Locus 719

Sequence ID 2R_DroMel_CAF1
Location 3,532,230 – 3,532,392
Length 162
Max. P 0.965920
window1263 window1264 window1265 window1266 window1267

overview

Window 3

Location 3,532,230 – 3,532,321
Length 91
Sequences 3
Columns 91
Reading direction forward
Mean pairwise identity 99.27
Mean single sequence MFE -32.63
Consensus MFE -30.73
Energy contribution -31.07
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.97
Structure conservation index 0.94
SVM decision value 0.58
SVM RNA-class probability 0.789107
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3532230 91 + 20766785
AUGGCGAGUCCAGCCCUCUCUAUGACAUUGAUGGGCAUUGACGACGCUGGUGAUGGGAUGGUGAUCAUCAGCGAGAGCGUCAUCAUCAUCA
..((((.(((..((((((...........)).))))...)))..))))((((((((((((.....)))).((....))....)))))))). ( -32.10)
>DroSec_CAF1 3590 91 + 1
AUGGCGAGUCCAGCCCUCUCUAUGACAUUGAUGGGCAUUGACGACGCUGCUGAUGGGAUGGUGAUCAUCAGCGAGAGCGUCAUCAUCAUCA
(((..(((((..((((((...........)).))))...)))((((((((((((((........))))))))...)))))).))..))).. ( -32.90)
>DroSim_CAF1 1 91 + 1
AUGGCGAGUCCAGCCCUCUCUAUGACAUUGAUGGGCAUUGACGACGCUGCUGAUGGGAUGGUGAUCAUCAGCGAGAGCGUCAUCAUCAUCA
(((..(((((..((((((...........)).))))...)))((((((((((((((........))))))))...)))))).))..))).. ( -32.90)
>consensus
AUGGCGAGUCCAGCCCUCUCUAUGACAUUGAUGGGCAUUGACGACGCUGCUGAUGGGAUGGUGAUCAUCAGCGAGAGCGUCAUCAUCAUCA
(((..(((((..((((((...........)).))))...)))((((((((((((((........))))))))...)))))).))..))).. (-30.73 = -31.07 +   0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,532,230 – 3,532,321
Length 91
Sequences 3
Columns 91
Reading direction reverse
Mean pairwise identity 99.27
Mean single sequence MFE -30.90
Consensus MFE -30.93
Energy contribution -31.27
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.38
Structure conservation index 1.00
SVM decision value 1.59
SVM RNA-class probability 0.965920
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3532230 91 - 20766785
UGAUGAUGAUGACGCUCUCGCUGAUGAUCACCAUCCCAUCACCAGCGUCGUCAAUGCCCAUCAAUGUCAUAGAGAGGGCUGGACUCGCCAU
......((((((((((...(.(((((..........))))).)))))))))))..((((.((.........))..))))(((.....))). ( -26.50)
>DroSec_CAF1 3590 91 - 1
UGAUGAUGAUGACGCUCUCGCUGAUGAUCACCAUCCCAUCAGCAGCGUCGUCAAUGCCCAUCAAUGUCAUAGAGAGGGCUGGACUCGCCAU
......((((((((((...(((((((..........)))))))))))))))))..((((.((.........))..))))(((.....))). ( -33.10)
>DroSim_CAF1 1 91 - 1
UGAUGAUGAUGACGCUCUCGCUGAUGAUCACCAUCCCAUCAGCAGCGUCGUCAAUGCCCAUCAAUGUCAUAGAGAGGGCUGGACUCGCCAU
......((((((((((...(((((((..........)))))))))))))))))..((((.((.........))..))))(((.....))). ( -33.10)
>consensus
UGAUGAUGAUGACGCUCUCGCUGAUGAUCACCAUCCCAUCAGCAGCGUCGUCAAUGCCCAUCAAUGUCAUAGAGAGGGCUGGACUCGCCAU
......((((((((((...(((((((..........)))))))))))))))))..((((.((.........))..))))(((.....))). (-30.93 = -31.27 +   0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,532,247 – 3,532,353
Length 106
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 86.09
Mean single sequence MFE -29.65
Consensus MFE -20.28
Energy contribution -19.79
Covariance contribution -0.50
Combinations/Pair 1.14
Mean z-score -3.11
Structure conservation index 0.68
SVM decision value 1.54
SVM RNA-class probability 0.962389
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3532247 106 - 20766785
UUCAUCGUCAUUCCCUGCCACAUUCCCAGCUCUGAUGAUGAUGACGCUCUCGCUGAUGAUCACCAUCCCAUC------ACCAGCGUCGUCAAUGCCCAUCAAUGUCAUAGAG
.(((((((((....(((.........)))...)))))))))(((((....(((((.((((.........)))------).))))).)))))..................... ( -26.00)
>DroSec_CAF1 3607 106 - 1
UUCAUCGUCAUUCCCUGCCACAUUCCCAGCUCUGAUGAUGAUGACGCUCUCGCUGAUGAUCACCAUCCCAUC------AGCAGCGUCGUCAAUGCCCAUCAAUGUCAUAGAG
.(((((((((....(((.........)))...)))))))(((((((((...(((((((..........))))------))))))))))))...................)). ( -30.50)
>DroSim_CAF1 18 106 - 1
UUCAUCGUCAUUCCCUGCCACAUUCCCGGCUCUGAUGAUGAUGACGCUCUCGCUGAUGAUCACCAUCCCAUC------AGCAGCGUCGUCAAUGCCCAUCAAUGUCAUAGAG
.(((((((((......(((........)))..)))))))(((((((((...(((((((..........))))------))))))))))))...................)). ( -33.70)
>DroEre_CAF1 1 99 - 1
UUCAUCGUCAUUCCCUGCCACAUUCCCAGAGCUGAUGAUGAUGACACUGUUGAUGAUGAUCACCAUCCCGUGAUGACGACCAUCGUCGUCAAUGCCCAU-------------
.(((((((((((.((((.........))).)..)))))))))))....(((((((((((((..((((....))))..))...)))))))))))......------------- ( -28.40)
>consensus
UUCAUCGUCAUUCCCUGCCACAUUCCCAGCUCUGAUGAUGAUGACGCUCUCGCUGAUGAUCACCAUCCCAUC______ACCAGCGUCGUCAAUGCCCAUCAAUGUCAUAGAG
.(((((((((....(((.........)))...)))))))))(((((....(((((.........................))))).)))))..................... (-20.28 = -19.79 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,532,281 – 3,532,392
Length 111
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 95.52
Mean single sequence MFE -30.92
Consensus MFE -27.95
Energy contribution -28.95
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.70
Structure conservation index 0.90
SVM decision value 0.43
SVM RNA-class probability 0.732512
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3532281 111 + 20766785
GAUGGGAUGGUGAUCAUCAGCGAGAGCGUCAUCAUCAUCAGAGCUGGGAAUGUGGCAGGGAAUGACGAUGAAGUAACAAGGAG-AACGACAUUUCCAGCUAACGAAUUCAAU
..((((((((((((.....((....))...)))))))))..((((((((((((.(.........((......)).........-..).)))))))))))).......))).. ( -33.85)
>DroSec_CAF1 3641 111 + 1
GAUGGGAUGGUGAUCAUCAGCGAGAGCGUCAUCAUCAUCAGAGCUGGGAAUGUGGCAGGGAAUGACGAUGAAGUAACAAGGAG-AACGACAUUUCCAGCUAACGAAUUCAAU
..((((((((((((.....((....))...)))))))))..((((((((((((.(.........((......)).........-..).)))))))))))).......))).. ( -33.85)
>DroSim_CAF1 52 111 + 1
GAUGGGAUGGUGAUCAUCAGCGAGAGCGUCAUCAUCAUCAGAGCCGGGAAUGUGGCAGGGAAUGACGAUGAAGUAACAAGGAG-AACGACAUUUCCAGCUAACGAAUUCAAU
.....(((((((((.....((....))...)))))))))........((((.((((.(((((((.((................-..)).))))))).))))....))))... ( -29.67)
>DroEre_CAF1 28 112 + 1
CACGGGAUGGUGAUCAUCAUCAACAGUGUCAUCAUCAUCAGCUCUGGGAAUGUGGCAGGGAAUGACGAUGAAGUAACAAGGAGGAACGACAUUUCCAGCUAACGAAUUCAAU
.....(((((((((...(((.....)))..)))))))))........((((.((((.(((((((.((...................)).))))))).))))....))))... ( -26.31)
>consensus
GAUGGGAUGGUGAUCAUCAGCGAGAGCGUCAUCAUCAUCAGAGCUGGGAAUGUGGCAGGGAAUGACGAUGAAGUAACAAGGAG_AACGACAUUUCCAGCUAACGAAUUCAAU
.....(((((((((.....((....))...)))))))))..((((((((((((.(((.....))((......))............).))))))))))))............ (-27.95 = -28.95 +   1.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,532,281 – 3,532,392
Length 111
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 95.52
Mean single sequence MFE -26.35
Consensus MFE -22.98
Energy contribution -22.85
Covariance contribution -0.13
Combinations/Pair 1.06
Mean z-score -1.76
Structure conservation index 0.87
SVM decision value 0.32
SVM RNA-class probability 0.687400
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3532281 111 - 20766785
AUUGAAUUCGUUAGCUGGAAAUGUCGUU-CUCCUUGUUACUUCAUCGUCAUUCCCUGCCACAUUCCCAGCUCUGAUGAUGAUGACGCUCUCGCUGAUGAUCACCAUCCCAUC
..(((..((((((((.(((..((((((.-(.....)..)).(((((((((....(((.........)))...))))))))).)))).))).))))))))))).......... ( -25.40)
>DroSec_CAF1 3641 111 - 1
AUUGAAUUCGUUAGCUGGAAAUGUCGUU-CUCCUUGUUACUUCAUCGUCAUUCCCUGCCACAUUCCCAGCUCUGAUGAUGAUGACGCUCUCGCUGAUGAUCACCAUCCCAUC
..(((..((((((((.(((..((((((.-(.....)..)).(((((((((....(((.........)))...))))))))).)))).))).))))))))))).......... ( -25.40)
>DroSim_CAF1 52 111 - 1
AUUGAAUUCGUUAGCUGGAAAUGUCGUU-CUCCUUGUUACUUCAUCGUCAUUCCCUGCCACAUUCCCGGCUCUGAUGAUGAUGACGCUCUCGCUGAUGAUCACCAUCCCAUC
..(((..((((((((.(((.........-.)))........(((((((((((....(((........)))...))))))))))).......))))))))))).......... ( -29.50)
>DroEre_CAF1 28 112 - 1
AUUGAAUUCGUUAGCUGGAAAUGUCGUUCCUCCUUGUUACUUCAUCGUCAUUCCCUGCCACAUUCCCAGAGCUGAUGAUGAUGACACUGUUGAUGAUGAUCACCAUCCCGUG
..(((..((((((((.((((......))))....(((((..(((((((((..(.(((.........))).).))))))))))))))..))))))))...))).......... ( -25.10)
>consensus
AUUGAAUUCGUUAGCUGGAAAUGUCGUU_CUCCUUGUUACUUCAUCGUCAUUCCCUGCCACAUUCCCAGCUCUGAUGAUGAUGACGCUCUCGCUGAUGAUCACCAUCCCAUC
..(((..((((((((.(((...........))).(((((..(((((((((....(((.........)))...)))))))))))))).....))))))))))).......... (-22.98 = -22.85 +  -0.13)

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 09:45:32 2006