Locus 2104

Sequence ID 3L_DroMel_CAF1
Location 5,764,164 – 5,764,274
Length 110
Max. P 0.975798
window3273 window3274

overview

Window 3

Location 5,764,164 – 5,764,274
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.32
Mean single sequence MFE -22.48
Consensus MFE -18.20
Energy contribution -18.60
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.20
Structure conservation index 0.81
SVM decision value 1.76
SVM RNA-class probability 0.975798
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5764164 110 + 23771897
UACAUUUAGUUUUCAAAUGAAAUCAUUUAAAAAUA--GUUUGAUUUACAAAAACUAGAAGCUACAUAA--AAACCGCGUCACGAUCU-CGCGGCACUCAUAAUGAGAUGCUU-----UUG
........(((((.(((((....))))).)))))(--((((.........)))))((((((.......--...(((((.........-)))))..(((.....)))..))))-----)). ( -21.00)
>DroSec_CAF1 6728 107 + 1
UACAUUUAGUUUUCAAAUUAAAUCAUUUAAAAAUA--GUUUGAUUUACAAAAACUAGAAGCUACA-----AAACCGCGUGACGAUCU-CGCGGCACUCAUAAUGAGAUGCUU-----UUA
......(((((((.(((((((((.(((....))).--)))))))))...)))))))(((((....-----...(((((.(.....).-)))))..(((.....)))..))))-----).. ( -23.80)
>DroSim_CAF1 6585 110 + 1
UACAUUUAGUUUUCAAAUUAAAUCAUUUAAAAAUA--GUUUGAUUUACAAAAACUAGAAGCUACAUAA--AAACCGCGCGACGAUCU-CGCGGCACUCAUAAUGAGAUGCUU-----UUG
......(((((((.(((((((((.(((....))).--)))))))))...)))))))(((((.......--...(((((.(.....).-)))))..(((.....)))..))))-----).. ( -23.50)
>DroEre_CAF1 6676 109 + 1
UACAUUUAGUUUUCA-AUUAAAUCAUUUAAAAAUA--GUUUGAUUUACAAAAACUAGAAGCUACAUAA--AAACCGCGUCACGAUCU-CGCGGCACUCAUAAUGAGAUGCGU-----UUG
....(((((((((..-..(((((((..........--...)))))))..)))))))))..........--((((((((.........-))))((((((.....))).)))))-----)). ( -21.62)
>DroAna_CAF1 7213 120 + 1
UACAUUUAGUUUCCAAAUUAAAUCAUUUAAAAAUAGAGUUUGAUUUACAAAAACUAGAAGCUAAAUAAAAAAACCGCGAUAAGUUCUCCGCGGCACUCAUAAUGAGAUGCUUUUUUUUUG
...((((((((((.....(((((((...............))))))).........))))))))))(((((((.((((..........))))((((((.....))).)))..))))))). ( -22.50)
>consensus
UACAUUUAGUUUUCAAAUUAAAUCAUUUAAAAAUA__GUUUGAUUUACAAAAACUAGAAGCUACAUAA__AAACCGCGUCACGAUCU_CGCGGCACUCAUAAUGAGAUGCUU_____UUG
....(((((((((.....(((((((...............)))))))..))))))))).((............(((((..........)))))..(((.....)))..)).......... (-18.20 = -18.60 +   0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,764,164 – 5,764,274
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.32
Mean single sequence MFE -23.74
Consensus MFE -19.32
Energy contribution -19.56
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.57
Structure conservation index 0.81
SVM decision value 0.54
SVM RNA-class probability 0.776381
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5764164 110 - 23771897
CAA-----AAGCAUCUCAUUAUGAGUGCCGCG-AGAUCGUGACGCGGUUU--UUAUGUAGCUUCUAGUUUUUGUAAAUCAAAC--UAUUUUUAAAUGAUUUCAUUUGAAAACUAAAUGUA
(((-----((((.......((((((.((((((-.........)))))).)--))))).........)))))))..........--..((((((((((....))))))))))......... ( -23.29)
>DroSec_CAF1 6728 107 - 1
UAA-----AAGCAUCUCAUUAUGAGUGCCGCG-AGAUCGUCACGCGGUUU-----UGUAGCUUCUAGUUUUUGUAAAUCAAAC--UAUUUUUAAAUGAUUUAAUUUGAAAACUAAAUGUA
...-----..((((........(((.((..((-((((((.....))))))-----))..)))))((((((((.(((((((...--..........)))))))....)))))))).)))). ( -24.42)
>DroSim_CAF1 6585 110 - 1
CAA-----AAGCAUCUCAUUAUGAGUGCCGCG-AGAUCGUCGCGCGGUUU--UUAUGUAGCUUCUAGUUUUUGUAAAUCAAAC--UAUUUUUAAAUGAUUUAAUUUGAAAACUAAAUGUA
...-----..((((.....((((((.((((((-.(.....).)))))).)--))))).......((((((((.(((((((...--..........)))))))....)))))))).)))). ( -24.32)
>DroEre_CAF1 6676 109 - 1
CAA-----ACGCAUCUCAUUAUGAGUGCCGCG-AGAUCGUGACGCGGUUU--UUAUGUAGCUUCUAGUUUUUGUAAAUCAAAC--UAUUUUUAAAUGAUUUAAU-UGAAAACUAAAUGUA
...-----..((((.....((((((.((((((-.........)))))).)--))))).......((((((((.(((((((...--..........)))))))..-.)))))))).)))). ( -23.02)
>DroAna_CAF1 7213 120 - 1
CAAAAAAAAAGCAUCUCAUUAUGAGUGCCGCGGAGAACUUAUCGCGGUUUUUUUAUUUAGCUUCUAGUUUUUGUAAAUCAAACUCUAUUUUUAAAUGAUUUAAUUUGGAAACUAAAUGUA
...((((((((((.(((.....))))))(((((........))))).)))))))((((((.((((((......(((((((...............)))))))..)))))).))))))... ( -23.66)
>consensus
CAA_____AAGCAUCUCAUUAUGAGUGCCGCG_AGAUCGUCACGCGGUUU__UUAUGUAGCUUCUAGUUUUUGUAAAUCAAAC__UAUUUUUAAAUGAUUUAAUUUGAAAACUAAAUGUA
........((((..(((.....))).((((((..........))))))...........)))).((((((((.(((((((...............)))))))....))))))))...... (-19.32 = -19.56 +   0.24)

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 10:24:27 2006