Locus 5608

Sequence ID 3L_DroMel_CAF1
Location 15,381,130 – 15,381,220
Length 90
Max. P 0.941484
window8864 window8865

overview

Window 4

Location 15,381,130 – 15,381,220
Length 90
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 87.09
Mean single sequence MFE -24.10
Consensus MFE -19.60
Energy contribution -20.35
Covariance contribution 0.75
Combinations/Pair 1.08
Mean z-score -3.17
Structure conservation index 0.81
SVM decision value 1.32
SVM RNA-class probability 0.941484
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15381130 90 + 23771897
-----UGCAGCGGUGCUUAAACAAUUUAAUUUUGAUUUAAGUGCGAAAUUAAAUGUCAGGCUAUUCUGAAAUUUUAUCCC-CACACUGCUGCUUUG
-----.(((((((((........(((((((((((((....)).))))))))))).(((((....)))))...........-..))))))))).... ( -25.70)
>DroSec_CAF1 112891 90 + 1
-----UGCAGCGGUGCUUAAACAAUUUAAUUUUGAUUUAAGUGCGAAAUUAAAUGUCAGGCUAUUCUGACAUUUUACCCC-CACACUCCUGCUUUG
-----.((((.((..(((((((((.......))).))))))..)......((((((((((....))))))))))......-......))))).... ( -24.10)
>DroSim_CAF1 115233 90 + 1
-----UGCAGCGGUGCUUAAACAAUUUAAUUUUGAUUUAAGUGCGAAAUUAAAUGUCAGGCUAUUCUGACAUUUUACCCC-CACACUCCUGCUUUG
-----.((((.((..(((((((((.......))).))))))..)......((((((((((....))))))))))......-......))))).... ( -24.10)
>DroEre_CAF1 113729 88 + 1
-----UGCAGCGGUGCUUAAACAAUUUAAUUUUGAUUUAAGUGCGAAAUUAAAUGUCAGGCCAUUCUGACAUUUU-CC-C-CGCACUCCUGCCUCC
-----.((((.(((((((((((((.......))).)))))))(((.....((((((((((....)))))))))).-..-.-)))))).)))).... ( -27.60)
>DroYak_CAF1 116300 89 + 1
-----UGCAGCGGUGCUUAAACAAUUUAAUUUUGAUUUAAGUGCGAAAUUAAAUGUCAGGCUAUUCUGACAUUUU-CCAC-CACACUCCUGCCUCG
-----.((((.((..(((((((((.......))).))))))..)......((((((((((....)))))))))).-....-......))))).... ( -23.70)
>DroAna_CAF1 259455 94 + 1
GCAGCUGCAGCGGUGCUUAAACAAUUUAAUUUUGAUUUAAGUACGAAAUUAAAUGUCAGGAAAAUGCGCUUUCUUUCCUCUCUAAUAUCUGCU--G
.......(((((((((((((((((.......))).)))))))))((.((((...(..((((((..........))))))..))))).))))))--) ( -19.40)
>consensus
_____UGCAGCGGUGCUUAAACAAUUUAAUUUUGAUUUAAGUGCGAAAUUAAAUGUCAGGCUAUUCUGACAUUUUACCCC_CACACUCCUGCUUUG
......((((..((((((((((((.......))).)))))))))......((((((((((....))))))))))..............)))).... (-19.60 = -20.35 +   0.75)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,381,130 – 15,381,220
Length 90
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 87.09
Mean single sequence MFE -26.22
Consensus MFE -17.90
Energy contribution -19.32
Covariance contribution 1.42
Combinations/Pair 1.20
Mean z-score -3.47
Structure conservation index 0.68
SVM decision value 0.09
SVM RNA-class probability 0.578957
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15381130 90 - 23771897
CAAAGCAGCAGUGUG-GGGAUAAAAUUUCAGAAUAGCCUGACAUUUAAUUUCGCACUUAAAUCAAAAUUAAAUUGUUUAAGCACCGCUGCA-----
....(((((.(((((-(..((.((((.((((......)))).)))).))..).))((((((.(((.......)))))))))))).))))).----- ( -24.40)
>DroSec_CAF1 112891 90 - 1
CAAAGCAGGAGUGUG-GGGGUAAAAUGUCAGAAUAGCCUGACAUUUAAUUUCGCACUUAAAUCAAAAUUAAAUUGUUUAAGCACCGCUGCA-----
....(((((((((((-..(...(((((((((......)))))))))..)..)))))))...............(((....)))...)))).----- ( -29.20)
>DroSim_CAF1 115233 90 - 1
CAAAGCAGGAGUGUG-GGGGUAAAAUGUCAGAAUAGCCUGACAUUUAAUUUCGCACUUAAAUCAAAAUUAAAUUGUUUAAGCACCGCUGCA-----
....(((((((((((-..(...(((((((((......)))))))))..)..)))))))...............(((....)))...)))).----- ( -29.20)
>DroEre_CAF1 113729 88 - 1
GGAGGCAGGAGUGCG-G-GG-AAAAUGUCAGAAUGGCCUGACAUUUAAUUUCGCACUUAAAUCAAAAUUAAAUUGUUUAAGCACCGCUGCA-----
....(((((((((((-.-.(-.(((((((((......)))))))))..)..)))))))...............(((....)))...)))).----- ( -29.60)
>DroYak_CAF1 116300 89 - 1
CGAGGCAGGAGUGUG-GUGG-AAAAUGUCAGAAUAGCCUGACAUUUAAUUUCGCACUUAAAUCAAAAUUAAAUUGUUUAAGCACCGCUGCA-----
....(((((((((((-(...-.(((((((((......)))))))))....))))))))...............(((....)))...)))).----- ( -26.60)
>DroAna_CAF1 259455 94 - 1
C--AGCAGAUAUUAGAGAGGAAAGAAAGCGCAUUUUCCUGACAUUUAAUUUCGUACUUAAAUCAAAAUUAAAUUGUUUAAGCACCGCUGCAGCUGC
(--(((.((.((((((.(((((((........)))))))....)))))).))((.((((((.(((.......))))))))).)).))))....... ( -18.30)
>consensus
CAAAGCAGGAGUGUG_GGGGUAAAAUGUCAGAAUAGCCUGACAUUUAAUUUCGCACUUAAAUCAAAAUUAAAUUGUUUAAGCACCGCUGCA_____
....(((((((((((.((....(((((((((......)))))))))..)).)))))))...............(((....)))...))))...... (-17.90 = -19.32 +   1.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:33 2006