Locus 6625

Sequence ID 2R_DroMel_CAF1
Location 20,714,261 – 20,714,420
Length 159
Max. P 0.999948
window10549 window10550 window10551 window10552

overview

Window 9

Location 20,714,261 – 20,714,380
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.66
Mean single sequence MFE -37.16
Consensus MFE -35.64
Energy contribution -36.24
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.92
Structure conservation index 0.96
SVM decision value 4.47
SVM RNA-class probability 0.999904
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20714261 119 + 20766785
UGCUGCUGCUUUUUCUGUCAAA-AAAUAAGGGGAAAAGCAACGAAAAAGCAAAUGGGUUGGCAGCAUAGGGUUGGUGUGGUUCGCACCACCACAAGGAUUACUUGUGGGAGAAGAGGGUA
((((((((((((((((.(....-.....).)))))))))........(((......))))))))))......(((((((...)))))))(((((((.....)))))))............ ( -39.10)
>DroSec_CAF1 147851 120 + 1
UGCUGCUGCUUUUUCUGUCAAAAAAAUAAGGGGAAAAGCAACGAAAAAGCAAAUGGGUUGGCAGCAUAGGGUUGGUGUGGUUCGCACCACCACAAGGGUUACUUGUGGGAGAAGAGGGUA
((((((((((((((((.(..........).)))))))))........(((......))))))))))......(((((((...)))))))(((((((.....)))))))............ ( -39.00)
>DroSim_CAF1 152920 120 + 1
UGCUGCUGCUUUUUCUGUCAAAAAAAUAAGGGGAAAAGCAACGAAAAAGCAAAUGGGUUGGCAGCAUAGGGUUGGUGUGGUUCGCACCACCACAAGGGUUACUUGUGGGAGAAGAGGGUA
((((((((((((((((.(..........).)))))))))........(((......))))))))))......(((((((...)))))))(((((((.....)))))))............ ( -39.00)
>DroEre_CAF1 188982 119 + 1
UGCUGCUGCUUUUUCUGUCAAA-AAAUAAGGGGAAAAGCAACGAAAAAGCAAAUGGGUUGACAGCAUGGGGUUGGUGUGGUUCGCACCACCACAAGGGUUACUUGUGGGAGAAGAGGGUA
(((((.((((((((((.(....-.....).)))))))))).......(((......)))..)))))......(((((((...)))))))(((((((.....)))))))............ ( -34.90)
>DroYak_CAF1 153902 118 + 1
UGCUGCUGCUU-UUCUGUCAAA-AAAUAAGGGGAAAAGCAACGAAAAAGCAAAUGGGUUGACAGCAUAGGGUUGGUGUGGUUUGCACCACCACAAGGGUUACUUGUGGGAGAAGAGGGUA
(((((.(((((-((((.(....-......).))))))))).......(((......)))..)))))......((((((.....))))))(((((((.....)))))))............ ( -33.80)
>consensus
UGCUGCUGCUUUUUCUGUCAAA_AAAUAAGGGGAAAAGCAACGAAAAAGCAAAUGGGUUGGCAGCAUAGGGUUGGUGUGGUUCGCACCACCACAAGGGUUACUUGUGGGAGAAGAGGGUA
((((((((((((((((.(..........).)))))))))........(((......))))))))))......((((((.....))))))(((((((.....)))))))............ (-35.64 = -36.24 +   0.60)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,714,261 – 20,714,380
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.66
Mean single sequence MFE -30.40
Consensus MFE -30.27
Energy contribution -30.23
Covariance contribution -0.04
Combinations/Pair 1.03
Mean z-score -4.03
Structure conservation index 1.00
SVM decision value 4.77
SVM RNA-class probability 0.999948
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20714261 119 - 20766785
UACCCUCUUCUCCCACAAGUAAUCCUUGUGGUGGUGCGAACCACACCAACCCUAUGCUGCCAACCCAUUUGCUUUUUCGUUGCUUUUCCCCUUAUUU-UUUGACAGAAAAAGCAGCAGCA
............(((((((.....)))))))(((((.......)))))......((((((.........((((((((((((................-...))).))))))))))))))) ( -31.21)
>DroSec_CAF1 147851 120 - 1
UACCCUCUUCUCCCACAAGUAACCCUUGUGGUGGUGCGAACCACACCAACCCUAUGCUGCCAACCCAUUUGCUUUUUCGUUGCUUUUCCCCUUAUUUUUUUGACAGAAAAAGCAGCAGCA
............(((((((.....)))))))(((((.......)))))......((((((.........((((((((((((....................))).))))))))))))))) ( -31.15)
>DroSim_CAF1 152920 120 - 1
UACCCUCUUCUCCCACAAGUAACCCUUGUGGUGGUGCGAACCACACCAACCCUAUGCUGCCAACCCAUUUGCUUUUUCGUUGCUUUUCCCCUUAUUUUUUUGACAGAAAAAGCAGCAGCA
............(((((((.....)))))))(((((.......)))))......((((((.........((((((((((((....................))).))))))))))))))) ( -31.15)
>DroEre_CAF1 188982 119 - 1
UACCCUCUUCUCCCACAAGUAACCCUUGUGGUGGUGCGAACCACACCAACCCCAUGCUGUCAACCCAUUUGCUUUUUCGUUGCUUUUCCCCUUAUUU-UUUGACAGAAAAAGCAGCAGCA
............(((((((.....)))))))(((((.......)))))......((((((.........((((((((((((................-...))).))))))))))))))) ( -29.81)
>DroYak_CAF1 153902 118 - 1
UACCCUCUUCUCCCACAAGUAACCCUUGUGGUGGUGCAAACCACACCAACCCUAUGCUGUCAACCCAUUUGCUUUUUCGUUGCUUUUCCCCUUAUUU-UUUGACAGAA-AAGCAGCAGCA
............(((((((.....)))))))(((((.......)))))......(((((.(((.....))))......((((((((((...(((...-..)))..)))-))))))))))) ( -28.70)
>consensus
UACCCUCUUCUCCCACAAGUAACCCUUGUGGUGGUGCGAACCACACCAACCCUAUGCUGCCAACCCAUUUGCUUUUUCGUUGCUUUUCCCCUUAUUU_UUUGACAGAAAAAGCAGCAGCA
............(((((((.....)))))))(((((.......)))))......((((((.........((((((((((((....................))).))))))))))))))) (-30.27 = -30.23 +  -0.04)

alignment

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secondary structure

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Window 1

Location 20,714,300 – 20,714,420
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.83
Mean single sequence MFE -31.10
Consensus MFE -30.24
Energy contribution -29.68
Covariance contribution -0.56
Combinations/Pair 1.10
Mean z-score -1.35
Structure conservation index 0.97
SVM decision value 0.88
SVM RNA-class probability 0.873673
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20714300 120 + 20766785
ACGAAAAAGCAAAUGGGUUGGCAGCAUAGGGUUGGUGUGGUUCGCACCACCACAAGGAUUACUUGUGGGAGAAGAGGGUAACAUGUCUAAAUUUGCUAAAAAUGAAGCGGACUAUCGAUU
.(((....((..((...(((((((..((((..(((((((...)))))))(((((((.....))))))).................))))...)))))))..))...))......)))... ( -31.00)
>DroSec_CAF1 147891 120 + 1
ACGAAAAAGCAAAUGGGUUGGCAGCAUAGGGUUGGUGUGGUUCGCACCACCACAAGGGUUACUUGUGGGAGAAGAGGGUAACAUGUCUAAAUUUGCUAAAAAUGAAGCGGACUAUCGAUU
.(((....((..((...(((((((..((((..(((((((...)))))))(((((((.....))))))).................))))...)))))))..))...))......)))... ( -31.00)
>DroSim_CAF1 152960 120 + 1
ACGAAAAAGCAAAUGGGUUGGCAGCAUAGGGUUGGUGUGGUUCGCACCACCACAAGGGUUACUUGUGGGAGAAGAGGGUAACAUGUCUAAAUUUGCUAAAAAUGAAGCGAACUAUCGAUU
.......(((((((.....((((.........(((((((...)))))))(((((((.....)))))))...............))))...)))))))..........(((....)))... ( -31.10)
>DroEre_CAF1 189021 120 + 1
ACGAAAAAGCAAAUGGGUUGACAGCAUGGGGUUGGUGUGGUUCGCACCACCACAAGGGUUACUUGUGGGAGAAGAGGGUAACAUGUAUAAAUUUGCUAAAAAUGAAGCGGACUAUCGAUU
.(((...(((((((..((.....(((((....(((((((...)))))))(((((((.....))))))).............)))))))..)))))))........((....)).)))... ( -31.60)
>DroYak_CAF1 153940 120 + 1
ACGAAAAAGCAAAUGGGUUGACAGCAUAGGGUUGGUGUGGUUUGCACCACCACAAGGGUUACUUGUGGGAGAAGAGGGUAACAUGUCUAAAUUUGCUAAAAAUGAAGCGGACUAUCGAUU
.(((...(((((((.....((((.........((((((.....))))))(((((((.....)))))))...............))))...)))))))........((....)).)))... ( -30.80)
>consensus
ACGAAAAAGCAAAUGGGUUGGCAGCAUAGGGUUGGUGUGGUUCGCACCACCACAAGGGUUACUUGUGGGAGAAGAGGGUAACAUGUCUAAAUUUGCUAAAAAUGAAGCGGACUAUCGAUU
.(((................(((.((......)).)))(((((((.(..(((((((.....)))))))..).....(((((.((......))))))).........))))))).)))... (-30.24 = -29.68 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,714,300 – 20,714,420
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.83
Mean single sequence MFE -23.24
Consensus MFE -21.66
Energy contribution -21.70
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.69
Structure conservation index 0.93
SVM decision value 1.66
SVM RNA-class probability 0.970782
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20714300 120 - 20766785
AAUCGAUAGUCCGCUUCAUUUUUAGCAAAUUUAGACAUGUUACCCUCUUCUCCCACAAGUAAUCCUUGUGGUGGUGCGAACCACACCAACCCUAUGCUGCCAACCCAUUUGCUUUUUCGU
...(((.(((..(((........))).....(((.((((.............(((((((.....)))))))(((((.......)))))....)))))))...........)))...))). ( -22.40)
>DroSec_CAF1 147891 120 - 1
AAUCGAUAGUCCGCUUCAUUUUUAGCAAAUUUAGACAUGUUACCCUCUUCUCCCACAAGUAACCCUUGUGGUGGUGCGAACCACACCAACCCUAUGCUGCCAACCCAUUUGCUUUUUCGU
...(((.(((..(((........))).....(((.((((.............(((((((.....)))))))(((((.......)))))....)))))))...........)))...))). ( -22.40)
>DroSim_CAF1 152960 120 - 1
AAUCGAUAGUUCGCUUCAUUUUUAGCAAAUUUAGACAUGUUACCCUCUUCUCCCACAAGUAACCCUUGUGGUGGUGCGAACCACACCAACCCUAUGCUGCCAACCCAUUUGCUUUUUCGU
...(((.(((..(((........))).....(((.((((.............(((((((.....)))))))(((((.......)))))....)))))))...........)))...))). ( -22.40)
>DroEre_CAF1 189021 120 - 1
AAUCGAUAGUCCGCUUCAUUUUUAGCAAAUUUAUACAUGUUACCCUCUUCUCCCACAAGUAACCCUUGUGGUGGUGCGAACCACACCAACCCCAUGCUGUCAACCCAUUUGCUUUUUCGU
....(((((...(((........))).........((((.............(((((((.....)))))))(((((.......)))))....)))))))))................... ( -24.70)
>DroYak_CAF1 153940 120 - 1
AAUCGAUAGUCCGCUUCAUUUUUAGCAAAUUUAGACAUGUUACCCUCUUCUCCCACAAGUAACCCUUGUGGUGGUGCAAACCACACCAACCCUAUGCUGUCAACCCAUUUGCUUUUUCGU
...(((.(((..(((........))).......((((.((............(((((((.....)))))))(((((.......))))).......)))))).........)))...))). ( -24.30)
>consensus
AAUCGAUAGUCCGCUUCAUUUUUAGCAAAUUUAGACAUGUUACCCUCUUCUCCCACAAGUAACCCUUGUGGUGGUGCGAACCACACCAACCCUAUGCUGCCAACCCAUUUGCUUUUUCGU
...(((.(((..(((........))).....(((.((((.............(((((((.....)))))))(((((.......)))))....)))))))...........)))...))). (-21.66 = -21.70 +   0.04)

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 12:15:32 2006