Multiple sequence alignment - TraesCS3D01G524200

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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 TraesCS3D01G524200 chr3D 100.000 2714 0 0 1 2714 604364354 604361641 0.000000e+00 5012.0
1 TraesCS3D01G524200 chr3A 90.893 1746 72 33 4 1714 734005215 734003522 0.000000e+00 2263.0
2 TraesCS3D01G524200 chr3A 86.236 356 18 10 2386 2714 734002504 734002153 9.240000e-95 357.0
3 TraesCS3D01G524200 chrUn 87.934 1815 89 62 1 1710 42189798 42191587 0.000000e+00 2019.0
4 TraesCS3D01G524200 chrUn 86.867 632 45 20 2012 2620 42191798 42192414 0.000000e+00 673.0
5 TraesCS3D01G524200 chr5A 86.071 280 30 6 4 282 231068743 231069014 2.640000e-75 292.0
6 TraesCS3D01G524200 chr5A 89.404 151 15 1 316 466 231091759 231091908 3.570000e-44 189.0
7 TraesCS3D01G524200 chr7A 81.481 297 39 9 4 297 594570769 594570486 2.100000e-56 230.0
8 TraesCS3D01G524200 chr4D 77.616 411 56 20 100 482 306379987 306379585 1.640000e-52 217.0
9 TraesCS3D01G524200 chr6D 76.167 407 49 27 103 476 472405225 472404834 1.290000e-38 171.0
10 TraesCS3D01G524200 chr1D 88.462 78 9 0 2476 2553 10257706 10257783 8.000000e-16 95.3


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 TraesCS3D01G524200 chr3D 604361641 604364354 2713 True 5012 5012 100.0000 1 2714 1 chr3D.!!$R1 2713
1 TraesCS3D01G524200 chr3A 734002153 734005215 3062 True 1310 2263 88.5645 4 2714 2 chr3A.!!$R1 2710
2 TraesCS3D01G524200 chrUn 42189798 42192414 2616 False 1346 2019 87.4005 1 2620 2 chrUn.!!$F1 2619

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
891 946 0.255318 AATGAGCCCAGGAGAAGCTG 59.745 55.0 0.0 0.0 36.87 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 2553 0.031178 GCCTTTGTCTTGCAGTGTGG 59.969 55.0 0.0 0.0 0.0 4.17 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
36 37 1.227556 GACGGCCTGCGGAATGTAT 60.228 57.895 0.00 0.00 0.00 2.29
42 43 1.392589 CCTGCGGAATGTATGCCTTT 58.607 50.000 0.00 0.00 0.00 3.11
45 46 3.206150 CTGCGGAATGTATGCCTTTAGT 58.794 45.455 0.00 0.00 0.00 2.24
171 172 1.630244 CCTTGAACGCCAGCTTCTCG 61.630 60.000 0.00 0.00 0.00 4.04
268 269 1.534697 GGACCCTGACAAACCACCA 59.465 57.895 0.00 0.00 0.00 4.17
519 562 2.032528 TCGGCAGCACTCTTTGGG 59.967 61.111 0.00 0.00 0.00 4.12
564 607 2.789917 CCTCGCACAGCTGCAATC 59.210 61.111 15.27 0.00 44.50 2.67
622 665 2.500098 AGGGCGACTAAATACAAGCAGA 59.500 45.455 0.00 0.00 0.00 4.26
792 847 1.202663 GGGAAGGAATAGTTCGGCTCC 60.203 57.143 0.00 0.00 0.00 4.70
882 937 1.447643 CCCGGTAGAATGAGCCCAG 59.552 63.158 0.00 0.00 0.00 4.45
886 941 1.794714 GGTAGAATGAGCCCAGGAGA 58.205 55.000 0.00 0.00 0.00 3.71
889 944 0.545646 AGAATGAGCCCAGGAGAAGC 59.454 55.000 0.00 0.00 0.00 3.86
891 946 0.255318 AATGAGCCCAGGAGAAGCTG 59.745 55.000 0.00 0.00 36.87 4.24
902 957 2.439156 GAAGCTGCCGGCCATTCT 60.439 61.111 26.77 12.52 43.05 2.40
905 960 3.880846 GCTGCCGGCCATTCTTCG 61.881 66.667 26.77 2.88 34.27 3.79
908 963 2.125106 GCCGGCCATTCTTCGTCT 60.125 61.111 18.11 0.00 0.00 4.18
909 964 2.174319 GCCGGCCATTCTTCGTCTC 61.174 63.158 18.11 0.00 0.00 3.36
912 976 0.457851 CGGCCATTCTTCGTCTCTCT 59.542 55.000 2.24 0.00 0.00 3.10
936 1000 3.382083 TTTTTCCCTGCCTTATCCTCC 57.618 47.619 0.00 0.00 0.00 4.30
940 1004 1.369321 CCTGCCTTATCCTCCGAGC 59.631 63.158 0.00 0.00 0.00 5.03
941 1005 1.402896 CCTGCCTTATCCTCCGAGCA 61.403 60.000 0.00 0.00 0.00 4.26
942 1006 0.465705 CTGCCTTATCCTCCGAGCAA 59.534 55.000 0.00 0.00 0.00 3.91
972 1047 3.249189 AGCCTCCGTTGCTTCCCA 61.249 61.111 0.00 0.00 34.87 4.37
973 1048 2.282180 GCCTCCGTTGCTTCCCAA 60.282 61.111 0.00 0.00 0.00 4.12
988 1063 0.875059 CCCAACGCTCCTCTGTTTTC 59.125 55.000 0.00 0.00 0.00 2.29
1023 1100 2.832201 GCCTCCATGCTCAAGCCC 60.832 66.667 0.00 0.00 41.18 5.19
1156 1243 0.400213 TGGTTGCTTACTGTCCTGGG 59.600 55.000 0.00 0.00 0.00 4.45
1174 1261 2.586792 GAGCGAGCTCCACCCATT 59.413 61.111 13.73 0.00 37.11 3.16
1197 1285 3.059884 CTCTCACACGCTGCTTCTTTTA 58.940 45.455 0.00 0.00 0.00 1.52
1203 1291 4.739716 CACACGCTGCTTCTTTTACATTTT 59.260 37.500 0.00 0.00 0.00 1.82
1391 1513 4.587189 CTACTACAGGGCGGCGGC 62.587 72.222 26.59 26.59 38.90 6.53
1710 1841 1.614824 CCAGCAAGTCTCCCCCTCT 60.615 63.158 0.00 0.00 0.00 3.69
1715 1846 1.872773 CAAGTCTCCCCCTCTTAGCT 58.127 55.000 0.00 0.00 0.00 3.32
1717 1848 3.375699 CAAGTCTCCCCCTCTTAGCTTA 58.624 50.000 0.00 0.00 0.00 3.09
1718 1849 3.322191 AGTCTCCCCCTCTTAGCTTAG 57.678 52.381 0.00 0.00 0.00 2.18
1721 1852 2.585900 TCTCCCCCTCTTAGCTTAGTCA 59.414 50.000 0.00 0.00 0.00 3.41
1725 1856 3.906846 CCCCCTCTTAGCTTAGTCATCAT 59.093 47.826 0.00 0.00 0.00 2.45
1729 1860 6.183361 CCCCTCTTAGCTTAGTCATCATCTTT 60.183 42.308 0.00 0.00 0.00 2.52
1730 1861 7.278875 CCCTCTTAGCTTAGTCATCATCTTTT 58.721 38.462 0.00 0.00 0.00 2.27
1731 1862 8.424918 CCCTCTTAGCTTAGTCATCATCTTTTA 58.575 37.037 0.00 0.00 0.00 1.52
1732 1863 9.995003 CCTCTTAGCTTAGTCATCATCTTTTAT 57.005 33.333 0.00 0.00 0.00 1.40
1760 1906 8.470657 TCTCTTGTCAGTGTAATATATGAGCT 57.529 34.615 0.00 0.00 0.00 4.09
1761 1907 8.918116 TCTCTTGTCAGTGTAATATATGAGCTT 58.082 33.333 0.00 0.00 0.00 3.74
1775 1921 6.702449 ATATGAGCTTATTATGGGTGTGGA 57.298 37.500 0.00 0.00 0.00 4.02
1776 1922 4.150897 TGAGCTTATTATGGGTGTGGAC 57.849 45.455 0.00 0.00 0.00 4.02
1777 1923 3.131396 GAGCTTATTATGGGTGTGGACG 58.869 50.000 0.00 0.00 0.00 4.79
1778 1924 2.769663 AGCTTATTATGGGTGTGGACGA 59.230 45.455 0.00 0.00 0.00 4.20
1779 1925 3.199071 AGCTTATTATGGGTGTGGACGAA 59.801 43.478 0.00 0.00 0.00 3.85
1803 1956 2.845486 TCGACATTCGAAATTTTGCCG 58.155 42.857 0.00 0.00 46.90 5.69
1822 1975 7.401484 TTGCCGAAATTTATCAAAAACAGTC 57.599 32.000 0.00 0.00 0.00 3.51
1823 1976 6.744112 TGCCGAAATTTATCAAAAACAGTCT 58.256 32.000 0.00 0.00 0.00 3.24
1824 1977 7.206687 TGCCGAAATTTATCAAAAACAGTCTT 58.793 30.769 0.00 0.00 0.00 3.01
1825 1978 7.708752 TGCCGAAATTTATCAAAAACAGTCTTT 59.291 29.630 0.00 0.00 0.00 2.52
1835 1988 5.478679 TCAAAAACAGTCTTTTCAACTCCCA 59.521 36.000 0.00 0.00 0.00 4.37
1837 1990 3.644966 ACAGTCTTTTCAACTCCCACA 57.355 42.857 0.00 0.00 0.00 4.17
1839 1992 3.694566 ACAGTCTTTTCAACTCCCACAAC 59.305 43.478 0.00 0.00 0.00 3.32
1840 1993 2.943033 AGTCTTTTCAACTCCCACAACG 59.057 45.455 0.00 0.00 0.00 4.10
1841 1994 2.940410 GTCTTTTCAACTCCCACAACGA 59.060 45.455 0.00 0.00 0.00 3.85
1842 1995 3.564225 GTCTTTTCAACTCCCACAACGAT 59.436 43.478 0.00 0.00 0.00 3.73
1843 1996 3.813166 TCTTTTCAACTCCCACAACGATC 59.187 43.478 0.00 0.00 0.00 3.69
1844 1997 2.178912 TTCAACTCCCACAACGATCC 57.821 50.000 0.00 0.00 0.00 3.36
1845 1998 1.052617 TCAACTCCCACAACGATCCA 58.947 50.000 0.00 0.00 0.00 3.41
1846 1999 1.001974 TCAACTCCCACAACGATCCAG 59.998 52.381 0.00 0.00 0.00 3.86
1847 2000 1.001974 CAACTCCCACAACGATCCAGA 59.998 52.381 0.00 0.00 0.00 3.86
1848 2001 1.348064 ACTCCCACAACGATCCAGAA 58.652 50.000 0.00 0.00 0.00 3.02
1849 2002 1.697432 ACTCCCACAACGATCCAGAAA 59.303 47.619 0.00 0.00 0.00 2.52
1850 2003 2.105821 ACTCCCACAACGATCCAGAAAA 59.894 45.455 0.00 0.00 0.00 2.29
1851 2004 3.146066 CTCCCACAACGATCCAGAAAAA 58.854 45.455 0.00 0.00 0.00 1.94
1852 2005 3.758554 CTCCCACAACGATCCAGAAAAAT 59.241 43.478 0.00 0.00 0.00 1.82
1853 2006 4.148838 TCCCACAACGATCCAGAAAAATT 58.851 39.130 0.00 0.00 0.00 1.82
1854 2007 4.586841 TCCCACAACGATCCAGAAAAATTT 59.413 37.500 0.00 0.00 0.00 1.82
1855 2008 4.923281 CCCACAACGATCCAGAAAAATTTC 59.077 41.667 0.00 0.00 37.45 2.17
1857 2010 5.858581 CCACAACGATCCAGAAAAATTTCTC 59.141 40.000 5.45 0.00 45.23 2.87
1858 2011 5.858581 CACAACGATCCAGAAAAATTTCTCC 59.141 40.000 5.45 0.00 45.23 3.71
1859 2012 5.048013 ACAACGATCCAGAAAAATTTCTCCC 60.048 40.000 5.45 0.00 45.23 4.30
1860 2013 3.689649 ACGATCCAGAAAAATTTCTCCCG 59.310 43.478 5.45 8.97 45.23 5.14
1861 2014 3.938963 CGATCCAGAAAAATTTCTCCCGA 59.061 43.478 5.45 3.15 45.23 5.14
1862 2015 4.576463 CGATCCAGAAAAATTTCTCCCGAT 59.424 41.667 5.45 7.22 45.23 4.18
1863 2016 5.504665 CGATCCAGAAAAATTTCTCCCGATG 60.505 44.000 5.45 0.00 45.23 3.84
1864 2017 3.443681 TCCAGAAAAATTTCTCCCGATGC 59.556 43.478 5.45 0.00 45.23 3.91
1865 2018 3.193267 CCAGAAAAATTTCTCCCGATGCA 59.807 43.478 5.45 0.00 45.23 3.96
1866 2019 4.321899 CCAGAAAAATTTCTCCCGATGCAA 60.322 41.667 5.45 0.00 45.23 4.08
1867 2020 5.229423 CAGAAAAATTTCTCCCGATGCAAA 58.771 37.500 5.45 0.00 45.23 3.68
1868 2021 5.119125 CAGAAAAATTTCTCCCGATGCAAAC 59.881 40.000 5.45 0.00 45.23 2.93
1869 2022 2.919666 AATTTCTCCCGATGCAAACG 57.080 45.000 9.21 9.21 0.00 3.60
1870 2023 2.107950 ATTTCTCCCGATGCAAACGA 57.892 45.000 16.17 0.00 31.90 3.85
1871 2024 1.885560 TTTCTCCCGATGCAAACGAA 58.114 45.000 16.17 5.29 31.90 3.85
1872 2025 1.885560 TTCTCCCGATGCAAACGAAA 58.114 45.000 16.17 5.00 31.90 3.46
1873 2026 1.153353 TCTCCCGATGCAAACGAAAC 58.847 50.000 16.17 0.00 31.90 2.78
1874 2027 0.871722 CTCCCGATGCAAACGAAACA 59.128 50.000 16.17 0.00 31.90 2.83
1875 2028 0.871722 TCCCGATGCAAACGAAACAG 59.128 50.000 16.17 1.76 31.90 3.16
1876 2029 0.871722 CCCGATGCAAACGAAACAGA 59.128 50.000 16.17 0.00 31.90 3.41
1877 2030 1.135972 CCCGATGCAAACGAAACAGAG 60.136 52.381 16.17 0.57 31.90 3.35
1878 2031 1.595609 CGATGCAAACGAAACAGAGC 58.404 50.000 10.41 0.00 31.90 4.09
1879 2032 1.725931 CGATGCAAACGAAACAGAGCC 60.726 52.381 10.41 0.00 31.90 4.70
1880 2033 1.537202 GATGCAAACGAAACAGAGCCT 59.463 47.619 0.00 0.00 0.00 4.58
1881 2034 0.662619 TGCAAACGAAACAGAGCCTG 59.337 50.000 0.00 1.16 37.52 4.85
1882 2035 0.040067 GCAAACGAAACAGAGCCTGG 60.040 55.000 7.06 0.00 35.51 4.45
1883 2036 1.593196 CAAACGAAACAGAGCCTGGA 58.407 50.000 0.00 0.00 35.51 3.86
1884 2037 1.946768 CAAACGAAACAGAGCCTGGAA 59.053 47.619 0.00 0.00 35.51 3.53
1885 2038 1.594331 AACGAAACAGAGCCTGGAAC 58.406 50.000 0.00 0.00 35.51 3.62
1886 2039 0.468226 ACGAAACAGAGCCTGGAACA 59.532 50.000 0.00 0.00 35.51 3.18
1903 2333 6.146021 CCTGGAACAAAAACTTGCATATTCAC 59.854 38.462 0.00 0.00 38.70 3.18
1920 2370 7.414429 GCATATTCACACTCAACTAATGAAGCA 60.414 37.037 0.00 0.00 37.67 3.91
1965 2416 2.559668 CACAGGTTGCAACAATCATCCT 59.440 45.455 29.55 13.85 34.81 3.24
1966 2417 3.006110 CACAGGTTGCAACAATCATCCTT 59.994 43.478 29.55 5.61 32.80 3.36
1967 2418 4.218200 CACAGGTTGCAACAATCATCCTTA 59.782 41.667 29.55 0.00 32.80 2.69
1968 2419 4.218417 ACAGGTTGCAACAATCATCCTTAC 59.782 41.667 29.55 8.73 32.80 2.34
1969 2420 4.460382 CAGGTTGCAACAATCATCCTTACT 59.540 41.667 29.55 10.85 32.80 2.24
1972 2423 6.151144 AGGTTGCAACAATCATCCTTACTTAC 59.849 38.462 29.55 7.11 31.46 2.34
1977 2428 6.672357 GCAACAATCATCCTTACTTACACGAC 60.672 42.308 0.00 0.00 0.00 4.34
1981 2432 4.726416 TCATCCTTACTTACACGACGAAC 58.274 43.478 0.00 0.00 0.00 3.95
1984 2435 2.660236 CCTTACTTACACGACGAACTGC 59.340 50.000 0.00 0.00 0.00 4.40
1996 2447 0.871722 CGAACTGCGAAACCATTCCA 59.128 50.000 0.00 0.00 44.57 3.53
2035 2486 1.626654 CTCGGCACAAAATCGACGCT 61.627 55.000 0.00 0.00 0.00 5.07
2036 2487 1.206578 CGGCACAAAATCGACGCTT 59.793 52.632 0.00 0.00 0.00 4.68
2038 2489 0.517316 GGCACAAAATCGACGCTTCT 59.483 50.000 0.00 0.00 0.00 2.85
2039 2490 1.595609 GCACAAAATCGACGCTTCTG 58.404 50.000 0.00 0.00 0.00 3.02
2040 2491 1.194547 GCACAAAATCGACGCTTCTGA 59.805 47.619 0.00 0.00 0.00 3.27
2041 2492 2.827555 CACAAAATCGACGCTTCTGAC 58.172 47.619 0.00 0.00 0.00 3.51
2042 2493 2.476619 CACAAAATCGACGCTTCTGACT 59.523 45.455 0.00 0.00 0.00 3.41
2045 2497 0.888619 AATCGACGCTTCTGACTCCA 59.111 50.000 0.00 0.00 0.00 3.86
2047 2499 1.797933 CGACGCTTCTGACTCCACG 60.798 63.158 0.00 0.00 0.00 4.94
2061 2515 3.426615 ACTCCACGAACAGAAGAGATCT 58.573 45.455 0.00 0.00 39.68 2.75
2080 2534 0.321346 TGAAATCAGCAGGCGACTCA 59.679 50.000 0.00 0.00 40.21 3.41
2099 2553 5.041940 ACTCAGTCGACACAGAACTAAAAC 58.958 41.667 19.50 0.00 0.00 2.43
2104 2558 3.866910 TCGACACAGAACTAAAACCACAC 59.133 43.478 0.00 0.00 0.00 3.82
2119 2573 0.317269 CACACTGCAAGACAAAGGCG 60.317 55.000 0.00 0.00 37.43 5.52
2120 2574 1.370900 CACTGCAAGACAAAGGCGC 60.371 57.895 0.00 0.00 37.43 6.53
2132 2586 0.678048 AAAGGCGCCATCAGGAAGAC 60.678 55.000 31.54 0.00 36.89 3.01
2164 2618 9.802039 TTGAACTAGTTGATATTTACAAAGGGT 57.198 29.630 14.14 0.00 0.00 4.34
2167 2621 8.937634 ACTAGTTGATATTTACAAAGGGTACG 57.062 34.615 0.00 0.00 0.00 3.67
2168 2622 8.534496 ACTAGTTGATATTTACAAAGGGTACGT 58.466 33.333 0.00 0.00 0.00 3.57
2176 2630 1.070105 AAAGGGTACGTGCTTCGCA 59.930 52.632 3.01 0.00 44.19 5.10
2224 2683 2.894879 CGCCGCCATTCGATTCCA 60.895 61.111 0.00 0.00 41.67 3.53
2238 2697 1.952296 GATTCCAGCGGCAAATCTGAT 59.048 47.619 1.45 0.00 32.26 2.90
2239 2698 1.382522 TTCCAGCGGCAAATCTGATC 58.617 50.000 1.45 0.00 32.26 2.92
2242 2701 1.660167 CAGCGGCAAATCTGATCTCA 58.340 50.000 1.45 0.00 32.26 3.27
2374 2878 1.661341 AGGCTGCTGCTTCTATTTCG 58.339 50.000 15.64 0.00 39.59 3.46
2489 3002 2.435372 TTGAACACAGCTCCCACTTT 57.565 45.000 0.00 0.00 0.00 2.66
2563 3076 6.542370 GCAGGCCTCTGTAAAACAAATAGATA 59.458 38.462 0.00 0.00 42.78 1.98
2565 3078 8.956426 CAGGCCTCTGTAAAACAAATAGATAAA 58.044 33.333 0.00 0.00 36.30 1.40
2585 3112 1.818642 AGAAGGCTTCAGCATCACAC 58.181 50.000 27.70 0.00 44.36 3.82
2587 3114 1.881973 GAAGGCTTCAGCATCACACAA 59.118 47.619 21.99 0.00 44.36 3.33
2591 3118 3.322828 AGGCTTCAGCATCACACAATTTT 59.677 39.130 0.30 0.00 44.36 1.82
2592 3119 3.430895 GGCTTCAGCATCACACAATTTTG 59.569 43.478 0.30 0.00 44.36 2.44
2631 3169 2.432444 CACGAGGGGCATAAAGAAACA 58.568 47.619 0.00 0.00 0.00 2.83
2664 3202 3.750130 GGACATGGAAATCAGATCCGATG 59.250 47.826 0.00 6.34 39.98 3.84
2698 3236 2.158827 TGTGTTAACTTGCAGAGGCTCA 60.159 45.455 18.26 0.00 41.91 4.26
2709 3247 2.484594 GCAGAGGCTCAGGAGGATAAAC 60.485 54.545 18.26 0.00 36.96 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 1.616865 AGCTACGACACACTAAAGGCA 59.383 47.619 0.00 0.00 0.00 4.75
42 43 3.005554 GGTCTACAGCTACGACACACTA 58.994 50.000 10.26 0.00 0.00 2.74
45 46 1.900245 TGGTCTACAGCTACGACACA 58.100 50.000 10.26 4.75 0.00 3.72
326 360 3.143515 GAGGACGTCCCGGTACCC 61.144 72.222 30.82 4.01 40.87 3.69
564 607 1.462616 TTCTGGGATGGATTGCGTTG 58.537 50.000 0.00 0.00 0.00 4.10
635 680 3.625897 TGAGCCCACTGACCACCG 61.626 66.667 0.00 0.00 0.00 4.94
636 681 2.032681 GTGAGCCCACTGACCACC 59.967 66.667 0.00 0.00 40.10 4.61
641 686 2.431683 GCAAGGTGAGCCCACTGA 59.568 61.111 0.00 0.00 42.77 3.41
642 687 3.052082 CGCAAGGTGAGCCCACTG 61.052 66.667 0.00 0.00 42.77 3.66
748 797 4.154347 CCTCCTCCACGGCAGCTC 62.154 72.222 0.00 0.00 0.00 4.09
859 914 1.364171 CTCATTCTACCGGGCCTCG 59.636 63.158 6.32 4.41 38.88 4.63
882 937 4.496336 ATGGCCGGCAGCTTCTCC 62.496 66.667 30.85 8.62 43.05 3.71
886 941 2.036256 AAGAATGGCCGGCAGCTT 59.964 55.556 30.85 20.97 43.05 3.74
889 944 2.436646 ACGAAGAATGGCCGGCAG 60.437 61.111 30.85 10.52 0.00 4.85
891 946 2.125106 AGACGAAGAATGGCCGGC 60.125 61.111 21.18 21.18 0.00 6.13
921 985 2.053618 CTCGGAGGATAAGGCAGGG 58.946 63.158 0.00 0.00 0.00 4.45
922 986 1.369321 GCTCGGAGGATAAGGCAGG 59.631 63.158 7.20 0.00 0.00 4.85
936 1000 2.680913 CGTGGCCTTCCTTTGCTCG 61.681 63.158 3.32 0.00 0.00 5.03
940 1004 3.267974 GCTCGTGGCCTTCCTTTG 58.732 61.111 3.32 0.00 34.27 2.77
972 1047 1.694696 AGAGGAAAACAGAGGAGCGTT 59.305 47.619 0.00 0.00 0.00 4.84
973 1048 1.001406 CAGAGGAAAACAGAGGAGCGT 59.999 52.381 0.00 0.00 0.00 5.07
975 1050 1.447945 GCAGAGGAAAACAGAGGAGC 58.552 55.000 0.00 0.00 0.00 4.70
1023 1100 4.154347 GGAGGGAGCAGCACCGAG 62.154 72.222 2.39 0.00 0.00 4.63
1112 1198 4.681978 ACCGTCCGACCTTGCTGC 62.682 66.667 0.00 0.00 0.00 5.25
1169 1256 1.081892 CAGCGTGTGAGAGAAATGGG 58.918 55.000 0.00 0.00 0.00 4.00
1174 1261 0.676184 AGAAGCAGCGTGTGAGAGAA 59.324 50.000 0.00 0.00 0.00 2.87
1203 1291 0.881118 GGTTCTGCTCGATTGGCAAA 59.119 50.000 3.01 0.00 39.30 3.68
1206 1295 1.424493 CGAGGTTCTGCTCGATTGGC 61.424 60.000 0.00 0.00 44.85 4.52
1718 1849 9.809096 TGACAAGAGAGTATAAAAGATGATGAC 57.191 33.333 0.00 0.00 0.00 3.06
1721 1852 9.814899 CACTGACAAGAGAGTATAAAAGATGAT 57.185 33.333 0.00 0.00 0.00 2.45
1734 1865 8.575589 AGCTCATATATTACACTGACAAGAGAG 58.424 37.037 0.00 0.00 0.00 3.20
1735 1866 8.470657 AGCTCATATATTACACTGACAAGAGA 57.529 34.615 0.00 0.00 0.00 3.10
1760 1906 6.183360 CGAAAATTCGTCCACACCCATAATAA 60.183 38.462 7.37 0.00 45.09 1.40
1761 1907 5.294799 CGAAAATTCGTCCACACCCATAATA 59.705 40.000 7.37 0.00 45.09 0.98
1762 1908 4.095782 CGAAAATTCGTCCACACCCATAAT 59.904 41.667 7.37 0.00 45.09 1.28
1763 1909 3.437395 CGAAAATTCGTCCACACCCATAA 59.563 43.478 7.37 0.00 45.09 1.90
1765 1911 1.810151 CGAAAATTCGTCCACACCCAT 59.190 47.619 7.37 0.00 45.09 4.00
1766 1912 1.231221 CGAAAATTCGTCCACACCCA 58.769 50.000 7.37 0.00 45.09 4.51
1810 1963 6.154363 TGGGAGTTGAAAAGACTGTTTTTGAT 59.846 34.615 0.00 0.00 30.78 2.57
1822 1975 3.058224 GGATCGTTGTGGGAGTTGAAAAG 60.058 47.826 0.00 0.00 0.00 2.27
1823 1976 2.882137 GGATCGTTGTGGGAGTTGAAAA 59.118 45.455 0.00 0.00 0.00 2.29
1824 1977 2.158740 TGGATCGTTGTGGGAGTTGAAA 60.159 45.455 0.00 0.00 0.00 2.69
1825 1978 1.418264 TGGATCGTTGTGGGAGTTGAA 59.582 47.619 0.00 0.00 0.00 2.69
1827 1980 1.001974 TCTGGATCGTTGTGGGAGTTG 59.998 52.381 0.00 0.00 0.00 3.16
1828 1981 1.348064 TCTGGATCGTTGTGGGAGTT 58.652 50.000 0.00 0.00 0.00 3.01
1829 1982 1.348064 TTCTGGATCGTTGTGGGAGT 58.652 50.000 0.00 0.00 0.00 3.85
1831 1984 2.940994 TTTTCTGGATCGTTGTGGGA 57.059 45.000 0.00 0.00 0.00 4.37
1832 1985 4.519540 AATTTTTCTGGATCGTTGTGGG 57.480 40.909 0.00 0.00 0.00 4.61
1835 1988 5.048013 GGGAGAAATTTTTCTGGATCGTTGT 60.048 40.000 10.16 0.00 46.84 3.32
1837 1990 4.156008 CGGGAGAAATTTTTCTGGATCGTT 59.844 41.667 10.16 0.00 46.84 3.85
1839 1992 3.938963 TCGGGAGAAATTTTTCTGGATCG 59.061 43.478 10.16 8.33 46.84 3.69
1840 1993 5.734503 GCATCGGGAGAAATTTTTCTGGATC 60.735 44.000 10.16 0.00 46.84 3.36
1841 1994 4.098501 GCATCGGGAGAAATTTTTCTGGAT 59.901 41.667 10.16 8.37 46.84 3.41
1842 1995 3.443681 GCATCGGGAGAAATTTTTCTGGA 59.556 43.478 10.16 6.68 46.84 3.86
1843 1996 3.193267 TGCATCGGGAGAAATTTTTCTGG 59.807 43.478 10.16 1.96 46.84 3.86
1844 1997 4.439305 TGCATCGGGAGAAATTTTTCTG 57.561 40.909 10.16 0.99 46.84 3.02
1846 1999 4.089923 CGTTTGCATCGGGAGAAATTTTTC 59.910 41.667 0.06 0.06 45.37 2.29
1847 2000 3.987220 CGTTTGCATCGGGAGAAATTTTT 59.013 39.130 0.00 0.00 45.37 1.94
1848 2001 3.254657 TCGTTTGCATCGGGAGAAATTTT 59.745 39.130 10.93 0.00 45.37 1.82
1849 2002 2.817258 TCGTTTGCATCGGGAGAAATTT 59.183 40.909 10.93 0.00 45.37 1.82
1850 2003 2.432444 TCGTTTGCATCGGGAGAAATT 58.568 42.857 10.93 0.00 45.37 1.82
1851 2004 2.107950 TCGTTTGCATCGGGAGAAAT 57.892 45.000 10.93 0.00 45.37 2.17
1852 2005 1.885560 TTCGTTTGCATCGGGAGAAA 58.114 45.000 10.93 0.00 45.37 2.52
1853 2006 1.533731 GTTTCGTTTGCATCGGGAGAA 59.466 47.619 10.93 0.00 45.37 2.87
1854 2007 1.153353 GTTTCGTTTGCATCGGGAGA 58.847 50.000 10.93 0.00 46.90 3.71
1855 2008 0.871722 TGTTTCGTTTGCATCGGGAG 59.128 50.000 10.93 0.00 0.00 4.30
1856 2009 0.871722 CTGTTTCGTTTGCATCGGGA 59.128 50.000 10.93 0.13 0.00 5.14
1857 2010 0.871722 TCTGTTTCGTTTGCATCGGG 59.128 50.000 10.93 0.00 0.00 5.14
1858 2011 1.725931 GCTCTGTTTCGTTTGCATCGG 60.726 52.381 10.93 0.00 0.00 4.18
1859 2012 1.595609 GCTCTGTTTCGTTTGCATCG 58.404 50.000 5.62 5.62 0.00 3.84
1860 2013 1.537202 AGGCTCTGTTTCGTTTGCATC 59.463 47.619 0.00 0.00 0.00 3.91
1861 2014 1.267806 CAGGCTCTGTTTCGTTTGCAT 59.732 47.619 0.00 0.00 0.00 3.96
1862 2015 0.662619 CAGGCTCTGTTTCGTTTGCA 59.337 50.000 0.00 0.00 0.00 4.08
1863 2016 0.040067 CCAGGCTCTGTTTCGTTTGC 60.040 55.000 0.00 0.00 0.00 3.68
1864 2017 1.593196 TCCAGGCTCTGTTTCGTTTG 58.407 50.000 0.00 0.00 0.00 2.93
1865 2018 1.947456 GTTCCAGGCTCTGTTTCGTTT 59.053 47.619 0.00 0.00 0.00 3.60
1866 2019 1.134220 TGTTCCAGGCTCTGTTTCGTT 60.134 47.619 0.00 0.00 0.00 3.85
1867 2020 0.468226 TGTTCCAGGCTCTGTTTCGT 59.532 50.000 0.00 0.00 0.00 3.85
1868 2021 1.593196 TTGTTCCAGGCTCTGTTTCG 58.407 50.000 0.00 0.00 0.00 3.46
1869 2022 4.112634 GTTTTTGTTCCAGGCTCTGTTTC 58.887 43.478 0.00 0.00 0.00 2.78
1870 2023 3.769300 AGTTTTTGTTCCAGGCTCTGTTT 59.231 39.130 0.00 0.00 0.00 2.83
1871 2024 3.365472 AGTTTTTGTTCCAGGCTCTGTT 58.635 40.909 0.00 0.00 0.00 3.16
1872 2025 3.018423 AGTTTTTGTTCCAGGCTCTGT 57.982 42.857 0.00 0.00 0.00 3.41
1873 2026 3.709987 CAAGTTTTTGTTCCAGGCTCTG 58.290 45.455 0.00 0.00 0.00 3.35
1874 2027 2.101415 GCAAGTTTTTGTTCCAGGCTCT 59.899 45.455 0.00 0.00 36.65 4.09
1875 2028 2.159114 TGCAAGTTTTTGTTCCAGGCTC 60.159 45.455 0.00 0.00 36.65 4.70
1876 2029 1.830477 TGCAAGTTTTTGTTCCAGGCT 59.170 42.857 0.00 0.00 36.65 4.58
1877 2030 2.307934 TGCAAGTTTTTGTTCCAGGC 57.692 45.000 0.00 0.00 36.65 4.85
1878 2031 6.146021 GTGAATATGCAAGTTTTTGTTCCAGG 59.854 38.462 0.00 0.00 36.65 4.45
1879 2032 6.700960 TGTGAATATGCAAGTTTTTGTTCCAG 59.299 34.615 0.00 0.00 36.65 3.86
1880 2033 6.478344 GTGTGAATATGCAAGTTTTTGTTCCA 59.522 34.615 0.00 0.00 36.65 3.53
1881 2034 6.701400 AGTGTGAATATGCAAGTTTTTGTTCC 59.299 34.615 0.00 0.00 36.65 3.62
1882 2035 7.434897 TGAGTGTGAATATGCAAGTTTTTGTTC 59.565 33.333 0.00 0.00 36.65 3.18
1883 2036 7.264221 TGAGTGTGAATATGCAAGTTTTTGTT 58.736 30.769 0.00 0.00 36.65 2.83
1884 2037 6.804677 TGAGTGTGAATATGCAAGTTTTTGT 58.195 32.000 0.00 0.00 36.65 2.83
1885 2038 7.436080 AGTTGAGTGTGAATATGCAAGTTTTTG 59.564 33.333 0.00 0.00 37.36 2.44
1886 2039 7.491682 AGTTGAGTGTGAATATGCAAGTTTTT 58.508 30.769 0.00 0.00 0.00 1.94
1903 2333 4.728882 GCGGAATGCTTCATTAGTTGAGTG 60.729 45.833 0.00 0.00 41.73 3.51
1920 2370 2.435805 TCTTTCTCCATAGCAGCGGAAT 59.564 45.455 0.00 0.00 0.00 3.01
1923 2373 2.141517 CATCTTTCTCCATAGCAGCGG 58.858 52.381 0.00 0.00 0.00 5.52
1930 2380 4.264253 CAACCTGTGCATCTTTCTCCATA 58.736 43.478 0.00 0.00 0.00 2.74
1932 2382 2.507484 CAACCTGTGCATCTTTCTCCA 58.493 47.619 0.00 0.00 0.00 3.86
1960 2411 4.557690 CAGTTCGTCGTGTAAGTAAGGATG 59.442 45.833 0.00 0.00 0.00 3.51
1961 2412 4.730657 CAGTTCGTCGTGTAAGTAAGGAT 58.269 43.478 0.00 0.00 0.00 3.24
1962 2413 3.610114 GCAGTTCGTCGTGTAAGTAAGGA 60.610 47.826 0.00 0.00 0.00 3.36
1963 2414 2.660236 GCAGTTCGTCGTGTAAGTAAGG 59.340 50.000 0.00 0.00 0.00 2.69
1965 2416 2.032117 TCGCAGTTCGTCGTGTAAGTAA 60.032 45.455 0.00 0.00 39.67 2.24
1966 2417 1.530720 TCGCAGTTCGTCGTGTAAGTA 59.469 47.619 0.00 0.00 39.67 2.24
1967 2418 0.308684 TCGCAGTTCGTCGTGTAAGT 59.691 50.000 0.00 0.00 39.67 2.24
1968 2419 1.401530 TTCGCAGTTCGTCGTGTAAG 58.598 50.000 0.00 0.00 39.67 2.34
1969 2420 1.518102 GTTTCGCAGTTCGTCGTGTAA 59.482 47.619 0.00 0.00 39.67 2.41
1972 2423 1.200839 GGTTTCGCAGTTCGTCGTG 59.799 57.895 0.00 0.00 39.67 4.35
1977 2428 0.871722 TGGAATGGTTTCGCAGTTCG 59.128 50.000 0.00 0.00 40.15 3.95
1981 2432 3.120580 GCAAATTTGGAATGGTTTCGCAG 60.121 43.478 19.47 0.00 32.28 5.18
1984 2435 5.671742 AAAGCAAATTTGGAATGGTTTCG 57.328 34.783 19.47 0.00 39.73 3.46
1996 2447 6.625081 GCCGAGTTCATACCTAAAGCAAATTT 60.625 38.462 0.00 0.00 34.72 1.82
2035 2486 2.956333 TCTTCTGTTCGTGGAGTCAGAA 59.044 45.455 0.00 0.00 42.21 3.02
2036 2487 2.554462 CTCTTCTGTTCGTGGAGTCAGA 59.446 50.000 0.00 0.00 35.54 3.27
2038 2489 2.583143 TCTCTTCTGTTCGTGGAGTCA 58.417 47.619 0.00 0.00 0.00 3.41
2039 2490 3.442273 AGATCTCTTCTGTTCGTGGAGTC 59.558 47.826 0.00 0.00 31.79 3.36
2040 2491 3.192422 CAGATCTCTTCTGTTCGTGGAGT 59.808 47.826 0.00 0.00 45.79 3.85
2041 2492 3.768406 CAGATCTCTTCTGTTCGTGGAG 58.232 50.000 0.00 0.00 45.79 3.86
2042 2493 3.857549 CAGATCTCTTCTGTTCGTGGA 57.142 47.619 0.00 0.00 45.79 4.02
2061 2515 0.321346 TGAGTCGCCTGCTGATTTCA 59.679 50.000 0.00 0.00 0.00 2.69
2063 2517 0.322975 ACTGAGTCGCCTGCTGATTT 59.677 50.000 0.00 0.00 0.00 2.17
2080 2534 4.117685 GTGGTTTTAGTTCTGTGTCGACT 58.882 43.478 17.92 0.00 0.00 4.18
2087 2541 3.616219 TGCAGTGTGGTTTTAGTTCTGT 58.384 40.909 0.00 0.00 0.00 3.41
2099 2553 0.031178 GCCTTTGTCTTGCAGTGTGG 59.969 55.000 0.00 0.00 0.00 4.17
2104 2558 1.870055 ATGGCGCCTTTGTCTTGCAG 61.870 55.000 29.70 0.00 0.00 4.41
2119 2573 3.440173 TCAAAATTCGTCTTCCTGATGGC 59.560 43.478 0.00 0.00 32.70 4.40
2120 2574 5.182001 AGTTCAAAATTCGTCTTCCTGATGG 59.818 40.000 0.00 0.00 32.70 3.51
2224 2683 1.209019 AGTGAGATCAGATTTGCCGCT 59.791 47.619 0.00 0.00 0.00 5.52
2238 2697 7.176690 TGTTCTCATACAGAATACACAGTGAGA 59.823 37.037 7.81 0.00 43.33 3.27
2239 2698 7.315890 TGTTCTCATACAGAATACACAGTGAG 58.684 38.462 7.81 0.00 43.33 3.51
2242 2701 7.896811 TCTTGTTCTCATACAGAATACACAGT 58.103 34.615 0.00 0.00 43.33 3.55
2374 2878 1.098050 CAATAGTCACCTTGCTGCCC 58.902 55.000 0.00 0.00 0.00 5.36
2451 2964 1.710013 ATCAACCACTAGTCGTTGCG 58.290 50.000 23.72 6.45 39.36 4.85
2563 3076 3.005155 GTGTGATGCTGAAGCCTTCTTTT 59.995 43.478 5.96 0.00 41.18 2.27
2565 3078 2.157738 GTGTGATGCTGAAGCCTTCTT 58.842 47.619 5.96 0.00 41.18 2.52
2585 3112 4.431986 CGCGTCTTTCTGAATGCAAAATTG 60.432 41.667 0.00 0.00 0.00 2.32
2587 3114 3.058293 TCGCGTCTTTCTGAATGCAAAAT 60.058 39.130 5.77 0.00 0.00 1.82
2591 3118 0.790207 GTCGCGTCTTTCTGAATGCA 59.210 50.000 5.77 0.00 0.00 3.96
2592 3119 0.095417 GGTCGCGTCTTTCTGAATGC 59.905 55.000 5.77 0.00 0.00 3.56
2621 3148 5.081032 TCCCACGGGATTTTGTTTCTTTAT 58.919 37.500 0.00 0.00 39.76 1.40
2622 3149 4.471548 TCCCACGGGATTTTGTTTCTTTA 58.528 39.130 0.00 0.00 39.76 1.85
2647 3185 1.202806 GGGCATCGGATCTGATTTCCA 60.203 52.381 23.90 0.00 32.45 3.53


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

AutoCloner maintained by Alex Coulton.