Locus 2302

Sequence ID X_DroMel_CAF1
Location 6,232,117 – 6,232,266
Length 149
Max. P 0.991579
window3729 window3730 window3731

overview

Window 9

Location 6,232,117 – 6,232,226
Length 109
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.75
Mean single sequence MFE -36.17
Consensus MFE -22.52
Energy contribution -23.58
Covariance contribution 1.06
Combinations/Pair 1.07
Mean z-score -2.77
Structure conservation index 0.62
SVM decision value 1.05
SVM RNA-class probability 0.906413
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6232117 109 + 22224390
---------UAUGGUUCGAUG--GUGUAUGGUUGUGGAUAUGUGGUUAUAUCCAGCUUGCCUGCACCAAAUUAUUGCCUUUUACAAUUACAAUUGUAAUUGAGAAUGAGAGUUUUACGGC
---------..........((--(((((.(((.(((((((((....)))))))).)..)))))))))).......(((.....(((((((....)))))))(((((....)))))..))) ( -34.50)
>DroSec_CAF1 5163 116 + 1
UG----GGGAAUGGUUCGAGGGGGCGUAGGGUUGUGGAUAUGUGGUUAUAUCCAGCUCGCCUGCACCAAAUUAUUGCCUUUUACAAUUACAAUUGUAAUUGAGAAUGAGAGUUUUACGAC
.(----((.(((((((.(.(.(((((...(((..((((((((....)))))))))))))))).)..).))))))).)))....(((((((....)))))))(((((....)))))..... ( -34.60)
>DroSim_CAF1 7235 116 + 1
UG----GGGAAUGGUUCGUGGGGGCGUGGGGUUGUGGAUAUGUGGUUAUAUCCAGCUCGCCUGCACCAAAUUAUUGCCUUUUACAAUUACAAUUGUAAUUGAGAAUGAGAGUUUUACGGC
.(----((.(((((((.(((.(((((...(((..((((((((....)))))))))))))))).)))..))))))).)))....(((((((....)))))))(((((....)))))..... ( -39.20)
>DroYak_CAF1 12605 110 + 1
GGGAAUGGGAAUGGUGCG--GUGGCGUAUGGUUGUGGAUU--------CAUGCAACUCGCCUGCGCCAAAUUAUUGCCUUUUACAAUUACAAUUGUAAUUGAGAAUGAGAGUUUUACGGC
((.(((((...(((((((--..((((...(((((((....--------..))))))))))))))))))..))))).)).....(((((((....)))))))(((((....)))))..... ( -36.40)
>consensus
UG____GGGAAUGGUUCGAGGGGGCGUAGGGUUGUGGAUAUGUGGUUAUAUCCAGCUCGCCUGCACCAAAUUAUUGCCUUUUACAAUUACAAUUGUAAUUGAGAAUGAGAGUUUUACGGC
............(((.......((((((.(((..((((((((....))))))))....)))))))))........))).....(((((((....)))))))................... (-22.52 = -23.58 +   1.06)

alignment

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secondary structure

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Window 0

Location 6,232,117 – 6,232,226
Length 109
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.75
Mean single sequence MFE -22.48
Consensus MFE -16.92
Energy contribution -17.18
Covariance contribution 0.25
Combinations/Pair 1.11
Mean z-score -2.16
Structure conservation index 0.75
SVM decision value 1.10
SVM RNA-class probability 0.915718
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6232117 109 - 22224390
GCCGUAAAACUCUCAUUCUCAAUUACAAUUGUAAUUGUAAAAGGCAAUAAUUUGGUGCAGGCAAGCUGGAUAUAACCACAUAUCCACAACCAUACAC--CAUCGAACCAUA---------
((((.....).....((..(((((((....)))))))..)).))).......(((((..((...(.(((((((......))))))))..))...)))--))..........--------- ( -22.30)
>DroSec_CAF1 5163 116 - 1
GUCGUAAAACUCUCAUUCUCAAUUACAAUUGUAAUUGUAAAAGGCAAUAAUUUGGUGCAGGCGAGCUGGAUAUAACCACAUAUCCACAACCCUACGCCCCCUCGAACCAUUCCC----CA
.(((...........((..(((((((....)))))))..))............((((.(((.(...(((((((......)))))))...)))).))))....))).........----.. ( -22.20)
>DroSim_CAF1 7235 116 - 1
GCCGUAAAACUCUCAUUCUCAAUUACAAUUGUAAUUGUAAAAGGCAAUAAUUUGGUGCAGGCGAGCUGGAUAUAACCACAUAUCCACAACCCCACGCCCCCACGAACCAUUCCC----CA
((((.....).....((..(((((((....)))))))..)).)))......((.(((..((((.(.(((((((......)))))))......).))))..))).))........----.. ( -23.90)
>DroYak_CAF1 12605 110 - 1
GCCGUAAAACUCUCAUUCUCAAUUACAAUUGUAAUUGUAAAAGGCAAUAAUUUGGCGCAGGCGAGUUGCAUG--------AAUCCACAACCAUACGCCAC--CGCACCAUUCCCAUUCCC
((((.....).....((..(((((((....)))))))..)).))).......(((.((.((((.((((..((--------....))))))....))))..--.)).)))........... ( -21.50)
>consensus
GCCGUAAAACUCUCAUUCUCAAUUACAAUUGUAAUUGUAAAAGGCAAUAAUUUGGUGCAGGCGAGCUGGAUAUAACCACAUAUCCACAACCAUACGCCCCCUCGAACCAUUCCC____CA
((((.....).....((..(((((((....)))))))..)).)))........((((..((...(.(((((((......))))))))..))...))))...................... (-16.92 = -17.18 +   0.25)

alignment

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secondary structure

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Window 1

Location 6,232,146 – 6,232,266
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.05
Mean single sequence MFE -30.10
Consensus MFE -27.42
Energy contribution -27.42
Covariance contribution 0.00
Combinations/Pair 1.09
Mean z-score -2.63
Structure conservation index 0.91
SVM decision value 2.28
SVM RNA-class probability 0.991579
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6232146 120 - 22224390
ACGCCGUUUUCCAUGUACCACGCACCCACUGUUAAAUUCAGCCGUAAAACUCUCAUUCUCAAUUACAAUUGUAAUUGUAAAAGGCAAUAAUUUGGUGCAGGCAAGCUGGAUAUAACCACA
...((((((.((.(((((((.(((.....)))........((((.....).....((..(((((((....)))))))..)).))).......))))))))).)))).))........... ( -24.80)
>DroSec_CAF1 5199 119 - 1
ACGCCGUUCGCCAUGUACCACGCAC-UACUGUUAAAUUCAGUCGUAAAACUCUCAUUCUCAAUUACAAUUGUAAUUGUAAAAGGCAAUAAUUUGGUGCAGGCGAGCUGGAUAUAACCACA
...(((((((((.(((((((...((-.((((.......)))).))..........((..(((((((....)))))))..))...........)))))))))))))).))........... ( -34.00)
>DroSim_CAF1 7271 119 - 1
ACGCCGUUCGCCAUGUACCACGCAC-CACUGUUAAAUUCAGCCGUAAAACUCUCAUUCUCAAUUACAAUUGUAAUUGUAAAAGGCAAUAAUUUGGUGCAGGCGAGCUGGAUAUAACCACA
...(((((((((.(((((((.(((.-...)))........((((.....).....((..(((((((....)))))))..)).))).......)))))))))))))).))........... ( -33.20)
>DroYak_CAF1 12643 111 - 1
ACGCCGUUCGCCAUGUACCACGCAC-CACUGUUAAACUCAGCCGUAAAACUCUCAUUCUCAAUUACAAUUGUAAUUGUAAAAGGCAAUAAUUUGGCGCAGGCGAGUUGCAUG--------
..((..((((((.((..(((.(((.-...)))........((((.....).....((..(((((((....)))))))..)).))).......)))..))))))))..))...-------- ( -28.40)
>consensus
ACGCCGUUCGCCAUGUACCACGCAC_CACUGUUAAAUUCAGCCGUAAAACUCUCAUUCUCAAUUACAAUUGUAAUUGUAAAAGGCAAUAAUUUGGUGCAGGCGAGCUGGAUAUAACCACA
...(((((((((.(((((((.(((.....)))........((((.....).....((..(((((((....)))))))..)).))).......)))))))))))))).))........... (-27.42 = -27.42 +   0.00)

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 10:31:02 2006