Locus 6093

Sequence ID 3L_DroMel_CAF1
Location 16,177,870 – 16,178,003
Length 133
Max. P 0.815722
window9790 window9791

overview

Window 0

Location 16,177,870 – 16,177,963
Length 93
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 84.89
Mean single sequence MFE -16.67
Consensus MFE -11.20
Energy contribution -11.57
Covariance contribution 0.38
Combinations/Pair 1.10
Mean z-score -2.09
Structure conservation index 0.67
SVM decision value 0.66
SVM RNA-class probability 0.815722
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16177870 93 + 23771897
UUUCACCACUUUUUUUUUUGUUGUAACAAAUGUGACAUGCAGAGUG---GAGUAUGUUUUUUUGGCAUUGCUAUGCUUCGUUUAUUUUUGAACAUU
.....(((((((......(((..((.....))..)))...))))))---)((((((((.....)))).)))).......(((((....)))))... ( -17.80)
>DroSec_CAF1 35533 94 + 1
UUUCCCCACUUUUUU-UUUGUUUUAACAAAUGUGACAUGCA-AGUUUUUUUGUAUGUUUUUUUGGCAUUGCUAUGCUUCGUUUAUUUUUGAACAUU
...............-..........((((...((((((((-((....))))))))))..))))((((....))))...(((((....)))))... ( -18.60)
>DroSim_CAF1 38153 86 + 1
UUUCCCCACUCUUCU------UUUAACAAAUGUGACAUGCA-AGUG---GAGUAUGUUUUUUUGGCAUUGCUAUGCUUCGUUUAUUUUUAAACAUU
...............------.....((((...(((((((.-....---..)))))))..))))((((....))))...(((((....)))))... ( -15.00)
>DroEre_CAF1 35911 84 + 1
UUUCCCUCAUAUU-U------UUUAACAAAUGUGACGUGCA-AGUG---GAGUAUUUUUUUUU-GCAUUGCUAUGCUUCGCUUAUUUUUGAACAUU
......(((((((-(------......)))))))).....(-((((---((((((........-........)))))))))))............. ( -15.29)
>consensus
UUUCCCCACUUUUUU______UUUAACAAAUGUGACAUGCA_AGUG___GAGUAUGUUUUUUUGGCAUUGCUAUGCUUCGUUUAUUUUUGAACAUU
..........................((((...(((((((...........)))))))..))))((((....))))...(((((....)))))... (-11.20 = -11.57 +   0.38)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,177,891 – 16,178,003
Length 112
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 92.00
Mean single sequence MFE -26.32
Consensus MFE -19.75
Energy contribution -20.38
Covariance contribution 0.62
Combinations/Pair 1.06
Mean z-score -1.96
Structure conservation index 0.75
SVM decision value 0.20
SVM RNA-class probability 0.630905
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16177891 112 + 23771897
UGUAACAAAUGUGACAUGCAGAGUG---GAGUAUGUUUUUUUGGCAUUGCUAUGCUUCGUUUAUUUUUGAACAUUUUUUCGCAUUCGGAUGUUGUUUUUGACAGGUAAACGAACU
.....((((...(((((((......---..)))))))..))))((((....))))(((((((((((..(((((....((((....))))...))))).....))))))))))).. ( -25.60)
>DroSec_CAF1 35553 113 + 1
UUUAACAAAUGUGACAUGCA-AGUUUUUUUGUAUGUUUUUUUGGCAUUGCUAUGCUUCGUUUAUUUUUGAACAUUU-GUCGCAUUCGGAUGUUGUUUUUGACAGGUAAACGAACU
.....((((...((((((((-((....))))))))))..))))((((....))))(((((((((((...(((((((-(.......))))))))(((...)))))))))))))).. ( -29.30)
>DroSim_CAF1 38168 110 + 1
UUUAACAAAUGUGACAUGCA-AGUG---GAGUAUGUUUUUUUGGCAUUGCUAUGCUUCGUUUAUUUUUAAACAUUU-GUCGCAUUCGGAUGUUGUUUUUGACAGGUAAACGAACU
.....((((...(((((((.-....---..)))))))..))))((((....))))(((((((((((...(((((((-(.......))))))))(((...)))))))))))))).. ( -25.70)
>DroEre_CAF1 35925 109 + 1
UUUAACAAAUGUGACGUGCA-AGUG---GAGUAUUUUUUUUU-GCAUUGCUAUGCUUCGCUUAUUUUUGAACAUUU-GUCGUGUUCAGAUGUUGUUUUUGACAGGUAAACGAACU
.....((((.(..((((..(-((((---((((((........-........)))))))))))....((((((((..-...))))))))))))..).))))............... ( -24.69)
>consensus
UUUAACAAAUGUGACAUGCA_AGUG___GAGUAUGUUUUUUUGGCAUUGCUAUGCUUCGUUUAUUUUUGAACAUUU_GUCGCAUUCGGAUGUUGUUUUUGACAGGUAAACGAACU
.....((((...(((((((...........)))))))..))))((((....))))(((((((((((..(((((....(((.......)))..))))).....))))))))))).. (-19.75 = -20.38 +   0.62)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:09:53 2006