Locus 1625

Sequence ID X_DroMel_CAF1
Location 4,636,931 – 4,637,122
Length 191
Max. P 0.747318
window2663 window2664 window2665

overview

Window 3

Location 4,636,931 – 4,637,045
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.22
Mean single sequence MFE -19.82
Consensus MFE -16.12
Energy contribution -16.12
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.59
Structure conservation index 0.81
SVM decision value 0.11
SVM RNA-class probability 0.588520
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4636931 114 + 22224390
AAUCUGGCAACA------GCAACAAAGUGAAUAAAGUGAUGACAAAAGUAAACUGUAUCCAAAACAAAACCCCAAUGAAGUUUAUGAUUUCGAUUCUGCUCAACUAGAGAAUCGAAUUCA
...(((....))------)............................(((((((........................)))))))((.(((((((((.((.....))))))))))).)). ( -19.86)
>DroSec_CAF1 23067 114 + 1
AAUCUGGCAACA------GCAACAAAGUGAAUAAAGUGAUGACAAAAGUAAACUGUAUCCAAAACAAAACCCCAAUGAAGUUUAUGAUUUCGAUUCUGCUCAACUAGAGAAUCGAAUUCA
...(((....))------)............................(((((((........................)))))))((.(((((((((.((.....))))))))))).)). ( -19.86)
>DroSim_CAF1 4686 114 + 1
AAUCUGGCAACA------GCAACAAAGUGAAUAAAGUGAUGACAAAAGUAAACUGUAUCCAAAACAAAACCCCAAUGAAGUUUAUGAUUUCGAUUCUGCUCAACUAGAGAAUCGAAUUCA
...(((....))------)............................(((((((........................)))))))((.(((((((((.((.....))))))))))).)). ( -19.86)
>DroEre_CAF1 21135 114 + 1
AAUCUGGCAACA------GCAACAAAGUGAAUAAAGUGAUGACAAAAGUAAACUGUAUCCAAAACAAAACCCCAAUGAAGUUUAUGAUUUCGAUUCUGUUCAACUAGAGAAUCGAAUUCA
...(((....))------)............................(((((((........................)))))))((.(((((((((.(......).))))))))).)). ( -20.56)
>DroYak_CAF1 22459 120 + 1
AAUCUGGCAACAGCAACAGCAACAAAGUGAAUAAAGUGAUGACAAAAGUAAACUGUAUCCAAAACAAACCCAUAAUGAAGUUUAUGAUUUCGAUUCUGCCCAACUAGAGAAUCGAAUUCA
...(((....)))..................................(((((((........................)))))))((.(((((((((..........))))))))).)). ( -18.96)
>consensus
AAUCUGGCAACA______GCAACAAAGUGAAUAAAGUGAUGACAAAAGUAAACUGUAUCCAAAACAAAACCCCAAUGAAGUUUAUGAUUUCGAUUCUGCUCAACUAGAGAAUCGAAUUCA
....((....))...................................(((((((........................)))))))((.(((((((((..........))))))))).)). (-16.12 = -16.12 +  -0.00)

alignment

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secondary structure

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Window 4

Location 4,637,005 – 4,637,122
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.49
Mean single sequence MFE -23.36
Consensus MFE -17.60
Energy contribution -18.08
Covariance contribution 0.48
Combinations/Pair 1.04
Mean z-score -1.92
Structure conservation index 0.75
SVM decision value 0.47
SVM RNA-class probability 0.747318
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4637005 117 + 22224390
UUUAUGAUUUCGAUUCUGCUCAACUAGAGAAUCGAAUUCAACUGUAGGUAUAUUAACAUUGAAUGCAAUUC-GUGCAGAGG--GCACACAACUAAAUUGUACAAUACAAAAAAUAUAUAA
....(((.(((((((((.((.....))))))))))).)))..((((.(((((........((((...))))-((((.....--))))..........)))))..))))............ ( -24.10)
>DroSec_CAF1 23141 115 + 1
UUUAUGAUUUCGAUUCUGCUCAACUAGAGAAUCGAAUUCAACUGUAGGUAUAUUAGCAUUGAAUGCAAUUC-GUGCAGAGGGAGCACACAACUAAACUGUACAAUAAAA----AAUAUAA
....(((.(((((((((.((.....))))))))))).)))........((((((.((((...)))).....-((((((....((.......))...)))))).......----)))))). ( -24.90)
>DroSim_CAF1 4760 115 + 1
UUUAUGAUUUCGAUUCUGCUCAACUAGAGAAUCGAAUUCAACUGUAGGUAUAUUAACAUUGAAUGCGAUUC-GUGCAGAGGGAGCACACAACUAAACUGUACAAUAAAA----AAUAUAA
....(((.(((((((((.((.....))))))))))).))).......(((((......(((..(((..(((-.....)))...)))..)))......))))).......----....... ( -22.50)
>DroEre_CAF1 21209 114 + 1
UUUAUGAUUUCGAUUCUGUUCAACUAGAGAAUCGAAUUCAACUGUAGGUAUAUUAACAUUGAAUGCAAUUCAAUGCAGAGG--GCACGAAACUAAAUUGUACAAUAAAA----UAAAAAA
....(((.(((((((((.(......).))))))))).))).......(((((....((((((((...))))))))....((--........))....))))).......----....... ( -22.30)
>DroYak_CAF1 22539 113 + 1
UUUAUGAUUUCGAUUCUGCCCAACUAGAGAAUCGAAUUCAACUGUAGGUAUAUUAACAUUGCAUGCCAUUC-AUGCUGAGG--GCACAAAACUAAACUGUACAAUAAAA----UAUAUAA
....(((.(((((((((..........))))))))).))).......(((((((...((((..((((.(((-.....))))--)))....((......)).))))..))----))))).. ( -23.00)
>consensus
UUUAUGAUUUCGAUUCUGCUCAACUAGAGAAUCGAAUUCAACUGUAGGUAUAUUAACAUUGAAUGCAAUUC_GUGCAGAGG__GCACACAACUAAACUGUACAAUAAAA____UAUAUAA
....(((.(((((((((..........))))))))).))).......(((((.....((((....))))...((((.......))))..........))))).................. (-17.60 = -18.08 +   0.48)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,637,005 – 4,637,122
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.49
Mean single sequence MFE -23.60
Consensus MFE -18.86
Energy contribution -19.06
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -1.58
Structure conservation index 0.80
SVM decision value 0.43
SVM RNA-class probability 0.732014
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4637005 117 - 22224390
UUAUAUAUUUUUUGUAUUGUACAAUUUAGUUGUGUGC--CCUCUGCAC-GAAUUGCAUUCAAUGUUAAUAUACCUACAGUUGAAUUCGAUUCUCUAGUUGAGCAGAAUCGAAAUCAUAAA
...((((((..(((...((((((((...)))))((((--.....))))-.....)))..)))....))))))........(((.(((((((((((.....)).))))))))).))).... ( -23.60)
>DroSec_CAF1 23141 115 - 1
UUAUAUU----UUUUAUUGUACAGUUUAGUUGUGUGCUCCCUCUGCAC-GAAUUGCAUUCAAUGCUAAUAUACCUACAGUUGAAUUCGAUUCUCUAGUUGAGCAGAAUCGAAAUCAUAAA
.((((((----...(((((...(((.(((((.(((((.......))))-)))))).))))))))..))))))........(((.(((((((((((.....)).))))))))).))).... ( -24.60)
>DroSim_CAF1 4760 115 - 1
UUAUAUU----UUUUAUUGUACAGUUUAGUUGUGUGCUCCCUCUGCAC-GAAUCGCAUUCAAUGUUAAUAUACCUACAGUUGAAUUCGAUUCUCUAGUUGAGCAGAAUCGAAAUCAUAAA
.((((((----...(((((.((((.....))))((((.......))))-..........)))))..))))))........(((.(((((((((((.....)).))))))))).))).... ( -23.80)
>DroEre_CAF1 21209 114 - 1
UUUUUUA----UUUUAUUGUACAAUUUAGUUUCGUGC--CCUCUGCAUUGAAUUGCAUUCAAUGUUAAUAUACCUACAGUUGAAUUCGAUUCUCUAGUUGAACAGAAUCGAAAUCAUAAA
.......----....((((((.......((.....))--.....(((((((((...))))))))).........))))))(((.(((((((((..........))))))))).))).... ( -19.60)
>DroYak_CAF1 22539 113 - 1
UUAUAUA----UUUUAUUGUACAGUUUAGUUUUGUGC--CCUCAGCAU-GAAUGGCAUGCAAUGUUAAUAUACCUACAGUUGAAUUCGAUUCUCUAGUUGGGCAGAAUCGAAAUCAUAAA
...((((----((.(((((((..(((....((..(((--.....))).-.)).))).)))))))..))))))........(((.(((((((((((.....)).))))))))).))).... ( -26.40)
>consensus
UUAUAUA____UUUUAUUGUACAGUUUAGUUGUGUGC__CCUCUGCAC_GAAUUGCAUUCAAUGUUAAUAUACCUACAGUUGAAUUCGAUUCUCUAGUUGAGCAGAAUCGAAAUCAUAAA
...............((((((..(((..((((.((((....((......))...)))).))))...))).....))))))(((.(((((((((((.....)).))))))))).))).... (-18.86 = -19.06 +   0.20)

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 10:15:03 2006