Locus 3213

Sequence ID 2L_DroMel_CAF1
Location 9,185,662 – 9,185,812
Length 150
Max. P 0.931803
window5105 window5106 window5107

overview

Window 5

Location 9,185,662 – 9,185,759
Length 97
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 89.15
Mean single sequence MFE -23.30
Consensus MFE -19.76
Energy contribution -20.51
Covariance contribution 0.75
Combinations/Pair 1.08
Mean z-score -2.32
Structure conservation index 0.85
SVM decision value 1.08
SVM RNA-class probability 0.911935
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9185662 97 + 22407834
GCACUUCGGUUUUGGUUCAAUUUUCAA--UUUUAACGACCGAGACUAAUUUUCACACCAGCAGCUAAUGUCAACACAAUCGUUGACAUUUUGUCAGUGG
.......((((((((((..........--.......))))))))))........(((..((((..(((((((((......)))))))))))))..))). ( -25.23)
>DroSec_CAF1 21610 97 + 1
ACACUUCGGUUUUGCUUCAAUUUUCAA--UUUUAACGACCGAGACUAAUUUUUAAACCAGCAGCUAAUGUCAACACAAUCGUUGACAUUUUGUCAGUGA
.((((((((((................--.......)))))).................((((..(((((((((......))))))))))))).)))). ( -19.40)
>DroSim_CAF1 22487 97 + 1
ACACUUCGGUUUUGCUUCAAUUUUCAA--UUUUAACGACCGAGACUAAUUUUCACACCAGCAGCUAAUGUCAACACAAUCGUUGACAUUUUGUCAGUGA
....(((((((................--.......)))))))...........(((..((((..(((((((((......)))))))))))))..))). ( -21.10)
>DroEre_CAF1 25324 97 + 1
ACACUUCGGUUUUGGUUCAGUUUUCAA--UUUUAACGACCGAGACUAAUUUUCACACCAGCAGCUAAUGUCAACACAAUCGUUGACAUUUUGUCAGUGA
.......((((((((((..(((.....--....)))))))))))))........(((..((((..(((((((((......)))))))))))))..))). ( -26.20)
>DroYak_CAF1 23503 97 + 1
ACAGUUCGGUUUUGGUUCAGUUUACAA--UUUUAACGACCGAGACUAAUUUUCACACCAGCAGCUAAUGUCAACACAAUCGUUGACAUUUUGUCAGUGA
.......((((((((((..(((.....--....)))))))))))))........(((..((((..(((((((((......)))))))))))))..))). ( -26.20)
>DroAna_CAF1 23454 97 + 1
A-ACUCUGGUUUUCGCUUA-UUUUCAACACUUUAAUGGCCAAGACUAAUUUUCACACCAGCGGCGAAUGUCAACAGGGCCAUUGACAGUUGGUCGGUGA
.-..........(((((..-...(((((...(((((((((..(((.....(((.(.......).))).))).....)))))))))..)))))..))))) ( -21.70)
>consensus
ACACUUCGGUUUUGGUUCAAUUUUCAA__UUUUAACGACCGAGACUAAUUUUCACACCAGCAGCUAAUGUCAACACAAUCGUUGACAUUUUGUCAGUGA
.......((((((((((...................))))))))))........(((..((((..(((((((((......)))))))))))))..))). (-19.76 = -20.51 +   0.75)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,185,719 – 9,185,812
Length 93
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 85.92
Mean single sequence MFE -19.60
Consensus MFE -14.10
Energy contribution -14.86
Covariance contribution 0.76
Combinations/Pair 1.05
Mean z-score -2.48
Structure conservation index 0.72
SVM decision value 1.22
SVM RNA-class probability 0.931803
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9185719 93 + 22407834
GCAGCUAAUGUCAACACAAUCGUUGACAUUUUGUCAGUGGAAGCAACUAGCCAAUUUGACAAGAAAAAGGCA-AAAAAAAAACAUUUCAAUUGG
...(((..(((((((......)))))))((((((((.(((..........)))...))))))))....))).-..................... ( -21.10)
>DroSec_CAF1 21667 83 + 1
GCAGCUAAUGUCAACACAAUCGUUGACAUUUUGUCAGUGAGAGCAACUAGCCAAUUUGAAAAA----------AAGAAAA-ACAUUUCAAUUGG
((((..(((((((((......)))))))))))))..((....))......((((((.((((..----------.......-...)))))))))) ( -17.70)
>DroSim_CAF1 22544 84 + 1
GCAGCUAAUGUCAACACAAUCGUUGACAUUUUGUCAGUGAGAGCAACUAGCCAAUUUGAAAAA----------AAGAAAAUACAUUUCAAUUGG
((((..(((((((((......)))))))))))))..((....))......((((((.((((..----------...........)))))))))) ( -17.62)
>DroEre_CAF1 25381 87 + 1
GCAGCUAAUGUCAACACAAUCGUUGACAUUUUGUCAGUGAAAGCAACUAGCCAACUUGACAUGAAAA-GGCAAA------AACAUUUCAAUUGG
...((((((((((((......))))))))).(((((((....((.....))..)).)))))......-)))...------.............. ( -19.40)
>DroYak_CAF1 23560 93 + 1
GCAGCUAAUGUCAACACAAUCGUUGACAUUUUGUCAGUGAAAGCAACUAGCCAACUUGACAAGAAAU-GGCACAAAAAAACACAUUUCAAUUGG
...((((.(((((((......)))))))((((((((((....((.....))..)).))))))))..)-)))....................... ( -22.20)
>consensus
GCAGCUAAUGUCAACACAAUCGUUGACAUUUUGUCAGUGAAAGCAACUAGCCAAUUUGACAAGAAA__GGCA_AAAAAAAAACAUUUCAAUUGG
....(((((((((((......)))))).(((((((((.....((.....))....))))))))).........................))))) (-14.10 = -14.86 +   0.76)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,185,719 – 9,185,812
Length 93
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 85.92
Mean single sequence MFE -20.24
Consensus MFE -15.98
Energy contribution -16.58
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.89
Structure conservation index 0.79
SVM decision value 0.76
SVM RNA-class probability 0.842709
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9185719 93 - 22407834
CCAAUUGAAAUGUUUUUUUUU-UGCCUUUUUCUUGUCAAAUUGGCUAGUUGCUUCCACUGACAAAAUGUCAACGAUUGUGUUGACAUUAGCUGC
.(((..((((....))))..)-))........((((((....(((.....))).....))))))((((((((((....))))))))))...... ( -20.40)
>DroSec_CAF1 21667 83 - 1
CCAAUUGAAAUGU-UUUUCUU----------UUUUUCAAAUUGGCUAGUUGCUCUCACUGACAAAAUGUCAACGAUUGUGUUGACAUUAGCUGC
.(((((((((...-.......----------..)))).)))))(((..(((.((.....)))))((((((((((....)))))))))))))... ( -17.20)
>DroSim_CAF1 22544 84 - 1
CCAAUUGAAAUGUAUUUUCUU----------UUUUUCAAAUUGGCUAGUUGCUCUCACUGACAAAAUGUCAACGAUUGUGUUGACAUUAGCUGC
.(((((((((...........----------..)))).)))))(((..(((.((.....)))))((((((((((....)))))))))))))... ( -17.12)
>DroEre_CAF1 25381 87 - 1
CCAAUUGAAAUGUU------UUUGCC-UUUUCAUGUCAAGUUGGCUAGUUGCUUUCACUGACAAAAUGUCAACGAUUGUGUUGACAUUAGCUGC
.....(((((.((.------...)).-.)))))(((((.((.(((.....)))...))))))).((((((((((....))))))))))...... ( -21.10)
>DroYak_CAF1 23560 93 - 1
CCAAUUGAAAUGUGUUUUUUUGUGCC-AUUUCUUGUCAAGUUGGCUAGUUGCUUUCACUGACAAAAUGUCAACGAUUGUGUUGACAUUAGCUGC
......((((((.((........)))-)))))((((((.((.(((.....)))...))))))))((((((((((....))))))))))...... ( -25.40)
>consensus
CCAAUUGAAAUGUUUUUUCUU_UGCC__UUUCUUGUCAAAUUGGCUAGUUGCUUUCACUGACAAAAUGUCAACGAUUGUGUUGACAUUAGCUGC
................................((((((....(((.....))).....))))))((((((((((....))))))))))...... (-15.98 = -16.58 +   0.60)

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 10:47:07 2006