Multiple sequence alignment - TraesCS5D01G441700

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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 TraesCS5D01G441700 chr5D 100.000 2737 0 0 1 2737 494182026 494184762 0.000000e+00 5055.0
1 TraesCS5D01G441700 chr5B 89.771 1877 99 36 1 1834 610294078 610295904 0.000000e+00 2316.0
2 TraesCS5D01G441700 chr5B 87.500 488 50 8 1982 2461 610298394 610298878 1.110000e-153 553.0
3 TraesCS5D01G441700 chr5B 90.435 115 9 2 2625 2737 610299162 610299276 1.700000e-32 150.0
4 TraesCS5D01G441700 chr5B 90.164 61 2 3 2472 2528 270772348 270772288 2.920000e-10 76.8
5 TraesCS5D01G441700 chr5A 87.442 1736 112 49 28 1723 617174224 617175893 0.000000e+00 1901.0
6 TraesCS5D01G441700 chr5A 89.563 1236 92 23 630 1835 617187800 617189028 0.000000e+00 1533.0
7 TraesCS5D01G441700 chr5A 89.529 382 30 6 1982 2353 617189090 617189471 2.470000e-130 475.0
8 TraesCS5D01G441700 chr5A 86.982 169 18 3 2461 2626 617189577 617189744 1.290000e-43 187.0
9 TraesCS5D01G441700 chr5A 89.916 119 12 0 2619 2737 617189813 617189931 1.310000e-33 154.0
10 TraesCS5D01G441700 chr3D 82.700 237 29 7 1 236 555333193 555333418 1.660000e-47 200.0
11 TraesCS5D01G441700 chr3D 84.848 99 11 3 1865 1963 5867001 5866907 2.240000e-16 97.1
12 TraesCS5D01G441700 chr3D 86.747 83 7 4 2154 2234 421702720 421702640 3.750000e-14 89.8
13 TraesCS5D01G441700 chr3B 80.169 237 30 9 1 236 738626617 738626837 7.840000e-36 161.0
14 TraesCS5D01G441700 chr3B 88.608 79 7 2 2486 2563 729027886 729027809 8.070000e-16 95.3
15 TraesCS5D01G441700 chr3B 78.195 133 21 6 2488 2614 526736967 526737097 8.130000e-11 78.7
16 TraesCS5D01G441700 chr2D 80.503 159 26 4 2459 2613 555952014 555951857 1.720000e-22 117.0
17 TraesCS5D01G441700 chr2A 75.836 269 43 15 2187 2446 754019205 754018950 1.720000e-22 117.0
18 TraesCS5D01G441700 chr7B 78.000 150 22 9 2472 2613 5997923 5997777 1.750000e-12 84.2
19 TraesCS5D01G441700 chr3A 82.759 87 11 4 2154 2238 529171803 529171887 1.050000e-09 75.0
20 TraesCS5D01G441700 chr6B 78.218 101 14 4 1870 1970 5789065 5788973 1.060000e-04 58.4


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 TraesCS5D01G441700 chr5D 494182026 494184762 2736 False 5055.000000 5055 100.000000 1 2737 1 chr5D.!!$F1 2736
1 TraesCS5D01G441700 chr5B 610294078 610299276 5198 False 1006.333333 2316 89.235333 1 2737 3 chr5B.!!$F1 2736
2 TraesCS5D01G441700 chr5A 617174224 617175893 1669 False 1901.000000 1901 87.442000 28 1723 1 chr5A.!!$F1 1695
3 TraesCS5D01G441700 chr5A 617187800 617189931 2131 False 587.250000 1533 88.997500 630 2737 4 chr5A.!!$F2 2107

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
558 575 0.113972 TGCATGTGGGTGATGGGAAA 59.886 50.0 0.0 0.0 0.0 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2387 4818 0.178767 CATGGCCGTGAAGGATGAGA 59.821 55.0 21.08 0.0 45.0 3.27 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
22 23 2.004733 TCTGCAGATCACAAGAATGCG 58.995 47.619 13.74 0.00 41.11 4.73
100 105 6.848451 TGAAAACAAACTGTTGGAAGTAGAC 58.152 36.000 1.05 0.00 40.14 2.59
408 425 4.666253 AGCACGGCCAGCACCAAT 62.666 61.111 18.34 0.00 0.00 3.16
413 430 1.677300 CGGCCAGCACCAATACCAA 60.677 57.895 2.24 0.00 0.00 3.67
508 525 6.631971 TTGAATGAGCAAATTACACTGTGA 57.368 33.333 15.86 0.00 0.00 3.58
556 573 1.220703 TATGCATGTGGGTGATGGGA 58.779 50.000 10.16 0.00 0.00 4.37
558 575 0.113972 TGCATGTGGGTGATGGGAAA 59.886 50.000 0.00 0.00 0.00 3.13
559 576 1.273154 TGCATGTGGGTGATGGGAAAT 60.273 47.619 0.00 0.00 0.00 2.17
560 577 2.024560 TGCATGTGGGTGATGGGAAATA 60.025 45.455 0.00 0.00 0.00 1.40
561 578 2.362077 GCATGTGGGTGATGGGAAATAC 59.638 50.000 0.00 0.00 0.00 1.89
562 579 3.630168 CATGTGGGTGATGGGAAATACA 58.370 45.455 0.00 0.00 0.00 2.29
563 580 3.080300 TGTGGGTGATGGGAAATACAC 57.920 47.619 0.00 0.00 0.00 2.90
564 581 2.647299 TGTGGGTGATGGGAAATACACT 59.353 45.455 0.00 0.00 34.28 3.55
565 582 3.075283 TGTGGGTGATGGGAAATACACTT 59.925 43.478 0.00 0.00 34.28 3.16
566 583 4.086457 GTGGGTGATGGGAAATACACTTT 58.914 43.478 0.00 0.00 34.28 2.66
567 584 4.082245 GTGGGTGATGGGAAATACACTTTG 60.082 45.833 0.00 0.00 34.28 2.77
568 585 3.447229 GGGTGATGGGAAATACACTTTGG 59.553 47.826 0.00 0.00 34.28 3.28
569 586 4.086457 GGTGATGGGAAATACACTTTGGT 58.914 43.478 0.00 0.00 34.28 3.67
570 587 5.258051 GGTGATGGGAAATACACTTTGGTA 58.742 41.667 0.00 0.00 34.28 3.25
571 588 5.357032 GGTGATGGGAAATACACTTTGGTAG 59.643 44.000 0.00 0.00 34.28 3.18
572 589 5.944007 GTGATGGGAAATACACTTTGGTAGT 59.056 40.000 0.00 0.00 37.68 2.73
684 701 2.259618 CGTTTAGGTGATCAGGACGTG 58.740 52.381 0.00 0.00 0.00 4.49
693 710 1.066303 GATCAGGACGTGAGGTAGCTG 59.934 57.143 0.00 0.00 39.07 4.24
715 735 2.544685 GACTGTGACCAGATGAATCCG 58.455 52.381 0.00 0.00 41.50 4.18
757 777 1.208535 TCTCTCTGTCTCGGAGACTCC 59.791 57.143 31.68 11.87 45.27 3.85
915 937 3.059884 TCAGTGTCAAGAACGAGAATGC 58.940 45.455 0.00 0.00 0.00 3.56
1010 1037 1.299648 CAAGTCCAATGGGAGCGGA 59.700 57.895 0.00 0.00 46.12 5.54
1172 1199 3.451894 CCTTTCCCCGTGCATGGC 61.452 66.667 20.27 0.00 0.00 4.40
1191 1218 1.739929 CTACATGTCGGGCAACGCA 60.740 57.895 0.00 0.00 43.86 5.24
1378 1405 1.374758 AGCCAGTGCGACTGTAAGC 60.375 57.895 13.06 10.09 44.50 3.09
1384 1411 1.301401 TGCGACTGTAAGCCCACAC 60.301 57.895 5.47 0.00 37.60 3.82
1406 1454 0.111442 CGCAAGTACGAACAACACCG 60.111 55.000 0.00 0.00 34.06 4.94
1520 1574 0.602905 GCAGGTACGTGCAGAACCTT 60.603 55.000 30.20 0.00 41.75 3.50
1566 1620 0.735632 GGAGATGATCGGAGCGCATC 60.736 60.000 11.47 4.03 37.80 3.91
1661 1715 1.380785 TCAGTACTCCCGCGGGAAT 60.381 57.895 43.77 38.63 44.66 3.01
1665 1719 2.777972 TACTCCCGCGGGAATGTCG 61.778 63.158 43.77 33.62 44.66 4.35
1746 1806 0.762418 TACACCCTGACACCTGTTGG 59.238 55.000 0.00 0.00 39.83 3.77
1772 1849 2.417516 CGGGGCCTGTATCTGACG 59.582 66.667 3.48 0.00 0.00 4.35
1783 1860 3.305516 TCTGACGCAGCAGAGGCA 61.306 61.111 1.65 0.00 44.61 4.75
1797 1874 0.611714 GAGGCAGAGACCCCGTTAAA 59.388 55.000 0.00 0.00 0.00 1.52
1835 1913 5.528043 TTTTAGCAAGCCTTGAATGAACA 57.472 34.783 9.04 0.00 0.00 3.18
1838 1916 2.961062 AGCAAGCCTTGAATGAACAGTT 59.039 40.909 9.04 0.00 0.00 3.16
1839 1917 3.385755 AGCAAGCCTTGAATGAACAGTTT 59.614 39.130 9.04 0.00 0.00 2.66
1840 1918 4.122046 GCAAGCCTTGAATGAACAGTTTT 58.878 39.130 9.04 0.00 0.00 2.43
1841 1919 5.068987 AGCAAGCCTTGAATGAACAGTTTTA 59.931 36.000 9.04 0.00 0.00 1.52
1842 1920 5.175673 GCAAGCCTTGAATGAACAGTTTTAC 59.824 40.000 9.04 0.00 0.00 2.01
1843 1921 6.507023 CAAGCCTTGAATGAACAGTTTTACT 58.493 36.000 0.00 0.00 0.00 2.24
1844 1922 7.648142 CAAGCCTTGAATGAACAGTTTTACTA 58.352 34.615 0.00 0.00 0.00 1.82
1845 1923 7.817418 AGCCTTGAATGAACAGTTTTACTAA 57.183 32.000 0.00 0.00 0.00 2.24
1847 1925 7.502561 AGCCTTGAATGAACAGTTTTACTAAGT 59.497 33.333 0.00 0.00 0.00 2.24
1848 1926 8.780249 GCCTTGAATGAACAGTTTTACTAAGTA 58.220 33.333 0.00 0.00 0.00 2.24
1868 1946 9.737427 CTAAGTACTGATACTGACAAAATCGAT 57.263 33.333 0.00 0.00 41.00 3.59
1869 1947 7.993821 AGTACTGATACTGACAAAATCGATG 57.006 36.000 0.00 0.00 40.32 3.84
1871 1949 5.423015 ACTGATACTGACAAAATCGATGCT 58.577 37.500 0.00 0.00 0.00 3.79
1872 1950 6.573434 ACTGATACTGACAAAATCGATGCTA 58.427 36.000 0.00 0.00 0.00 3.49
1873 1951 7.212976 ACTGATACTGACAAAATCGATGCTAT 58.787 34.615 0.00 0.00 0.00 2.97
1874 1952 7.712639 ACTGATACTGACAAAATCGATGCTATT 59.287 33.333 0.00 0.00 0.00 1.73
1875 1953 8.437360 TGATACTGACAAAATCGATGCTATTT 57.563 30.769 0.00 0.00 0.00 1.40
1876 1954 8.892723 TGATACTGACAAAATCGATGCTATTTT 58.107 29.630 0.00 0.00 37.08 1.82
1878 1956 6.555315 ACTGACAAAATCGATGCTATTTTCC 58.445 36.000 0.00 0.00 35.00 3.13
1879 1957 6.375455 ACTGACAAAATCGATGCTATTTTCCT 59.625 34.615 0.00 0.00 35.00 3.36
1880 1958 7.094205 ACTGACAAAATCGATGCTATTTTCCTT 60.094 33.333 0.00 0.00 35.00 3.36
1881 1959 7.601856 TGACAAAATCGATGCTATTTTCCTTT 58.398 30.769 0.00 0.00 35.00 3.11
1883 1961 7.601856 ACAAAATCGATGCTATTTTCCTTTGA 58.398 30.769 15.15 0.00 35.00 2.69
1884 1962 8.253113 ACAAAATCGATGCTATTTTCCTTTGAT 58.747 29.630 15.15 2.12 35.00 2.57
1885 1963 8.749499 CAAAATCGATGCTATTTTCCTTTGATC 58.251 33.333 0.00 0.00 35.00 2.92
1886 1964 7.814264 AATCGATGCTATTTTCCTTTGATCT 57.186 32.000 0.00 0.00 0.00 2.75
1887 1965 7.814264 ATCGATGCTATTTTCCTTTGATCTT 57.186 32.000 0.00 0.00 0.00 2.40
1888 1966 7.019774 TCGATGCTATTTTCCTTTGATCTTG 57.980 36.000 0.00 0.00 0.00 3.02
1890 1968 5.981088 TGCTATTTTCCTTTGATCTTGCA 57.019 34.783 0.00 0.00 0.00 4.08
1891 1969 6.534475 TGCTATTTTCCTTTGATCTTGCAT 57.466 33.333 0.00 0.00 0.00 3.96
1892 1970 6.334989 TGCTATTTTCCTTTGATCTTGCATG 58.665 36.000 0.00 0.00 0.00 4.06
1893 1971 6.153170 TGCTATTTTCCTTTGATCTTGCATGA 59.847 34.615 4.57 4.57 0.00 3.07
1894 1972 7.037438 GCTATTTTCCTTTGATCTTGCATGAA 58.963 34.615 6.36 0.00 0.00 2.57
1895 1973 7.222224 GCTATTTTCCTTTGATCTTGCATGAAG 59.778 37.037 6.36 0.00 0.00 3.02
1896 1974 6.653526 TTTTCCTTTGATCTTGCATGAAGA 57.346 33.333 6.36 3.41 45.03 2.87
1909 1987 8.437360 TCTTGCATGAAGATTCGTATACAATT 57.563 30.769 3.32 0.00 35.64 2.32
1911 1989 9.507280 CTTGCATGAAGATTCGTATACAATTTT 57.493 29.630 3.32 4.11 32.82 1.82
1913 1991 9.502145 TGCATGAAGATTCGTATACAATTTTTC 57.498 29.630 3.32 9.88 0.00 2.29
1914 1992 9.722056 GCATGAAGATTCGTATACAATTTTTCT 57.278 29.630 3.32 0.00 0.00 2.52
1969 4121 7.468141 ACTATATCACTTGACTGACACTTGA 57.532 36.000 0.00 0.00 0.00 3.02
1970 4122 7.896811 ACTATATCACTTGACTGACACTTGAA 58.103 34.615 0.00 0.00 0.00 2.69
1974 4126 9.725019 ATATCACTTGACTGACACTTGAATAAA 57.275 29.630 0.00 0.00 0.00 1.40
1976 4128 8.450578 TCACTTGACTGACACTTGAATAAATT 57.549 30.769 0.00 0.00 0.00 1.82
1978 4130 7.113965 CACTTGACTGACACTTGAATAAATTGC 59.886 37.037 0.00 0.00 0.00 3.56
1979 4131 6.631971 TGACTGACACTTGAATAAATTGCA 57.368 33.333 0.00 0.00 0.00 4.08
1980 4132 6.437928 TGACTGACACTTGAATAAATTGCAC 58.562 36.000 0.00 0.00 0.00 4.57
2061 4482 5.523438 TTACAACCACAACCTCCATTTTC 57.477 39.130 0.00 0.00 0.00 2.29
2074 4495 6.856895 ACCTCCATTTTCGAAATCTCAAATC 58.143 36.000 12.12 0.00 0.00 2.17
2077 4498 7.225784 TCCATTTTCGAAATCTCAAATCCAA 57.774 32.000 12.12 0.00 0.00 3.53
2101 4522 4.530388 CAAATACATGCACGTCCATCATC 58.470 43.478 0.00 0.00 0.00 2.92
2112 4533 5.119279 GCACGTCCATCATCTGATAATACAC 59.881 44.000 0.00 0.00 32.63 2.90
2137 4558 6.419116 CGATAACAGTGAGTGAATACCTCATG 59.581 42.308 0.00 0.00 36.14 3.07
2142 4563 4.940046 AGTGAGTGAATACCTCATGCAAAG 59.060 41.667 0.00 0.00 36.14 2.77
2145 4566 6.094603 GTGAGTGAATACCTCATGCAAAGAAT 59.905 38.462 0.00 0.00 36.14 2.40
2148 4569 8.579850 AGTGAATACCTCATGCAAAGAATAAA 57.420 30.769 0.00 0.00 36.14 1.40
2275 4706 1.095228 CACGTGCACCTGTTGGTCTT 61.095 55.000 12.15 0.00 46.60 3.01
2316 4747 6.014584 TCTCTAGAAAGTTCACAACATGCCTA 60.015 38.462 0.00 0.00 0.00 3.93
2370 4801 6.227522 TCCGAACTTCTCAAAATCATGTGTA 58.772 36.000 0.00 0.00 0.00 2.90
2371 4802 6.147164 TCCGAACTTCTCAAAATCATGTGTAC 59.853 38.462 0.00 0.00 0.00 2.90
2378 4809 3.057876 TCAAAATCATGTGTACGGGTTGC 60.058 43.478 0.00 0.00 0.00 4.17
2379 4810 1.459450 AATCATGTGTACGGGTTGCC 58.541 50.000 0.00 0.00 0.00 4.52
2393 4824 1.680249 GGTTGCCCCTTCACTCTCATC 60.680 57.143 0.00 0.00 0.00 2.92
2411 4842 0.888736 TCCTTCACGGCCATGTTGTG 60.889 55.000 2.24 1.84 34.96 3.33
2424 4855 5.276270 GCCATGTTGTGCAAGATTACATAG 58.724 41.667 0.00 0.00 0.00 2.23
2437 4871 6.111669 AGATTACATAGCATGTCATCAGCT 57.888 37.500 17.79 3.41 43.14 4.24
2438 4872 5.932883 AGATTACATAGCATGTCATCAGCTG 59.067 40.000 7.63 7.63 43.14 4.24
2439 4873 3.555527 ACATAGCATGTCATCAGCTGT 57.444 42.857 14.67 0.00 39.92 4.40
2440 4874 3.882444 ACATAGCATGTCATCAGCTGTT 58.118 40.909 14.67 1.65 39.92 3.16
2457 4891 3.252458 GCTGTTACAATGTTTCGGTTCCT 59.748 43.478 0.00 0.00 0.00 3.36
2473 4949 1.451387 CCTGCACACCGAATACCCC 60.451 63.158 0.00 0.00 0.00 4.95
2484 4960 3.009695 ACCGAATACCCCTTTCACATTCA 59.990 43.478 0.00 0.00 0.00 2.57
2532 5008 5.240844 GCAAAGACACATTGTTACCTACCTT 59.759 40.000 0.00 0.00 0.00 3.50
2535 5011 4.595781 AGACACATTGTTACCTACCTTGGA 59.404 41.667 0.00 0.00 0.00 3.53
2540 5016 2.897350 TGTTACCTACCTTGGAGCTCA 58.103 47.619 17.19 0.00 0.00 4.26
2583 5063 2.358267 GCCGGTAGGATAGATACCATCG 59.642 54.545 1.90 0.00 42.45 3.84
2587 5067 3.381908 GGTAGGATAGATACCATCGGCAG 59.618 52.174 0.00 0.00 42.01 4.85
2595 5075 0.978667 TACCATCGGCAGGGTAGCAA 60.979 55.000 0.00 0.00 38.60 3.91
2634 5190 5.296780 GTGTCTTTTCATTGTGAGAACCAGA 59.703 40.000 0.00 0.00 0.00 3.86
2648 5206 3.960102 AGAACCAGACATGCCAAAGAAAA 59.040 39.130 0.00 0.00 0.00 2.29
2649 5207 3.733443 ACCAGACATGCCAAAGAAAAC 57.267 42.857 0.00 0.00 0.00 2.43
2651 5209 2.289010 CCAGACATGCCAAAGAAAACCC 60.289 50.000 0.00 0.00 0.00 4.11
2653 5211 1.339929 GACATGCCAAAGAAAACCCGT 59.660 47.619 0.00 0.00 0.00 5.28
2665 5223 4.721132 AGAAAACCCGTCTAATCCACAAA 58.279 39.130 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.803555 CAAGTTCTTGTCTGTCGCATTC 58.196 45.455 4.58 0.00 0.00 2.67
19 20 0.937304 GCAAGTTCTTGTCTGTCGCA 59.063 50.000 13.04 0.00 0.00 5.10
20 21 1.221414 AGCAAGTTCTTGTCTGTCGC 58.779 50.000 13.04 0.00 0.00 5.19
21 22 2.032549 CCAAGCAAGTTCTTGTCTGTCG 60.033 50.000 13.04 5.14 41.29 4.35
22 23 2.945668 ACCAAGCAAGTTCTTGTCTGTC 59.054 45.455 13.04 0.00 41.29 3.51
82 87 3.247648 CCGTGTCTACTTCCAACAGTTTG 59.752 47.826 0.00 0.00 0.00 2.93
86 91 2.609737 GGTCCGTGTCTACTTCCAACAG 60.610 54.545 0.00 0.00 0.00 3.16
92 97 1.135344 GCAGAGGTCCGTGTCTACTTC 60.135 57.143 0.00 0.00 0.00 3.01
100 105 2.126307 CGTCTGCAGAGGTCCGTG 60.126 66.667 24.86 3.53 0.00 4.94
294 299 1.111116 TCAACTTCGTGACGGGGAGT 61.111 55.000 4.70 4.46 0.00 3.85
490 507 4.713553 TCCTTCACAGTGTAATTTGCTCA 58.286 39.130 0.00 0.00 0.00 4.26
501 518 1.811266 CGCGGGATCCTTCACAGTG 60.811 63.158 12.58 0.00 0.00 3.66
556 573 5.818857 ACACGACAACTACCAAAGTGTATTT 59.181 36.000 0.00 0.00 39.23 1.40
558 575 4.748102 CACACGACAACTACCAAAGTGTAT 59.252 41.667 0.00 0.00 39.02 2.29
559 576 4.114073 CACACGACAACTACCAAAGTGTA 58.886 43.478 0.00 0.00 39.02 2.90
560 577 2.933906 CACACGACAACTACCAAAGTGT 59.066 45.455 0.00 0.00 41.31 3.55
561 578 2.933906 ACACACGACAACTACCAAAGTG 59.066 45.455 0.00 0.00 38.88 3.16
562 579 2.933906 CACACACGACAACTACCAAAGT 59.066 45.455 0.00 0.00 41.49 2.66
563 580 2.933906 ACACACACGACAACTACCAAAG 59.066 45.455 0.00 0.00 0.00 2.77
564 581 2.975266 ACACACACGACAACTACCAAA 58.025 42.857 0.00 0.00 0.00 3.28
565 582 2.676632 ACACACACGACAACTACCAA 57.323 45.000 0.00 0.00 0.00 3.67
566 583 3.797451 TTACACACACGACAACTACCA 57.203 42.857 0.00 0.00 0.00 3.25
567 584 4.114794 AGTTTACACACACGACAACTACC 58.885 43.478 0.00 0.00 0.00 3.18
568 585 5.973565 ACTAGTTTACACACACGACAACTAC 59.026 40.000 0.00 0.00 0.00 2.73
569 586 5.972973 CACTAGTTTACACACACGACAACTA 59.027 40.000 0.00 0.00 0.00 2.24
570 587 4.802039 CACTAGTTTACACACACGACAACT 59.198 41.667 0.00 0.00 0.00 3.16
571 588 4.563976 ACACTAGTTTACACACACGACAAC 59.436 41.667 0.00 0.00 0.00 3.32
572 589 4.563580 CACACTAGTTTACACACACGACAA 59.436 41.667 0.00 0.00 0.00 3.18
684 701 0.533032 GTCACAGTCCCAGCTACCTC 59.467 60.000 0.00 0.00 0.00 3.85
693 710 2.420687 GGATTCATCTGGTCACAGTCCC 60.421 54.545 0.00 0.00 45.14 4.46
915 937 5.642919 AGCTCTCTGATTTTGTAGCAAGAAG 59.357 40.000 0.00 0.00 32.42 2.85
981 1006 4.772100 CCCATTGGACTTGTTGTAATTCCT 59.228 41.667 3.62 0.00 0.00 3.36
1010 1037 1.299926 GCCGAGACGCCGTTATGAT 60.300 57.895 0.00 0.00 0.00 2.45
1158 1185 3.012119 TAGGCCATGCACGGGGAA 61.012 61.111 5.01 0.00 0.00 3.97
1161 1188 2.188829 CATGTAGGCCATGCACGGG 61.189 63.158 5.01 0.53 44.21 5.28
1172 1199 2.461110 GCGTTGCCCGACATGTAGG 61.461 63.158 17.45 17.45 39.56 3.18
1378 1405 2.667318 CGTACTTGCGCAGTGTGGG 61.667 63.158 22.61 13.10 35.97 4.61
1384 1411 0.579630 TGTTGTTCGTACTTGCGCAG 59.420 50.000 11.31 7.81 0.00 5.18
1406 1454 4.079710 GCACGACGTTATTTTCTACTTGC 58.920 43.478 0.00 0.00 0.00 4.01
1520 1574 4.322650 GGCCTATTCCAAAACATTTGCAGA 60.323 41.667 0.00 0.00 0.00 4.26
1566 1620 0.872021 GCTCCGATTAGCTCACCGTG 60.872 60.000 0.00 0.00 39.50 4.94
1661 1715 0.539669 TCCTTCCTGCTCTGTCGACA 60.540 55.000 18.88 18.88 0.00 4.35
1665 1719 1.899142 ACTTCTCCTTCCTGCTCTGTC 59.101 52.381 0.00 0.00 0.00 3.51
1728 1788 0.986019 TCCAACAGGTGTCAGGGTGT 60.986 55.000 2.70 0.00 0.00 4.16
1729 1789 0.401738 ATCCAACAGGTGTCAGGGTG 59.598 55.000 2.70 0.00 0.00 4.61
1761 1821 1.535649 CCTCTGCTGCGTCAGATACAG 60.536 57.143 10.46 8.25 41.73 2.74
1772 1849 2.125188 GGTCTCTGCCTCTGCTGC 60.125 66.667 0.00 0.00 38.71 5.25
1783 1860 4.041198 TCATTCAAGTTTAACGGGGTCTCT 59.959 41.667 0.00 0.00 0.00 3.10
1821 1899 7.502561 ACTTAGTAAAACTGTTCATTCAAGGCT 59.497 33.333 0.00 0.00 0.00 4.58
1840 1918 9.999009 CGATTTTGTCAGTATCAGTACTTAGTA 57.001 33.333 0.00 0.00 39.12 1.82
1841 1919 8.737175 TCGATTTTGTCAGTATCAGTACTTAGT 58.263 33.333 0.00 0.00 39.12 2.24
1842 1920 9.737427 ATCGATTTTGTCAGTATCAGTACTTAG 57.263 33.333 0.00 0.00 39.12 2.18
1843 1921 9.516314 CATCGATTTTGTCAGTATCAGTACTTA 57.484 33.333 0.00 0.00 39.12 2.24
1844 1922 7.010552 GCATCGATTTTGTCAGTATCAGTACTT 59.989 37.037 0.00 0.00 39.12 2.24
1845 1923 6.477033 GCATCGATTTTGTCAGTATCAGTACT 59.523 38.462 0.00 0.00 41.84 2.73
1847 1925 6.573434 AGCATCGATTTTGTCAGTATCAGTA 58.427 36.000 0.00 0.00 0.00 2.74
1848 1926 5.423015 AGCATCGATTTTGTCAGTATCAGT 58.577 37.500 0.00 0.00 0.00 3.41
1849 1927 5.980698 AGCATCGATTTTGTCAGTATCAG 57.019 39.130 0.00 0.00 0.00 2.90
1850 1928 8.437360 AAATAGCATCGATTTTGTCAGTATCA 57.563 30.769 0.00 0.00 0.00 2.15
1851 1929 9.374960 GAAAATAGCATCGATTTTGTCAGTATC 57.625 33.333 0.00 0.00 36.78 2.24
1852 1930 8.345565 GGAAAATAGCATCGATTTTGTCAGTAT 58.654 33.333 0.00 0.00 36.78 2.12
1854 1932 6.375455 AGGAAAATAGCATCGATTTTGTCAGT 59.625 34.615 0.00 0.00 36.78 3.41
1855 1933 6.789262 AGGAAAATAGCATCGATTTTGTCAG 58.211 36.000 0.00 0.00 36.78 3.51
1857 1935 7.754924 TCAAAGGAAAATAGCATCGATTTTGTC 59.245 33.333 0.00 0.00 36.78 3.18
1858 1936 7.601856 TCAAAGGAAAATAGCATCGATTTTGT 58.398 30.769 0.00 0.00 36.78 2.83
1859 1937 8.638685 ATCAAAGGAAAATAGCATCGATTTTG 57.361 30.769 0.00 0.27 36.78 2.44
1860 1938 8.689972 AGATCAAAGGAAAATAGCATCGATTTT 58.310 29.630 0.00 0.00 38.81 1.82
1861 1939 8.230472 AGATCAAAGGAAAATAGCATCGATTT 57.770 30.769 0.00 0.00 0.00 2.17
1863 1941 7.646314 CAAGATCAAAGGAAAATAGCATCGAT 58.354 34.615 0.00 0.00 0.00 3.59
1865 1943 5.684626 GCAAGATCAAAGGAAAATAGCATCG 59.315 40.000 0.00 0.00 0.00 3.84
1868 1946 5.981088 TGCAAGATCAAAGGAAAATAGCA 57.019 34.783 0.00 0.00 0.00 3.49
1869 1947 6.567050 TCATGCAAGATCAAAGGAAAATAGC 58.433 36.000 0.00 0.00 0.00 2.97
1871 1949 8.352137 TCTTCATGCAAGATCAAAGGAAAATA 57.648 30.769 0.00 0.00 36.08 1.40
1872 1950 7.235935 TCTTCATGCAAGATCAAAGGAAAAT 57.764 32.000 0.00 0.00 36.08 1.82
1873 1951 6.653526 TCTTCATGCAAGATCAAAGGAAAA 57.346 33.333 0.00 0.00 36.08 2.29
1884 1962 8.437360 AATTGTATACGAATCTTCATGCAAGA 57.563 30.769 9.18 9.18 45.60 3.02
1885 1963 9.507280 AAAATTGTATACGAATCTTCATGCAAG 57.493 29.630 0.00 0.00 0.00 4.01
1886 1964 9.853555 AAAAATTGTATACGAATCTTCATGCAA 57.146 25.926 0.00 0.00 0.00 4.08
1887 1965 9.502145 GAAAAATTGTATACGAATCTTCATGCA 57.498 29.630 0.00 0.00 0.00 3.96
1888 1966 9.722056 AGAAAAATTGTATACGAATCTTCATGC 57.278 29.630 0.00 0.00 0.00 4.06
1943 4095 9.190317 TCAAGTGTCAGTCAAGTGATATAGTAT 57.810 33.333 0.00 0.00 0.00 2.12
1944 4096 8.575649 TCAAGTGTCAGTCAAGTGATATAGTA 57.424 34.615 0.00 0.00 0.00 1.82
1945 4097 7.468141 TCAAGTGTCAGTCAAGTGATATAGT 57.532 36.000 0.00 0.00 0.00 2.12
1946 4098 8.939201 ATTCAAGTGTCAGTCAAGTGATATAG 57.061 34.615 0.00 0.00 0.00 1.31
1949 4101 9.725019 ATTTATTCAAGTGTCAGTCAAGTGATA 57.275 29.630 0.00 0.00 0.00 2.15
1950 4102 8.627208 ATTTATTCAAGTGTCAGTCAAGTGAT 57.373 30.769 0.00 0.00 0.00 3.06
1952 4104 7.113965 GCAATTTATTCAAGTGTCAGTCAAGTG 59.886 37.037 0.00 0.00 32.75 3.16
1953 4105 7.141363 GCAATTTATTCAAGTGTCAGTCAAGT 58.859 34.615 0.00 0.00 32.75 3.16
1954 4106 7.113965 GTGCAATTTATTCAAGTGTCAGTCAAG 59.886 37.037 0.00 0.00 32.75 3.02
1956 4108 6.039159 TGTGCAATTTATTCAAGTGTCAGTCA 59.961 34.615 0.00 0.00 32.75 3.41
1957 4109 6.360681 GTGTGCAATTTATTCAAGTGTCAGTC 59.639 38.462 0.00 0.00 32.75 3.51
1958 4110 6.208644 GTGTGCAATTTATTCAAGTGTCAGT 58.791 36.000 0.00 0.00 32.75 3.41
1959 4111 5.340403 CGTGTGCAATTTATTCAAGTGTCAG 59.660 40.000 0.00 0.00 32.75 3.51
1960 4112 5.211454 CGTGTGCAATTTATTCAAGTGTCA 58.789 37.500 0.00 0.00 32.75 3.58
1961 4113 5.212194 ACGTGTGCAATTTATTCAAGTGTC 58.788 37.500 0.00 0.00 32.75 3.67
1962 4114 5.181690 ACGTGTGCAATTTATTCAAGTGT 57.818 34.783 0.00 0.00 32.75 3.55
1963 4115 4.616802 GGACGTGTGCAATTTATTCAAGTG 59.383 41.667 0.00 0.00 33.35 3.16
1964 4116 4.277174 TGGACGTGTGCAATTTATTCAAGT 59.723 37.500 0.00 0.00 0.00 3.16
1965 4117 4.616802 GTGGACGTGTGCAATTTATTCAAG 59.383 41.667 0.00 0.00 31.21 3.02
1967 4119 3.364465 CGTGGACGTGTGCAATTTATTCA 60.364 43.478 0.00 0.00 31.21 2.57
1968 4120 3.160545 CGTGGACGTGTGCAATTTATTC 58.839 45.455 0.00 0.00 31.21 1.75
1969 4121 2.095466 CCGTGGACGTGTGCAATTTATT 60.095 45.455 0.00 0.00 37.74 1.40
1970 4122 1.466950 CCGTGGACGTGTGCAATTTAT 59.533 47.619 0.00 0.00 37.74 1.40
1972 4124 1.652012 CCGTGGACGTGTGCAATTT 59.348 52.632 0.00 0.00 37.74 1.82
1974 4126 2.668212 CCCGTGGACGTGTGCAAT 60.668 61.111 0.00 0.00 37.74 3.56
1976 4128 4.901123 CACCCGTGGACGTGTGCA 62.901 66.667 0.00 0.00 40.41 4.57
2020 4440 0.400213 AAAGAGAACATGGGCGGACA 59.600 50.000 0.00 0.00 0.00 4.02
2061 4482 7.312154 TGTATTTGGTTGGATTTGAGATTTCG 58.688 34.615 0.00 0.00 0.00 3.46
2074 4495 2.415357 GGACGTGCATGTATTTGGTTGG 60.415 50.000 12.53 0.00 0.00 3.77
2077 4498 2.192664 TGGACGTGCATGTATTTGGT 57.807 45.000 12.53 0.00 0.00 3.67
2101 4522 8.129211 TCACTCACTGTTATCGTGTATTATCAG 58.871 37.037 0.00 0.00 34.14 2.90
2112 4533 5.891451 TGAGGTATTCACTCACTGTTATCG 58.109 41.667 0.00 0.00 39.87 2.92
2180 4610 9.749490 GAATTTCATGTTTGAATTATGCACTTG 57.251 29.630 0.00 0.00 41.38 3.16
2275 4706 9.521503 CTTTCTAGAGATACATCGACAATTTCA 57.478 33.333 0.00 0.00 0.00 2.69
2316 4747 4.283212 GTCTGCCTCCTAGAATAAGATGCT 59.717 45.833 0.00 0.00 0.00 3.79
2378 4809 2.093235 GTGAAGGATGAGAGTGAAGGGG 60.093 54.545 0.00 0.00 0.00 4.79
2379 4810 2.417924 CGTGAAGGATGAGAGTGAAGGG 60.418 54.545 0.00 0.00 0.00 3.95
2384 4815 0.460987 GGCCGTGAAGGATGAGAGTG 60.461 60.000 0.00 0.00 45.00 3.51
2387 4818 0.178767 CATGGCCGTGAAGGATGAGA 59.821 55.000 21.08 0.00 45.00 3.27
2393 4824 1.580942 CACAACATGGCCGTGAAGG 59.419 57.895 31.74 20.25 44.97 3.46
2411 4842 6.549912 TGATGACATGCTATGTAATCTTGC 57.450 37.500 19.18 0.00 46.84 4.01
2424 4855 4.142534 ACATTGTAACAGCTGATGACATGC 60.143 41.667 23.35 3.41 0.00 4.06
2437 4871 3.003897 GCAGGAACCGAAACATTGTAACA 59.996 43.478 0.00 0.00 0.00 2.41
2438 4872 3.003897 TGCAGGAACCGAAACATTGTAAC 59.996 43.478 0.00 0.00 0.00 2.50
2439 4873 3.003897 GTGCAGGAACCGAAACATTGTAA 59.996 43.478 0.00 0.00 0.00 2.41
2440 4874 2.550606 GTGCAGGAACCGAAACATTGTA 59.449 45.455 0.00 0.00 0.00 2.41
2457 4891 0.402504 AAAGGGGTATTCGGTGTGCA 59.597 50.000 0.00 0.00 0.00 4.57
2473 4949 6.373774 AGAAGGTGCTAGAATGAATGTGAAAG 59.626 38.462 0.00 0.00 0.00 2.62
2484 4960 4.768968 ACAAATGCAAGAAGGTGCTAGAAT 59.231 37.500 0.00 0.00 45.17 2.40
2513 4989 4.901868 TCCAAGGTAGGTAACAATGTGTC 58.098 43.478 0.00 0.00 41.41 3.67
2524 5000 2.559381 ATCTGAGCTCCAAGGTAGGT 57.441 50.000 12.15 0.00 0.00 3.08
2532 5008 4.517075 CGTGAAGACTATATCTGAGCTCCA 59.483 45.833 12.15 0.00 37.88 3.86
2535 5011 6.701145 TTTCGTGAAGACTATATCTGAGCT 57.299 37.500 0.00 0.00 37.88 4.09
2540 5016 4.793353 GCGGCTTTCGTGAAGACTATATCT 60.793 45.833 0.00 0.00 41.56 1.98
2595 5075 7.001674 TGAAAAGACACAACTATACAATGGGT 58.998 34.615 0.00 0.00 32.30 4.51
2634 5190 1.339929 GACGGGTTTTCTTTGGCATGT 59.660 47.619 0.00 0.00 0.00 3.21
2648 5206 2.844348 AGGATTTGTGGATTAGACGGGT 59.156 45.455 0.00 0.00 0.00 5.28
2649 5207 3.560636 AGGATTTGTGGATTAGACGGG 57.439 47.619 0.00 0.00 0.00 5.28
2665 5223 4.025040 TGAAGCAGTGACATCAAAGGAT 57.975 40.909 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.