Locus 5482

Sequence ID 2R_DroMel_CAF1
Location 17,641,516 – 17,641,716
Length 200
Max. P 0.888167
window8743 window8744 window8745 window8746

overview

Window 3

Location 17,641,516 – 17,641,636
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 77.50
Mean single sequence MFE -25.90
Consensus MFE -14.13
Energy contribution -14.69
Covariance contribution 0.56
Combinations/Pair 1.10
Mean z-score -2.52
Structure conservation index 0.55
SVM decision value 0.95
SVM RNA-class probability 0.888167
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17641516 120 - 20766785
ACAUCUGUUAGAUGGCGCCACUAAGCCAAGCUUAUCUUUAAGCUAAGACAGCGAAAAAGCUAGUUUUAAAUUUAAGCUUACAUCAAACCCGUUUCACCUUAGCGCAAACAUUAAGAGCAU
.((((.....))))((((...(((((...(((((....)))))(((((((((......))).)))))).......)))))....(((....))).......))))............... ( -24.50)
>DroSim_CAF1 938 114 - 1
CCAUCUGUUAGAUGGCGCCACUAAGCCAAGCUUGUCUUUAAGCUGAGACAGCAAAAAAGCUAGUUUCAAAUGAAAGCUUACAUCAAGCC-----CACCUUAACGCUAACAUUAAAA-AAU
.....((((((.((((........)))).(((((....((((((((((((((......))).))))).......))))))...))))).-----..........))))))......-... ( -29.41)
>DroYak_CAF1 6267 114 - 1
CCAUCUGUUAGAUGGCGCCACUUACCCGAGCUUGUCUUUUAGCUGAGACAACUAAAAAGCUAGUUUAAAAUUAAAGCUUAAUUUAAACCCGUUUGAAU------CGAGCACUACAAAAAA
(((((.....)))))............(((((.(..((((((.((...)).))))))..).))))).........(((..(((((((....)))))))------..)))........... ( -23.80)
>consensus
CCAUCUGUUAGAUGGCGCCACUAAGCCAAGCUUGUCUUUAAGCUGAGACAGCAAAAAAGCUAGUUUAAAAUUAAAGCUUACAUCAAACCCGUUUCACCUUA_CGCAAACAUUAAAA_AAU
....(((((...((((........))))((((((....))))))..))))).....(((((.............)))))......................................... (-14.13 = -14.69 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,641,556 – 17,641,676
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 86.67
Mean single sequence MFE -32.13
Consensus MFE -24.09
Energy contribution -24.87
Covariance contribution 0.79
Combinations/Pair 1.16
Mean z-score -1.83
Structure conservation index 0.75
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17641556 120 + 20766785
UAAGCUUAAAUUUAAAACUAGCUUUUUCGCUGUCUUAGCUUAAAGAUAAGCUUGGCUUAGUGGCGCCAUCUAACAGAUGUUCUGCUCAAUUUUCAUGACCAACAGAUGGCGUAGCUUAGG
((((((.....................(((((.((.((((((....)))))).))..)))))(((((((((..(((.....))).(((.......))).....))))))))))))))).. ( -32.90)
>DroSim_CAF1 972 120 + 1
UAAGCUUUCAUUUGAAACUAGCUUUUUUGCUGUCUCAGCUUAAAGACAAGCUUGGCUUAGUGGCGCCAUCUAACAGAUGGUUUGCUCAAUUUUCAUGCCCAACAGAUGGCGUAACUAUGG
((((((......(((.((.(((......))))).)))((((......))))..))))))((.(((((((((....(.(((...((...........))))).)))))))))).))..... ( -30.90)
>DroYak_CAF1 6301 120 + 1
UAAGCUUUAAUUUUAAACUAGCUUUUUAGUUGUCUCAGCUAAAAGACAAGCUCGGGUAAGUGGCGCCAUCUAACAGAUGGUCUGCUCAAAUUUCUUAGCCAACAGAUGGCGUAAGUGAGU
...(((.....((((..(.(((((((((((((...))))))))....))))).)..)))).)))((((((.....))))))..(((((.....((((((((.....)))).))))))))) ( -32.60)
>consensus
UAAGCUUUAAUUUAAAACUAGCUUUUUAGCUGUCUCAGCUUAAAGACAAGCUUGGCUUAGUGGCGCCAUCUAACAGAUGGUCUGCUCAAUUUUCAUGACCAACAGAUGGCGUAACUAAGG
(((((((............(((......)))((((........)))))))))))....(((.(((((((((....(.(((((..............))))).)))))))))).))).... (-24.09 = -24.87 +   0.79)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,641,556 – 17,641,676
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 86.67
Mean single sequence MFE -32.79
Consensus MFE -24.62
Energy contribution -24.73
Covariance contribution 0.12
Combinations/Pair 1.10
Mean z-score -2.71
Structure conservation index 0.75
SVM decision value 0.88
SVM RNA-class probability 0.872641
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17641556 120 - 20766785
CCUAAGCUACGCCAUCUGUUGGUCAUGAAAAUUGAGCAGAACAUCUGUUAGAUGGCGCCACUAAGCCAAGCUUAUCUUUAAGCUAAGACAGCGAAAAAGCUAGUUUUAAAUUUAAGCUUA
..((((((.(((((((((....(((.......)))((((.....)))))))))))))............(((((....)))))(((((((((......))).))))))......)))))) ( -34.50)
>DroSim_CAF1 972 120 - 1
CCAUAGUUACGCCAUCUGUUGGGCAUGAAAAUUGAGCAAACCAUCUGUUAGAUGGCGCCACUAAGCCAAGCUUGUCUUUAAGCUGAGACAGCAAAAAAGCUAGUUUCAAAUGAAAGCUUA
...((((..(((((((((.(((..................))).....)))))))))..))))(((..((((((....))))))((((((((......))).)))))........))).. ( -34.17)
>DroYak_CAF1 6301 120 - 1
ACUCACUUACGCCAUCUGUUGGCUAAGAAAUUUGAGCAGACCAUCUGUUAGAUGGCGCCACUUACCCGAGCUUGUCUUUUAGCUGAGACAACUAAAAAGCUAGUUUAAAAUUAAAGCUUA
.....((((.((((.....)))))))).....((.((.(.(((((.....)))))))))).......(((((((((((......)))))(((((......)))))........)))))). ( -29.70)
>consensus
CCUAAGUUACGCCAUCUGUUGGCCAUGAAAAUUGAGCAGACCAUCUGUUAGAUGGCGCCACUAAGCCAAGCUUGUCUUUAAGCUGAGACAGCAAAAAAGCUAGUUUAAAAUUAAAGCUUA
.........((((((((.......((....))..(((((.....)))))))))))))..........(((((((((((......)))))(((......)))............)))))). (-24.62 = -24.73 +   0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,641,596 – 17,641,716
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 73.86
Mean single sequence MFE -25.69
Consensus MFE -14.88
Energy contribution -14.77
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -1.67
Structure conservation index 0.58
SVM decision value 0.26
SVM RNA-class probability 0.658744
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17641596 120 - 20766785
AAAACAUAAAAUAUACAUGACAGCUAUCUACGUCCGCUGUCCUAAGCUACGCCAUCUGUUGGUCAUGAAAAUUGAGCAGAACAUCUGUUAGAUGGCGCCACUAAGCCAAGCUUAUCUUUA
..................((((((...........)))))).((((((..((((((((....(((.......)))((((.....))))))))))))((......))..))))))...... ( -30.20)
>DroSim_CAF1 1012 100 - 1
-------AAACUAUACAUGACAGC-------------UGUCCAUAGUUACGCCAUCUGUUGGGCAUGAAAAUUGAGCAAACCAUCUGUUAGAUGGCGCCACUAAGCCAAGCUUGUCUUUA
-------...........((((((-------------(...(.((((..(((((((((.(((..................))).....)))))))))..)))).)...))).)))).... ( -27.17)
>DroYak_CAF1 6341 112 - 1
AAAACAUAAUCUAUUCAUGUCACGUAU--------AAUACACUCACUUACGCCAUCUGUUGGCUAAGAAAUUUGAGCAGACCAUCUGUUAGAUGGCGCCACUUACCCGAGCUUGUCUUUU
...........................--------......(((.((((.((((.....)))))))).....((.((.(.(((((.....)))))))))).......))).......... ( -19.70)
>consensus
AAAACAUAAACUAUACAUGACAGCUAU__________UGUCCUAAGUUACGCCAUCUGUUGGCCAUGAAAAUUGAGCAGACCAUCUGUUAGAUGGCGCCACUAAGCCAAGCUUGUCUUUA
.................................................((((((((.......((....))..(((((.....)))))))))))))....................... (-14.88 = -14.77 +  -0.11)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:58 2006