Locus 3098

Sequence ID 3R_DroMel_CAF1
Location 8,189,883 – 8,190,163
Length 280
Max. P 0.965134
window5028 window5029 window5030 window5031

overview

Window 8

Location 8,189,883 – 8,190,003
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.83
Mean single sequence MFE -50.74
Consensus MFE -45.34
Energy contribution -45.46
Covariance contribution 0.12
Combinations/Pair 1.16
Mean z-score -1.62
Structure conservation index 0.89
SVM decision value 1.58
SVM RNA-class probability 0.965134
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8189883 120 - 27905053
UGGCAGCCCGUAAUGGCAUUCGGGCCAUGGCCAACAGUGCUCUGGUGGGCUGUCUGGUGCUGGCCAUGAUUGAAGGAGCCGGUGCAGCAGUGGCCACCAUUAAUGCAGCCGACAAAGGUG
.(((((((((..(.((((((..(((....)))...)))))).)..)))))))))(((((.(((((((..(((..(....)....)))..))))))).))))).....(((......))). ( -50.40)
>DroSec_CAF1 4055 120 - 1
UGGCAGCCCGUAAUGGCAUUCGGGCCAUGGCCAACAGUGCUCUGGUGGGCUGUCUGGUGCUGGCCAUGAUUGAAGGAGCCGGUGCAGCAGUGGCCACCAUUAAUGCAGCCGACAAGGGUG
((((.(((((..........)))))....)))).....(((((.((.((((((.(((((.(((((((..(((..(....)....)))..))))))).)))))..)))))).)).))))). ( -51.90)
>DroSim_CAF1 4069 120 - 1
UGGCAGCCCGCAAUGGCAUUCGGGCCAUGGCCAACAGUGCACUGGUGGGCUGUCUGGUGCUGGCCAUGAUUGAAGGAGCCGGUGCAGCAGUGGCCACCAUUAAUGCAGCCGACAAGGGUG
.((((((((((....(((((..(((....)))...)))))....))))))))))(((((.(((((((..(((..(....)....)))..))))))).)))))...((.((.....)).)) ( -53.60)
>DroEre_CAF1 3977 120 - 1
UGGCAGCCCGUAAUGGCAUUCGGGCCAUGGCCAACAGUGCUCUGGUGGGCUGCCUGGUUCUGGCCAUGAUUGAAGGAGCAGGUGCAGCAGUGGCCACCAUUAAUGCAGCCGAUAAGGGGG
.(((((((((..(.((((((..(((....)))...)))))).)..)))))))))..(((((...((....))..))))).((((((..(((((...)))))..)))).)).......... ( -48.80)
>DroYak_CAF1 4015 120 - 1
UGGCCGCUCGUAAUGGCUUUCGGGCCAUGGCCAACAGUGCUCUUGUGGGCUGCCUGGUCCUGGCCAUGAUUGAAGGAGCAGGUGCAGCAGUGGCCACCAUCAAUGCAGCUGAUAAAGGCC
.((((((((.(.((((((...((((((.(((.......((((....)))).))))))))).))))))......).))))((.((((...((((...))))...)))).))......)))) ( -49.00)
>consensus
UGGCAGCCCGUAAUGGCAUUCGGGCCAUGGCCAACAGUGCUCUGGUGGGCUGUCUGGUGCUGGCCAUGAUUGAAGGAGCCGGUGCAGCAGUGGCCACCAUUAAUGCAGCCGACAAGGGUG
((((.(((((..........)))))....)))).....(((((.((.((((((.(((((.(((((((..(((............)))..))))))).)))))..)))))).)).))))). (-45.34 = -45.46 +   0.12)

alignment

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secondary structure

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Window 9

Location 8,189,923 – 8,190,043
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.75
Mean single sequence MFE -39.10
Consensus MFE -33.50
Energy contribution -33.90
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.49
Structure conservation index 0.86
SVM decision value 0.57
SVM RNA-class probability 0.786068
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8189923 120 + 27905053
GGCUCCUUCAAUCAUGGCCAGCACCAGACAGCCCACCAGAGCACUGUUGGCCAUGGCCCGAAUGCCAUUACGGGCUGCCAAUAUCCCACCAGUGGCCGCUCCACUGAGUAUCGAGUUCCA
(((.........(((((((((((.......((.(....).))..)))))))))))(((((..........))))).)))........((((((((.....)))))).))........... ( -39.50)
>DroSec_CAF1 4095 120 + 1
GGCUCCUUCAAUCAUGGCCAGCACCAGACAGCCCACCAGAGCACUGUUGGCCAUGGCCCGAAUGCCAUUACGGGCUGCCAAUAUCCCACCCGUGGCCGCUCCACUGAGUAUCGAGUUCCA
(((.........(((((((((((.......((.(....).))..)))))))))))(((((..........))))).)))......(((....)))..((((....))))........... ( -35.30)
>DroSim_CAF1 4109 120 + 1
GGCUCCUUCAAUCAUGGCCAGCACCAGACAGCCCACCAGUGCACUGUUGGCCAUGGCCCGAAUGCCAUUGCGGGCUGCCAAUAUCCCACCAGUGGCCGCUCCACUGAGUAUCGAGUUCCA
(((((.........((((.(((.((.(((((..((....))..))))).((.(((((......))))).))))))))))).......((((((((.....)))))).))...)))))... ( -40.40)
>DroEre_CAF1 4017 120 + 1
UGCUCCUUCAAUCAUGGCCAGAACCAGGCAGCCCACCAGAGCACUGUUGGCCAUGGCCCGAAUGCCAUUACGGGCUGCCAAUAUCCCACCAGUGGCCGCUCCACUGAGUAUCGAGUUCCA
.((((.........(((......)))((((((((.((((.......))))..(((((......)))))...))))))))........((((((((.....)))))).))...)))).... ( -40.20)
>DroYak_CAF1 4055 120 + 1
UGCUCCUUCAAUCAUGGCCAGGACCAGGCAGCCCACAAGAGCACUGUUGGCCAUGGCCCGAAAGCCAUUACGAGCGGCCAAUAUCCCACCAGUGGCCGCUCCACUGAGAAUCGAGUUCCA
.((((.(((....((((((((...(((((...........)).)))))))))))(((......))).....(((((((((............)))))))))......)))..)))).... ( -40.10)
>consensus
GGCUCCUUCAAUCAUGGCCAGCACCAGACAGCCCACCAGAGCACUGUUGGCCAUGGCCCGAAUGCCAUUACGGGCUGCCAAUAUCCCACCAGUGGCCGCUCCACUGAGUAUCGAGUUCCA
.((((.......(((((((((...(((...((.(....).)).))))))))))))(((((..........)))))..............((((((.....))))))......)))).... (-33.50 = -33.90 +   0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,189,923 – 8,190,043
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.75
Mean single sequence MFE -49.50
Consensus MFE -43.26
Energy contribution -43.50
Covariance contribution 0.24
Combinations/Pair 1.09
Mean z-score -1.47
Structure conservation index 0.87
SVM decision value 0.73
SVM RNA-class probability 0.836172
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8189923 120 - 27905053
UGGAACUCGAUACUCAGUGGAGCGGCCACUGGUGGGAUAUUGGCAGCCCGUAAUGGCAUUCGGGCCAUGGCCAACAGUGCUCUGGUGGGCUGUCUGGUGCUGGCCAUGAUUGAAGGAGCC
.((..((((((....(((((.....)))))(((.((.(((..((((((((..(.((((((..(((....)))...)))))).)..))))))).)..))))).)))...)))).))...)) ( -48.30)
>DroSec_CAF1 4095 120 - 1
UGGAACUCGAUACUCAGUGGAGCGGCCACGGGUGGGAUAUUGGCAGCCCGUAAUGGCAUUCGGGCCAUGGCCAACAGUGCUCUGGUGGGCUGUCUGGUGCUGGCCAUGAUUGAAGGAGCC
.((..((((((.....((((.....)))).(((.((.(((..((((((((..(.((((((..(((....)))...)))))).)..))))))).)..))))).)))...)))).))...)) ( -47.60)
>DroSim_CAF1 4109 120 - 1
UGGAACUCGAUACUCAGUGGAGCGGCCACUGGUGGGAUAUUGGCAGCCCGCAAUGGCAUUCGGGCCAUGGCCAACAGUGCACUGGUGGGCUGUCUGGUGCUGGCCAUGAUUGAAGGAGCC
.((..((((((....(((((.....)))))(((.((.(((..(((((((((....(((((..(((....)))...)))))....)))))))).)..))))).)))...)))).))...)) ( -51.40)
>DroEre_CAF1 4017 120 - 1
UGGAACUCGAUACUCAGUGGAGCGGCCACUGGUGGGAUAUUGGCAGCCCGUAAUGGCAUUCGGGCCAUGGCCAACAGUGCUCUGGUGGGCUGCCUGGUUCUGGCCAUGAUUGAAGGAGCA
......(((((....(((((.....)))))(((.(((....(((((((((..(.((((((..(((....)))...)))))).)..)))))))))....))).)))...)))))....... ( -50.50)
>DroYak_CAF1 4055 120 - 1
UGGAACUCGAUUCUCAGUGGAGCGGCCACUGGUGGGAUAUUGGCCGCUCGUAAUGGCUUUCGGGCCAUGGCCAACAGUGCUCUUGUGGGCUGCCUGGUCCUGGCCAUGAUUGAAGGAGCA
........(.((((((((.(((((((((.((......)).)))))))))...((((((...((((((.(((.......((((....)))).))))))))).)))))).)))).)))).). ( -49.70)
>consensus
UGGAACUCGAUACUCAGUGGAGCGGCCACUGGUGGGAUAUUGGCAGCCCGUAAUGGCAUUCGGGCCAUGGCCAACAGUGCUCUGGUGGGCUGUCUGGUGCUGGCCAUGAUUGAAGGAGCC
.....(((.......(((((.....)))))(((.((.....((((((((((...((((((..(((....)))...))))))...)))))))))).....)).)))..........))).. (-43.26 = -43.50 +   0.24)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,190,043 – 8,190,163
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.58
Mean single sequence MFE -40.74
Consensus MFE -34.12
Energy contribution -34.52
Covariance contribution 0.40
Combinations/Pair 1.11
Mean z-score -1.32
Structure conservation index 0.84
SVM decision value 0.10
SVM RNA-class probability 0.583828
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8190043 120 + 27905053
GGCAUCCUCCCUCUGGCGAUAGUGGACCAGGGCGCAAUCCACUGUGCUGAAAGUGGCACCCCAAACGGCAAAGCUGCCGGCAAUGGACGGCGUUCUCAUCUUCACCAAAUCAAUGCCACC
(((((........(((.((..(((....(((((((..((((..(((((......)))))......(((((....)))))....))))..))))))))))..)).))).....)))))... ( -41.22)
>DroSec_CAF1 4215 120 + 1
GGCAUCCUCCCGCUGGCGAUAGUGGACCAGGGCGCAGUCCACUGUGCUGAAUGUGGCACCCCAAACGGCAAAGCUGCCGGCAAUGCACGGCGUUCUCAUCUUCACCAAAUCAAUGCCACC
(((((....((((((....))))))....((((((((....)))))).((((((.(((.......(((((....)))))....)))...)))))).........))......)))))... ( -40.70)
>DroSim_CAF1 4229 120 + 1
GGCAUCCUCCCGCUGGCGAUAGUGGACCAGGGCGCAGUCCACUGUGCUGAAAGUGGCACCCCAAACGGCAAAGCUGCCGGCAAUGCACGGCGUUCUCAUCUUCACCAAAUCAAUGCCCCC
(((((....((((((....))))))....((((((((....))))))((((..(((.((.((...(((((....)))))((...))..)).)).).))..))))))......)))))... ( -39.90)
>DroEre_CAF1 4137 120 + 1
GGCGUCCUCCCUCUGCCGAUAGUGGACCAGGACACAAUCCACUGUGCUGAACGUGGCUCCCCAAACGGCAAAGCUGCCGGCAAUGGAGGGCGUCCUCAUCUUCACCGAAUCAAUUCCACC
((((((((((...(((((((((((((...(....)..)))))))).......(..(((..((....))...)))..))))))..)))))))))).......................... ( -43.40)
>DroYak_CAF1 4175 120 + 1
UGCAUCCUCCCUCUGGCGAUAGUGGACCAGGACGCAAUCCACUGUGCUGAAAGUGGCUCCCCAAACGGCAAAGCUGCCGGCAAUGGAGGGCGUUCUCAUCUUCACCGAAUCAAUGCCACC
.............(((((((.(((((..(((((((...(((((........)))))((((.....(((((....))))).....)))).)))))))....)))))...)))...)))).. ( -38.50)
>consensus
GGCAUCCUCCCUCUGGCGAUAGUGGACCAGGGCGCAAUCCACUGUGCUGAAAGUGGCACCCCAAACGGCAAAGCUGCCGGCAAUGGACGGCGUUCUCAUCUUCACCAAAUCAAUGCCACC
(((((........(((.((..(((....(((((((..((((.((((((......)))........(((((....)))))))).))))..))))))))))..)).))).....)))))... (-34.12 = -34.52 +   0.40)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:05 2006