Locus 9255

Sequence ID 3R_DroMel_CAF1
Location 24,674,187 – 24,674,361
Length 174
Max. P 0.961213
window14798 window14799 window14800 window14801

overview

Window 8

Location 24,674,187 – 24,674,307
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.67
Mean single sequence MFE -29.76
Consensus MFE -28.12
Energy contribution -28.36
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.69
Structure conservation index 0.94
SVM decision value 1.52
SVM RNA-class probability 0.961213
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24674187 120 - 27905053
UGUUAUUCUGAAGGAAGGAAGCGCUGCACAAAUUUGUGCGGCCAAAUGCAUAAAAUGAAUAUUAAAUUAAAGUUGAAACUGAAAUUGCCGCUGCGACAGCGGAAUUCGCUGGAAAAGGCA
.(((.((((......)))))))((((((((....))))))))..............((((....((((..(((....)))..)))).((((((...)))))).))))(((......))). ( -29.80)
>DroSec_CAF1 15204 120 - 1
UGUUAUUCUGAAGGAAGGAAGCGCUGCACAAAUUUGUGCGGCCAAAUGCAUAAAAUGAAUAUUAAAUUAAAGUUGAAACUGAAAUUGCCGCUGCGACAGCGGAAUUCGCUGGAAAAGGCA
.(((.((((......)))))))((((((((....))))))))..............((((....((((..(((....)))..)))).((((((...)))))).))))(((......))). ( -29.80)
>DroSim_CAF1 15245 120 - 1
UGUUAUUCUGAAGGAAGGAAGCGCUGCACAAAUUUGUGCGGCCAAAUGCAUAAAAUGAAUAUUAAAUUAAAGUUGAAACUGAAAUUGCCGCUGCGACAGCGGAAUUCGCUGGAAAAGGCA
.(((.((((......)))))))((((((((....))))))))..............((((....((((..(((....)))..)))).((((((...)))))).))))(((......))). ( -29.80)
>DroEre_CAF1 16685 120 - 1
CGUUAUUCUGAAGGAAGGAAGCGCUGCACAAAUUUGUGCGGCCAAAUGCAUAAAAUGAAUAUUAAAUUAAAGUUGAAACUGAAAUUGCCGCAGCGACAGCGGAAUUCGCUGGAAAAGGCA
.....((((......)))).(((((((.....((((((((......))))))))..........((((..(((....)))..))))...)))))..(((((.....)))))......)). ( -29.60)
>DroYak_CAF1 15619 120 - 1
CGUUAUUCUGAAGGAAGGAAGCGCUGCACAAAUUUGUGCGGCCAAAUGCAUAAAAUGAAUAUUAAAUUAAAGUUGAAACUGAAAUUGCCGCAGCGACAGCGGAAUUCGCUGGAAAAAGCA
.....((((......)))).(((((((.....((((((((......))))))))..........((((..(((....)))..))))...)))))..(((((.....)))))......)). ( -29.80)
>consensus
UGUUAUUCUGAAGGAAGGAAGCGCUGCACAAAUUUGUGCGGCCAAAUGCAUAAAAUGAAUAUUAAAUUAAAGUUGAAACUGAAAUUGCCGCUGCGACAGCGGAAUUCGCUGGAAAAGGCA
.(((.((((......)))))))((((((((....))))))))..............((((....((((..(((....)))..)))).((((((...)))))).))))(((......))). (-28.12 = -28.36 +   0.24)

alignment

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secondary structure

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Window 9

Location 24,674,227 – 24,674,332
Length 105
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 96.23
Mean single sequence MFE -26.90
Consensus MFE -26.36
Energy contribution -26.17
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -2.11
Structure conservation index 0.98
SVM decision value 1.44
SVM RNA-class probability 0.954036
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24674227 105 - 27905053
GU--GUGUGUGUGUGCGGUUGGUUGUGUGUUAUUCUGAAGGAAGGAAGCGCUGCACAAAUUUGUGCGGCCAAAUGCAUAAAAUGAAUAUUAAAUUAAAGUUGAAACU
((--((.....((((((.((((((..(((((.((((......))))))))).(((((....))))))))))).))))))......)))).................. ( -26.30)
>DroSec_CAF1 15244 101 - 1
GU------GUGUGUGCGGUUGGUUGUGUGUUAUUCUGAAGGAAGGAAGCGCUGCACAAAUUUGUGCGGCCAAAUGCAUAAAAUGAAUAUUAAAUUAAAGUUGAAACU
..------...((((((.((((((..(((((.((((......))))))))).(((((....))))))))))).))))))............................ ( -25.70)
>DroSim_CAF1 15285 105 - 1
GU--GUGUGUGUGUGCGGUUGGUUGUGUGUUAUUCUGAAGGAAGGAAGCGCUGCACAAAUUUGUGCGGCCAAAUGCAUAAAAUGAAUAUUAAAUUAAAGUUGAAACU
((--((.....((((((.((((((..(((((.((((......))))))))).(((((....))))))))))).))))))......)))).................. ( -26.30)
>DroEre_CAF1 16725 107 - 1
GUGUGUGUUUGUGUGCGGUUGGUUGUGCGUUAUUCUGAAGGAAGGAAGCGCUGCACAAAUUUGUGCGGCCAAAUGCAUAAAAUGAAUAUUAAAUUAAAGUUGAAACU
....((((((.((((((.((((((..(((((.((((......))))))))).(((((....))))))))))).))))))....)))))).................. ( -29.30)
>consensus
GU__GUGUGUGUGUGCGGUUGGUUGUGUGUUAUUCUGAAGGAAGGAAGCGCUGCACAAAUUUGUGCGGCCAAAUGCAUAAAAUGAAUAUUAAAUUAAAGUUGAAACU
...........((((((.((((((..(((((.((((......))))))))).(((((....))))))))))).))))))............................ (-26.36 = -26.17 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 0

Location 24,674,267 – 24,674,361
Length 94
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 95.79
Mean single sequence MFE -14.50
Consensus MFE -13.74
Energy contribution -13.74
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.07
Structure conservation index 0.95
SVM decision value 1.29
SVM RNA-class probability 0.938161
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24674267 94 + 27905053
CGCACAAAUUUGUGCAGCGCUUCCUUCCUUCAGAAUAACACACAACCAACCGCACACACACAC--ACACACACGAGUGCGCAUAAAAUUGAUUCAU
....(((.(((((((.((((((..(((.....)))................(......)....--........))))))))))))).)))...... ( -13.80)
>DroSec_CAF1 15284 90 + 1
CGCACAAAUUUGUGCAGCGCUUCCUUCCUUCAGAAUAACACACAACCAACCGCACACAC------ACACACACGAGUGCGCAUAAAAUUGAUUCAU
....(((.(((((((.((((((.....................................------........))))))))))))).)))...... ( -13.88)
>DroSim_CAF1 15325 94 + 1
CGCACAAAUUUGUGCAGCGCUUCCUUCCUUCAGAAUAACACACAACCAACCGCACACACACAC--ACACACACGAGUGCGCAUAAAAUUGAUUCAU
....(((.(((((((.((((((..(((.....)))................(......)....--........))))))))))))).)))...... ( -13.80)
>DroEre_CAF1 16765 96 + 1
CGCACAAAUUUGUGCAGCGCUUCCUUCCUUCAGAAUAACGCACAACCAACCGCACACAAACACACACACACACGAGUGCGCAUAAAAUUGAUUCAU
....(((.(((((((.((((((..(((.....)))....((..........))....................))))))))))))).)))...... ( -16.50)
>consensus
CGCACAAAUUUGUGCAGCGCUUCCUUCCUUCAGAAUAACACACAACCAACCGCACACACACAC__ACACACACGAGUGCGCAUAAAAUUGAUUCAU
....(((.(((((((.((((((...................................................))))))))))))).)))...... (-13.74 = -13.74 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 24,674,267 – 24,674,361
Length 94
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 95.79
Mean single sequence MFE -29.62
Consensus MFE -25.66
Energy contribution -26.22
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -2.57
Structure conservation index 0.87
SVM decision value 1.16
SVM RNA-class probability 0.923543
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24674267 94 - 27905053
AUGAAUCAAUUUUAUGCGCACUCGUGUGUGU--GUGUGUGUGUGCGGUUGGUUGUGUGUUAUUCUGAAGGAAGGAAGCGCUGCACAAAUUUGUGCG
...(((((((..(((((((((.((......)--).)))))))))..)))))))..(((((.((((......))))))))).(((((....))))). ( -30.00)
>DroSec_CAF1 15284 90 - 1
AUGAAUCAAUUUUAUGCGCACUCGUGUGUGU------GUGUGUGCGGUUGGUUGUGUGUUAUUCUGAAGGAAGGAAGCGCUGCACAAAUUUGUGCG
...(((((((..(((((((((........))------)))))))..)))))))..(((((.((((......))))))))).(((((....))))). ( -29.70)
>DroSim_CAF1 15325 94 - 1
AUGAAUCAAUUUUAUGCGCACUCGUGUGUGU--GUGUGUGUGUGCGGUUGGUUGUGUGUUAUUCUGAAGGAAGGAAGCGCUGCACAAAUUUGUGCG
...(((((((..(((((((((.((......)--).)))))))))..)))))))..(((((.((((......))))))))).(((((....))))). ( -30.00)
>DroEre_CAF1 16765 96 - 1
AUGAAUCAAUUUUAUGCGCACUCGUGUGUGUGUGUGUUUGUGUGCGGUUGGUUGUGCGUUAUUCUGAAGGAAGGAAGCGCUGCACAAAUUUGUGCG
...(((((((....(((((((.((..(....)..))...))))))))))))))..(((((.((((......))))))))).(((((....))))). ( -28.80)
>consensus
AUGAAUCAAUUUUAUGCGCACUCGUGUGUGU__GUGUGUGUGUGCGGUUGGUUGUGUGUUAUUCUGAAGGAAGGAAGCGCUGCACAAAUUUGUGCG
...(((((((....(((((((.((..(......)..)).))))))))))))))..(((((.((((......))))))))).(((((....))))). (-25.66 = -26.22 +   0.56)

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 13:30:03 2006