Locus 3035

Sequence ID 3R_DroMel_CAF1
Location 8,083,624 – 8,083,824
Length 200
Max. P 0.995005
window4883 window4884 window4885 window4886 window4887

overview

Window 3

Location 8,083,624 – 8,083,744
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.50
Mean single sequence MFE -45.90
Consensus MFE -43.82
Energy contribution -43.58
Covariance contribution -0.24
Combinations/Pair 1.03
Mean z-score -1.11
Structure conservation index 0.95
SVM decision value 0.13
SVM RNA-class probability 0.598385
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8083624 120 - 27905053
ACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGAUGGGGUGGUCAUCCGAUCGCCCCGAAGACAGCUGCCGUGUGCUGGAACCGGACAAUGUCCAAGGGACCCAUGGGCCACAAAAGUU
.(((.(((..(.(..(((((((....)).((((..((((((((((....))))))))))....((((........))))...)))).....)))))..).)))).)))............ ( -45.10)
>DroSec_CAF1 8567 120 - 1
ACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGAUGGGGUGGUCAUCCGAUCGCCCCGAAGACAGCUGCCGUGUGCUGGAACCGGACAAUAUCCAAGGGGCCCAUGGGCCACAAAAGUU
.((...(((.........((.....))..((((..((((((((((....))))))))))....((((........))))...))))......)))..))((((....))))......... ( -46.40)
>DroSim_CAF1 6984 120 - 1
ACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGAUGGGGUGGUCAUCCGAUCGCCCCGAAGACAGCUGCCGUGUGCUGGAACCGGACAACGUCCAAGGGACCCAUGGGCCACAAAAGUC
.(((.(((..(.(..(((((((....)).((((..((((((((((....))))))))))....((((........))))...)))).....)))))..).)))).)))............ ( -45.40)
>DroEre_CAF1 10343 120 - 1
ACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGAUGGGGUGGUCAUCCGAUCGCCCCGAAGACAGCUGCCGUGUGCUGGAACCGGCCAAUCUCCGAGGGACCCAUGGGCCACAAAAGUU
.(((.(((.........((((((.((((..(((..((((((((((....)))))))))).((....)).)))..))))....))))))..(((.....)))))).)))............ ( -47.00)
>DroYak_CAF1 3684 119 - 1
ACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGGUGGGGUGGUCAUCCGAUCGCCCCGAAGACAGCUGCCGUGUGCUGGAACCGGACCAUAUCCGAG-GACCCAUGGGCCACAAAAGUU
.(((.(((......((((((.....))..((((..((((((((((....))))))))))....((((........))))...)))).)))).((....-))))).)))............ ( -45.60)
>consensus
ACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGAUGGGGUGGUCAUCCGAUCGCCCCGAAGACAGCUGCCGUGUGCUGGAACCGGACAAUAUCCAAGGGACCCAUGGGCCACAAAAGUU
.(((.(((...((.....))((((.....((((..((((((((((....))))))))))....((((........))))...))))......)))).....))).)))............ (-43.82 = -43.58 +  -0.24)

alignment

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secondary structure

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Window 4

Location 8,083,664 – 8,083,784
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 99.67
Mean single sequence MFE -38.46
Consensus MFE -38.00
Energy contribution -38.20
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.23
Structure conservation index 0.99
SVM decision value -0.02
SVM RNA-class probability 0.525435
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8083664 120 + 27905053
CCAGCACACGGCAGCUGUCUUCGGGGCGAUCGGAUGACCACCCCAUCCCGGUCGCUUCCAGCCCAUUGCAUUCCCUUGGUCUGGUCUUUGUCCGGGAUUGUUUGCCUUCAAUUUGACUAC
.........((((((((.....((((((((((((((.......))).))))))))))))))).....(((.((((..((.(........).)))))).))).)))).............. ( -38.90)
>DroSec_CAF1 8607 120 + 1
CCAGCACACGGCAGCUGUCUUCGGGGCGAUCGGAUGACCACCCCAUCCCGGUCGCUUCCAGCCCAUUGCAUUCCCUUGGUCUGGUCUUUGUCCGGGAUUGUUUGCCUUCAAUUUGACUAC
.........((((((((.....((((((((((((((.......))).))))))))))))))).....(((.((((..((.(........).)))))).))).)))).............. ( -38.90)
>DroSim_CAF1 7024 120 + 1
CCAGCACACGGCAGCUGUCUUCGGGGCGAUCGGAUGACCACCCCAUCCCGGUCGCUUCCAGCCCAUUGCAUUCCCUUGGUCUGGUCUUUGUCCGGGAUUGUUUGCCUUCAAUUUGACUAC
.........((((((((.....((((((((((((((.......))).))))))))))))))).....(((.((((..((.(........).)))))).))).)))).............. ( -38.90)
>DroEre_CAF1 10383 120 + 1
CCAGCACACGGCAGCUGUCUUCGGGGCGAUCGGAUGACCACCCCAUCCCGGUCGCUUCCAGCCCAUUGCAUUCCCUUGGUCUGGUCUUUGUCCGGGAUUGUUUGCCUUCAAUUUGACUAC
.........((((((((.....((((((((((((((.......))).))))))))))))))).....(((.((((..((.(........).)))))).))).)))).............. ( -38.90)
>DroYak_CAF1 3723 120 + 1
CCAGCACACGGCAGCUGUCUUCGGGGCGAUCGGAUGACCACCCCACCCCGGUCGCUUCCAGCCCAUUGCAUUCCCUUGGUCUGGUCUUUGUCCGGGAUUGUUUGCCUUCAAUUUGACUAC
.........((((((((.....(((((((((((.((.......))..))))))))))))))).....(((.((((..((.(........).)))))).))).)))).............. ( -36.70)
>consensus
CCAGCACACGGCAGCUGUCUUCGGGGCGAUCGGAUGACCACCCCAUCCCGGUCGCUUCCAGCCCAUUGCAUUCCCUUGGUCUGGUCUUUGUCCGGGAUUGUUUGCCUUCAAUUUGACUAC
.........((((((((.....((((((((((((((.......))).))))))))))))))).....(((.((((..((.(........).)))))).))).)))).............. (-38.00 = -38.20 +   0.20)

alignment

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secondary structure

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Window 5

Location 8,083,664 – 8,083,784
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 99.67
Mean single sequence MFE -45.00
Consensus MFE -45.16
Energy contribution -45.00
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -2.05
Structure conservation index 1.00
SVM decision value 2.53
SVM RNA-class probability 0.995005
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8083664 120 - 27905053
GUAGUCAAAUUGAAGGCAAACAAUCCCGGACAAAGACCAGACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGAUGGGGUGGUCAUCCGAUCGCCCCGAAGACAGCUGCCGUGUGCUGG
((..((.....))..)).....(((((((.......((((.(((..(.....)..))).))))......)))))))(((((((((....))))))))).....((((........)))). ( -45.12)
>DroSec_CAF1 8607 120 - 1
GUAGUCAAAUUGAAGGCAAACAAUCCCGGACAAAGACCAGACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGAUGGGGUGGUCAUCCGAUCGCCCCGAAGACAGCUGCCGUGUGCUGG
((..((.....))..)).....(((((((.......((((.(((..(.....)..))).))))......)))))))(((((((((....))))))))).....((((........)))). ( -45.12)
>DroSim_CAF1 7024 120 - 1
GUAGUCAAAUUGAAGGCAAACAAUCCCGGACAAAGACCAGACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGAUGGGGUGGUCAUCCGAUCGCCCCGAAGACAGCUGCCGUGUGCUGG
((..((.....))..)).....(((((((.......((((.(((..(.....)..))).))))......)))))))(((((((((....))))))))).....((((........)))). ( -45.12)
>DroEre_CAF1 10383 120 - 1
GUAGUCAAAUUGAAGGCAAACAAUCCCGGACAAAGACCAGACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGAUGGGGUGGUCAUCCGAUCGCCCCGAAGACAGCUGCCGUGUGCUGG
((..((.....))..)).....(((((((.......((((.(((..(.....)..))).))))......)))))))(((((((((....))))))))).....((((........)))). ( -45.12)
>DroYak_CAF1 3723 120 - 1
GUAGUCAAAUUGAAGGCAAACAAUCCCGGACAAAGACCAGACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGGUGGGGUGGUCAUCCGAUCGCCCCGAAGACAGCUGCCGUGUGCUGG
((..((.....))..)).....(((((((.......((((.(((..(.....)..))).))))......)))))))(((((((((....))))))))).....((((........)))). ( -44.52)
>consensus
GUAGUCAAAUUGAAGGCAAACAAUCCCGGACAAAGACCAGACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGAUGGGGUGGUCAUCCGAUCGCCCCGAAGACAGCUGCCGUGUGCUGG
((..((.....))..)).....(((((((.......((((.(((..(.....)..))).))))......)))))))(((((((((....))))))))).....((((........)))). (-45.16 = -45.00 +  -0.16)

alignment

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secondary structure

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Window 6

Location 8,083,704 – 8,083,824
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 99.67
Mean single sequence MFE -31.10
Consensus MFE -30.60
Energy contribution -30.80
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.58
Structure conservation index 0.98
SVM decision value 1.13
SVM RNA-class probability 0.919795
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8083704 120 + 27905053
CCCCAUCCCGGUCGCUUCCAGCCCAUUGCAUUCCCUUGGUCUGGUCUUUGUCCGGGAUUGUUUGCCUUCAAUUUGACUACAAACCAUAAUUUAUCUUUUCAGACGUGUUGGUCAGCGCGA
....(((((((.((...((((.(((...........))).))))....)).))))))).(((((...((.....))...)))))...................((((((....)))))). ( -31.50)
>DroSec_CAF1 8647 120 + 1
CCCCAUCCCGGUCGCUUCCAGCCCAUUGCAUUCCCUUGGUCUGGUCUUUGUCCGGGAUUGUUUGCCUUCAAUUUGACUACAAACCAUAAUUUAUCUUUUCAGACGUGUUGGUCAGCGCGA
....(((((((.((...((((.(((...........))).))))....)).))))))).(((((...((.....))...)))))...................((((((....)))))). ( -31.50)
>DroSim_CAF1 7064 120 + 1
CCCCAUCCCGGUCGCUUCCAGCCCAUUGCAUUCCCUUGGUCUGGUCUUUGUCCGGGAUUGUUUGCCUUCAAUUUGACUACAAACCAUAAUUUAUCUUUUCAGACGUGUUGGUCAGCGCGA
....(((((((.((...((((.(((...........))).))))....)).))))))).(((((...((.....))...)))))...................((((((....)))))). ( -31.50)
>DroEre_CAF1 10423 120 + 1
CCCCAUCCCGGUCGCUUCCAGCCCAUUGCAUUCCCUUGGUCUGGUCUUUGUCCGGGAUUGUUUGCCUUCAAUUUGACUACAAACCAUAAUUUAUCUUUUCAGACGUGUUGGUCAGCGCGA
....(((((((.((...((((.(((...........))).))))....)).))))))).(((((...((.....))...)))))...................((((((....)))))). ( -31.50)
>DroYak_CAF1 3763 120 + 1
CCCCACCCCGGUCGCUUCCAGCCCAUUGCAUUCCCUUGGUCUGGUCUUUGUCCGGGAUUGUUUGCCUUCAAUUUGACUACAAACCAUAAUUUAUCUUUUCAGACGUGUUGGUCAGCGCGA
......(((((.((...((((.(((...........))).))))....)).)))))...(((((...((.....))...)))))...................((((((....)))))). ( -29.50)
>consensus
CCCCAUCCCGGUCGCUUCCAGCCCAUUGCAUUCCCUUGGUCUGGUCUUUGUCCGGGAUUGUUUGCCUUCAAUUUGACUACAAACCAUAAUUUAUCUUUUCAGACGUGUUGGUCAGCGCGA
....(((((((.((...((((.(((...........))).))))....)).))))))).(((((...((.....))...)))))...................((((((....)))))). (-30.60 = -30.80 +   0.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,083,704 – 8,083,824
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 99.67
Mean single sequence MFE -34.10
Consensus MFE -34.26
Energy contribution -34.10
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.53
Structure conservation index 1.00
SVM decision value 1.08
SVM RNA-class probability 0.911789
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8083704 120 - 27905053
UCGCGCUGACCAACACGUCUGAAAAGAUAAAUUAUGGUUUGUAGUCAAAUUGAAGGCAAACAAUCCCGGACAAAGACCAGACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGAUGGGG
.........((.....((((....))))........((((((..((.....))..)))))).(((((((.......((((.(((..(.....)..))).))))......))))))))).. ( -34.22)
>DroSec_CAF1 8647 120 - 1
UCGCGCUGACCAACACGUCUGAAAAGAUAAAUUAUGGUUUGUAGUCAAAUUGAAGGCAAACAAUCCCGGACAAAGACCAGACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGAUGGGG
.........((.....((((....))))........((((((..((.....))..)))))).(((((((.......((((.(((..(.....)..))).))))......))))))))).. ( -34.22)
>DroSim_CAF1 7064 120 - 1
UCGCGCUGACCAACACGUCUGAAAAGAUAAAUUAUGGUUUGUAGUCAAAUUGAAGGCAAACAAUCCCGGACAAAGACCAGACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGAUGGGG
.........((.....((((....))))........((((((..((.....))..)))))).(((((((.......((((.(((..(.....)..))).))))......))))))))).. ( -34.22)
>DroEre_CAF1 10423 120 - 1
UCGCGCUGACCAACACGUCUGAAAAGAUAAAUUAUGGUUUGUAGUCAAAUUGAAGGCAAACAAUCCCGGACAAAGACCAGACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGAUGGGG
.........((.....((((....))))........((((((..((.....))..)))))).(((((((.......((((.(((..(.....)..))).))))......))))))))).. ( -34.22)
>DroYak_CAF1 3763 120 - 1
UCGCGCUGACCAACACGUCUGAAAAGAUAAAUUAUGGUUUGUAGUCAAAUUGAAGGCAAACAAUCCCGGACAAAGACCAGACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGGUGGGG
.........((.....((((....))))........((((((..((.....))..)))))).(((((((.......((((.(((..(.....)..))).))))......))))))))).. ( -33.62)
>consensus
UCGCGCUGACCAACACGUCUGAAAAGAUAAAUUAUGGUUUGUAGUCAAAUUGAAGGCAAACAAUCCCGGACAAAGACCAGACCAAGGGAAUGCAAUGGGCUGGAAGCGACCGGGAUGGGG
.........((.....((((....))))........((((((..((.....))..)))))).(((((((.......((((.(((..(.....)..))).))))......))))))))).. (-34.26 = -34.10 +  -0.16)

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 10:50:47 2006