCGATAAAGTTCAGATTA 59.435 41.667 12.15 0.00 39.56 1.75
1972 2220 5.062934 CGTGCACCGATAAAGTTCAGATTAA 59.937 40.000 12.15 0.00 39.56 1.40
1973 2221 6.401688 CGTGCACCGATAAAGTTCAGATTAAA 60.402 38.462 12.15 0.00 39.56 1.52
1974 2222 6.961554 GTGCACCGATAAAGTTCAGATTAAAG 59.038 38.462 5.22 0.00 0.00 1.85
1975 2223 6.876789 TGCACCGATAAAGTTCAGATTAAAGA 59.123 34.615 0.00 0.00 0.00 2.52
2039 2295 6.821665 TCCAACGAAAGAAGAAAGAAAGAGAA 59.178 34.615 0.00 0.00 0.00 2.87
2048 2304 8.347004 AGAAGAAAGAAAGAGAAATTCCCATC 57.653 34.615 0.00 0.00 0.00 3.51
2121 2401 2.203126 GCAAGGATCGAGCTGGGG 60.203 66.667 0.00 0.00 0.00 4.96
2122 2402 2.203126 CAAGGATCGAGCTGGGGC 60.203 66.667 0.00 0.00 39.06 5.80
2135 2415 3.797353 GGGGCTGGATCCGCAGAA 61.797 66.667 23.67 0.20 38.75 3.02
2136 2416 2.514824 GGGCTGGATCCGCAGAAC 60.515 66.667 23.67 10.79 0.00 3.01
2137 2417 2.892425 GGCTGGATCCGCAGAACG 60.892 66.667 23.67 2.85 43.15 3.95
2139 2419 2.892425 CTGGATCCGCAGAACGCC 60.892 66.667 7.39 0.00 41.76 5.68
2145 2425 4.084888 CCGCAGAACGCCGAAACC 62.085 66.667 0.00 0.00 41.76 3.27
2150 2430 2.254350 GAACGCCGAAACCCAAGC 59.746 61.111 0.00 0.00 0.00 4.01
2156 2436 1.302192 CCGAAACCCAAGCGAGGAA 60.302 57.895 0.00 0.00 0.00 3.36
2157 2437 1.298859 CCGAAACCCAAGCGAGGAAG 61.299 60.000 0.00 0.00 0.00 3.46
2158 2438 0.320421 CGAAACCCAAGCGAGGAAGA 60.320 55.000 0.00 0.00 0.00 2.87
2182 2533 3.506067 AGACATTCCCCAAATCAAACGTC 59.494 43.478 0.00 0.00 0.00 4.34
2268 2625 2.043953 GGAATCACAGGGCCACCC 60.044 66.667 6.18 0.00 45.90 4.61
2279 2636 2.730094 GCCACCCTGTTGTTGCAG 59.270 61.111 0.00 0.00 36.31 4.41
2280 2637 2.730094 CCACCCTGTTGTTGCAGC 59.270 61.111 0.00 0.00 35.28 5.25
2281 2638 2.126596 CCACCCTGTTGTTGCAGCA 61.127 57.895 0.00 0.00 35.28 4.41
2283 2640 1.246649 CACCCTGTTGTTGCAGCATA 58.753 50.000 3.36 0.00 35.28 3.14
2284 2641 1.068333 CACCCTGTTGTTGCAGCATAC 60.068 52.381 3.36 6.51 35.28 2.39
2285 2642 0.527565 CCCTGTTGTTGCAGCATACC 59.472 55.000 3.36 0.00 35.28 2.73
2286 2643 1.246649 CCTGTTGTTGCAGCATACCA 58.753 50.000 3.36 1.13 35.28 3.25
2287 2644 1.820519 CCTGTTGTTGCAGCATACCAT 59.179 47.619 3.36 0.00 35.28 3.55
2288 2645 2.416296 CCTGTTGTTGCAGCATACCATG 60.416 50.000 3.36 0.00 35.28 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 4.042187 ACAATGGCTCACTAGGAAAGAGTT 59.958 41.667 0.00 0.00 0.00 3.01
53 54 1.021390 CGTCCCTGACAATGGCTCAC 61.021 60.000 0.00 0.00 32.09 3.51
55 56 2.109126 GCGTCCCTGACAATGGCTC 61.109 63.158 0.00 0.00 32.09 4.70
56 57 2.045926 GCGTCCCTGACAATGGCT 60.046 61.111 0.00 0.00 32.09 4.75
64 65 3.371097 GAGATTGCGGCGTCCCTGA 62.371 63.158 9.37 0.00 0.00 3.86
72 73 4.162690 AGACGGGGAGATTGCGGC 62.163 66.667 0.00 0.00 0.00 6.53
75 76 0.806492 GTTCGAGACGGGGAGATTGC 60.806 60.000 0.00 0.00 0.00 3.56
82 83 0.458543 CACTCATGTTCGAGACGGGG 60.459 60.000 0.00 0.00 36.47 5.73
90 91 6.147821 ACAAATTCTAACCTCACTCATGTTCG 59.852 38.462 0.00 0.00 0.00 3.95
119 120 3.191371 GGAACAAATGGAGTAGTTGCCTG 59.809 47.826 0.00 0.00 37.87 4.85
175 176 7.769970 ACTTGGTCAAAATTTGTGTGATTTGAT 59.230 29.630 5.56 0.00 41.99 2.57
181 182 6.148480 CCAAAACTTGGTCAAAATTTGTGTGA 59.852 34.615 5.56 0.00 45.93 3.58
217 219 7.542130 TGATATATGCGTGACATTGTAGATGTC 59.458 37.037 11.22 11.22 46.28 3.06
225 227 9.911980 GAATCTAATGATATATGCGTGACATTG 57.088 33.333 0.00 0.00 34.75 2.82
358 360 5.516996 TCCTCTATTTCATAACGTAGTGCG 58.483 41.667 0.00 0.00 45.00 5.34
360 362 9.448294 GTACTTCCTCTATTTCATAACGTAGTG 57.552 37.037 0.00 0.00 45.00 2.74
459 461 3.907474 TGACCCTGTGGAAACTGAGATAA 59.093 43.478 0.00 0.00 34.81 1.75
460 462 3.516586 TGACCCTGTGGAAACTGAGATA 58.483 45.455 0.00 0.00 34.81 1.98
475 477 2.030562 CGTTCGCCACTTGACCCT 59.969 61.111 0.00 0.00 0.00 4.34
609 631 2.049435 CGATGATGGGTCGATGGGA 58.951 57.895 0.00 0.00 41.40 4.37
618 640 3.576356 GGTGCGTGCGATGATGGG 61.576 66.667 0.00 0.00 0.00 4.00
673 697 1.045911 AGGCTCCCGAGAGATTGGAC 61.046 60.000 0.00 0.00 43.39 4.02
709 739 0.173708 GTCTAGGTGAGAGGCAACGG 59.826 60.000 0.00 0.00 39.91 4.44
724 755 0.808755 TTGCTGCTCGTGATCGTCTA 59.191 50.000 0.00 0.00 38.33 2.59
1215 1405 2.356313 CAGACGCACTTGGACGCT 60.356 61.111 0.00 0.00 0.00 5.07
1335 1539 1.595489 CGTCAGCCCATACGTACGTAC 60.595 57.143 28.99 16.66 34.48 3.67
1336 1540 0.657312 CGTCAGCCCATACGTACGTA 59.343 55.000 28.62 28.62 34.48 3.57
1337 1541 1.430632 CGTCAGCCCATACGTACGT 59.569 57.895 25.98 25.98 34.48 3.57
1344 1548 0.323302 TGAAGCAACGTCAGCCCATA 59.677 50.000 9.07 0.00 0.00 2.74
1399 1611 2.033299 CACCAGACACGCAAACAAGAAT 59.967 45.455 0.00 0.00 0.00 2.40
1655 1867 0.322997 TTGGTCAAAGGCCGGTATGG 60.323 55.000 1.90 0.00 42.50 2.74
1688 1900 4.036852 TCGATCTCTACAGCAATCAATCGT 59.963 41.667 0.00 0.00 36.89 3.73
1689 1901 4.381270 GTCGATCTCTACAGCAATCAATCG 59.619 45.833 0.00 0.00 36.89 3.34
1690 1902 4.381270 CGTCGATCTCTACAGCAATCAATC 59.619 45.833 0.00 0.00 0.00 2.67
1691 1903 4.294232 CGTCGATCTCTACAGCAATCAAT 58.706 43.478 0.00 0.00 0.00 2.57
1692 1904 3.489229 CCGTCGATCTCTACAGCAATCAA 60.489 47.826 0.00 0.00 0.00 2.57
1693 1905 2.033424 CCGTCGATCTCTACAGCAATCA 59.967 50.000 0.00 0.00 0.00 2.57
1694 1906 2.033550 ACCGTCGATCTCTACAGCAATC 59.966 50.000 0.00 0.00 0.00 2.67
1695 1907 2.025155 ACCGTCGATCTCTACAGCAAT 58.975 47.619 0.00 0.00 0.00 3.56
1703 1915 0.526662 GTGGTCAACCGTCGATCTCT 59.473 55.000 0.00 0.00 39.43 3.10
1706 1918 1.722011 ATTGTGGTCAACCGTCGATC 58.278 50.000 0.00 0.00 39.43 3.69
1709 1921 2.032302 TGAAAATTGTGGTCAACCGTCG 59.968 45.455 0.00 0.00 39.43 5.12
1710 1922 3.701532 TGAAAATTGTGGTCAACCGTC 57.298 42.857 0.00 0.00 39.43 4.79
1747 1959 2.158608 ACTTAAAGCCTGCCTGACAACT 60.159 45.455 0.00 0.00 0.00 3.16
1748 1960 2.230660 ACTTAAAGCCTGCCTGACAAC 58.769 47.619 0.00 0.00 0.00 3.32
1749 1961 2.656947 ACTTAAAGCCTGCCTGACAA 57.343 45.000 0.00 0.00 0.00 3.18
1750 1962 2.106511 AGAACTTAAAGCCTGCCTGACA 59.893 45.455 0.00 0.00 0.00 3.58
1751 1963 2.485814 CAGAACTTAAAGCCTGCCTGAC 59.514 50.000 0.00 0.00 0.00 3.51
1752 1964 2.371841 TCAGAACTTAAAGCCTGCCTGA 59.628 45.455 0.00 0.00 0.00 3.86
1753 1965 2.746362 CTCAGAACTTAAAGCCTGCCTG 59.254 50.000 0.00 0.00 0.00 4.85
1755 1967 1.470494 GCTCAGAACTTAAAGCCTGCC 59.530 52.381 0.00 0.00 0.00 4.85
1756 1968 2.154462 TGCTCAGAACTTAAAGCCTGC 58.846 47.619 0.00 0.00 33.79 4.85
1757 1969 5.181748 AGTATGCTCAGAACTTAAAGCCTG 58.818 41.667 0.00 0.00 33.79 4.85
1758 1970 5.188751 AGAGTATGCTCAGAACTTAAAGCCT 59.811 40.000 13.64 0.00 44.00 4.58
1767 1981 6.857956 TCTTCTGTTAGAGTATGCTCAGAAC 58.142 40.000 13.64 15.43 44.00 3.01
1803 2023 7.389803 GCTCTATGCATGTCTCTAATCTCTA 57.610 40.000 10.16 0.00 42.31 2.43
1819 2065 9.311916 CAGAGGTAATAATATTCTGCTCTATGC 57.688 37.037 0.00 0.00 43.25 3.14
1853 2099 8.833493 GCTAAAATGTCCTACCAAAACGTATAT 58.167 33.333 0.00 0.00 0.00 0.86
1854 2100 7.280652 GGCTAAAATGTCCTACCAAAACGTATA 59.719 37.037 0.00 0.00 0.00 1.47
1855 2101 6.094464 GGCTAAAATGTCCTACCAAAACGTAT 59.906 38.462 0.00 0.00 0.00 3.06
1856 2102 5.412286 GGCTAAAATGTCCTACCAAAACGTA 59.588 40.000 0.00 0.00 0.00 3.57
1857 2103 4.216902 GGCTAAAATGTCCTACCAAAACGT 59.783 41.667 0.00 0.00 0.00 3.99
1858 2104 4.457949 AGGCTAAAATGTCCTACCAAAACG 59.542 41.667 0.00 0.00 0.00 3.60
1859 2105 5.977489 AGGCTAAAATGTCCTACCAAAAC 57.023 39.130 0.00 0.00 0.00 2.43
1879 2125 1.081094 CGTTTTTGTAGGCCGGTAGG 58.919 55.000 1.90 0.00 41.62 3.18
1880 2126 1.728425 GACGTTTTTGTAGGCCGGTAG 59.272 52.381 1.90 0.00 0.00 3.18
1881 2127 1.344114 AGACGTTTTTGTAGGCCGGTA 59.656 47.619 1.90 0.00 0.00 4.02
1892 2138 9.855021 CTCCATTCCAAAATATAAGACGTTTTT 57.145 29.630 0.00 0.00 0.00 1.94
1920 2166 7.229228 TGTTTGCACAAGTAATATACTAGCG 57.771 36.000 0.00 0.00 38.26 4.26
1935 2181 2.103934 GCACGCCTTGTTTGCACA 59.896 55.556 0.00 0.00 36.22 4.57
1949 2195 4.946784 AATCTGAACTTTATCGGTGCAC 57.053 40.909 8.80 8.80 0.00 4.57
1951 2197 7.303634 TCTTTAATCTGAACTTTATCGGTGC 57.696 36.000 0.00 0.00 0.00 5.01
1969 2217 6.711277 ACTTCATCAGTGTATGCCTCTTTAA 58.289 36.000 0.00 0.00 32.83 1.52
1970 2218 6.299805 ACTTCATCAGTGTATGCCTCTTTA 57.700 37.500 0.00 0.00 32.83 1.85
1971 2219 5.171339 ACTTCATCAGTGTATGCCTCTTT 57.829 39.130 0.00 0.00 32.83 2.52
1972 2220 4.833478 ACTTCATCAGTGTATGCCTCTT 57.167 40.909 0.00 0.00 32.83 2.85
1973 2221 4.223700 TGAACTTCATCAGTGTATGCCTCT 59.776 41.667 0.00 0.00 35.12 3.69
1974 2222 4.507710 TGAACTTCATCAGTGTATGCCTC 58.492 43.478 0.00 0.00 35.12 4.70
1975 2223 4.223700 TCTGAACTTCATCAGTGTATGCCT 59.776 41.667 4.41 0.00 45.65 4.75
2039 2295 2.428171 CAAATCAGGTGCGATGGGAATT 59.572 45.455 0.00 0.00 0.00 2.17
2048 2304 6.324819 ACTAAATCAAATCAAATCAGGTGCG 58.675 36.000 0.00 0.00 0.00 5.34
2121 2401 3.567797 GCGTTCTGCGGATCCAGC 61.568 66.667 13.41 16.21 41.69 4.85
2130 2410 2.458006 CTTGGGTTTCGGCGTTCTGC 62.458 60.000 6.85 0.00 45.38 4.26
2131 2411 1.574428 CTTGGGTTTCGGCGTTCTG 59.426 57.895 6.85 0.00 0.00 3.02
2132 2412 2.258726 GCTTGGGTTTCGGCGTTCT 61.259 57.895 6.85 0.00 0.00 3.01
2133 2413 2.254350 GCTTGGGTTTCGGCGTTC 59.746 61.111 6.85 0.00 0.00 3.95
2134 2414 3.656045 CGCTTGGGTTTCGGCGTT 61.656 61.111 6.85 0.00 42.23 4.84
2135 2415 4.612412 TCGCTTGGGTTTCGGCGT 62.612 61.111 6.85 0.00 46.37 5.68
2137 2417 3.431725 CCTCGCTTGGGTTTCGGC 61.432 66.667 0.00 0.00 0.00 5.54
2139 2419 0.320421 TCTTCCTCGCTTGGGTTTCG 60.320 55.000 0.00 0.00 0.00 3.46
2145 2425 2.169832 TGTCTTTCTTCCTCGCTTGG 57.830 50.000 0.00 0.00 0.00 3.61
2150 2430 2.027192 TGGGGAATGTCTTTCTTCCTCG 60.027 50.000 1.72 0.00 43.74 4.63
2151 2431 3.721087 TGGGGAATGTCTTTCTTCCTC 57.279 47.619 1.72 0.00 41.60 3.71
2156 2436 5.278957 CGTTTGATTTGGGGAATGTCTTTCT 60.279 40.000 0.00 0.00 34.56 2.52
2157 2437 4.923281 CGTTTGATTTGGGGAATGTCTTTC 59.077 41.667 0.00 0.00 0.00 2.62
2158 2438 4.343814 ACGTTTGATTTGGGGAATGTCTTT 59.656 37.500 0.00 0.00 0.00 2.52
2268 2625 2.871133 CATGGTATGCTGCAACAACAG 58.129 47.619 6.36 0.00 40.80 3.16


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

AutoCloner maintained by Alex Coulton.