Locus 7626

Sequence ID 3L_DroMel_CAF1
Location 20,521,234 – 20,521,375
Length 141
Max. P 0.948501
window12391 window12392 window12393 window12394

overview

Window 1

Location 20,521,234 – 20,521,340
Length 106
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 80.84
Mean single sequence MFE -25.04
Consensus MFE -13.88
Energy contribution -15.86
Covariance contribution 1.98
Combinations/Pair 1.07
Mean z-score -2.14
Structure conservation index 0.55
SVM decision value 0.54
SVM RNA-class probability 0.776027
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20521234 106 + 23771897
AUUGGUUCAUUAGCCCUGCAGUA---GCUAGUAACAAAAGCGUAGUAAGCCAAAAGCAAUUAUAUUGGUUUUGGCCGA-GCGCAAAA--AAAGCAAGGCAGCCGAAAGAGAA
.((((((.....(((.(((.((.---.......))....((((.....(((((((.((((...)))).)))))))...-))))....--...))).)))))))))....... ( -29.20)
>DroSec_CAF1 63800 112 + 1
AUUGGUUCAUUAGCCCUGCAGUAGCAGCUAGUAAGAAAAGCGGAGUAAGCCAAAAGCAAUUAUAUUGGUUUUGGCCAAAACGCAAAGAAAGAGCAAGGCAGCCGAAAAAGAA
.((((((.....(((.((((((....)))..........(((......(((((((.((((...)))).))))))).....))).........))).)))))))))....... ( -29.70)
>DroSim_CAF1 63955 112 + 1
AUUGGUUCAUUAGCCCUGCAGUAGCAGCUAGUAACAAAAGCGGAGUAAGCCAAAAGCAAUUAUAUUGGUUUUGGCCAAAACGCAAAGAAAGAGCAAGGCAGCCGAAAAAGAA
.((((((.....(((.(((.((.((.....)).))....(((......(((((((.((((...)))).))))))).....))).........))).)))))))))....... ( -30.50)
>DroEre_CAF1 66296 103 + 1
AUUGGUUCAUUAGCCCUGCAGUA---GCUAGUAACGAAAACAGAGUAAGCCAAAAGCAAUUAUAUUGGUUUUGGCCAA-ACGGA-----AAAACGAGGCAGCCGAAAUAGAA
.((((((.((((((.........---))))))............((..(((((((.((((...)))).)))))))...-.((..-----....))..))))))))....... ( -21.70)
>DroAna_CAF1 61308 95 + 1
AUUGGUUCAUUAGCCCUGCAGUA---GCCAGUAACUGAAG------AAAUCCACAGCAAUUAGAUUGGAUUUUGCCAAAA---A-----AAAAAAAAGGAUUGGAAAAAAAA
.(..((((..........((((.---.......))))..(------(((((((...(.....)..)))))))).......---.-----........))))..)........ ( -14.10)
>consensus
AUUGGUUCAUUAGCCCUGCAGUA___GCUAGUAACAAAAGCGGAGUAAGCCAAAAGCAAUUAUAUUGGUUUUGGCCAAAACGCAAA___AAAGCAAGGCAGCCGAAAAAGAA
.(((((((((((((............)))))).......(((......(((((((.((((...)))).))))))).....)))..............).))))))....... (-13.88 = -15.86 +   1.98)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,521,234 – 20,521,340
Length 106
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 80.84
Mean single sequence MFE -24.28
Consensus MFE -16.94
Energy contribution -18.06
Covariance contribution 1.12
Combinations/Pair 1.19
Mean z-score -2.26
Structure conservation index 0.70
SVM decision value 1.38
SVM RNA-class probability 0.948501
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20521234 106 - 23771897
UUCUCUUUCGGCUGCCUUGCUUU--UUUUGCGC-UCGGCCAAAACCAAUAUAAUUGCUUUUGGCUUACUACGCUUUUGUUACUAGC---UACUGCAGGGCUAAUGAACCAAU
......((((...(((((((...--....(((.-..((((((((.((((...)))).)))))))).....)))....((.....))---....)))))))...))))..... ( -27.60)
>DroSec_CAF1 63800 112 - 1
UUCUUUUUCGGCUGCCUUGCUCUUUCUUUGCGUUUUGGCCAAAACCAAUAUAAUUGCUUUUGGCUUACUCCGCUUUUCUUACUAGCUGCUACUGCAGGGCUAAUGAACCAAU
......((((...(((((((.........((((...((((((((.((((...)))).)))))))).))...(((.........))).))....)))))))...))))..... ( -28.32)
>DroSim_CAF1 63955 112 - 1
UUCUUUUUCGGCUGCCUUGCUCUUUCUUUGCGUUUUGGCCAAAACCAAUAUAAUUGCUUUUGGCUUACUCCGCUUUUGUUACUAGCUGCUACUGCAGGGCUAAUGAACCAAU
......((((...(((((((.........(((....((((((((.((((...)))).)))))))).....)))....((........))....)))))))...))))..... ( -28.90)
>DroEre_CAF1 66296 103 - 1
UUCUAUUUCGGCUGCCUCGUUUU-----UCCGU-UUGGCCAAAACCAAUAUAAUUGCUUUUGGCUUACUCUGUUUUCGUUACUAGC---UACUGCAGGGCUAAUGAACCAAU
......((((...(((.......-----...((-..((((((((.((((...)))).)))))))).)).((((....((.....))---....)))))))...))))..... ( -22.00)
>DroAna_CAF1 61308 95 - 1
UUUUUUUUCCAAUCCUUUUUUUU-----U---UUUUGGCAAAAUCCAAUCUAAUUGCUGUGGAUUU------CUUCAGUUACUGGC---UACUGCAGGGCUAAUGAACCAAU
......................(-----(---(.(((((.(((((((..(.....)...)))))))------(((((((.......---.)))).)))))))).)))..... ( -14.60)
>consensus
UUCUUUUUCGGCUGCCUUGCUUU___UUUGCGUUUUGGCCAAAACCAAUAUAAUUGCUUUUGGCUUACUCCGCUUUUGUUACUAGC___UACUGCAGGGCUAAUGAACCAAU
......((((...(((((((................((((((((.((((...)))).))))))))......(((.........))).......)))))))...))))..... (-16.94 = -18.06 +   1.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,521,267 – 20,521,375
Length 108
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 81.30
Mean single sequence MFE -24.43
Consensus MFE -13.86
Energy contribution -15.86
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -1.96
Structure conservation index 0.57
SVM decision value -0.03
SVM RNA-class probability 0.518318
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20521267 108 + 23771897
AAAGCGUAGUAAGCCAAAAGCAAUUAUAUUGGUUUUGGCCGA-GCGCAAAA--AAAGCAAGGCAGCCGAAAGAGAAAUACGCCGAGAAUAAAGUGCUGUCCUCAAUGGGGA
...((((.....(((((((.((((...)))).)))))))...-))))....--..((((.(((...(....)(....)..)))..........)))).((((.....)))) ( -27.40)
>DroSec_CAF1 63836 111 + 1
AAAGCGGAGUAAGCCAAAAGCAAUUAUAUUGGUUUUGGCCAAAACGCAAAGAAAGAGCAAGGCAGCCGAAAAAGAAAUACGCCGAGAACGAUGUGCUGUCCUCAAUGGGGA
...(((......(((((((.((((...)))).))))))).....))).......(((...(((((((......)....(((.((....)).))))))))))))........ ( -26.10)
>DroSim_CAF1 63991 111 + 1
AAAGCGGAGUAAGCCAAAAGCAAUUAUAUUGGUUUUGGCCAAAACGCAAAGAAAGAGCAAGGCAGCCGAAAAAGAAAUACGCCGAAAACGAAGUGCUGUCCUCAAUGGGGA
...(((......(((((((.((((...)))).))))))).....))).......(((...(((((((.........................).)))))))))........ ( -25.11)
>DroEre_CAF1 66329 91 + 1
AAAACAGAGUAAGCCAAAAGCAAUUAUAUUGGUUUUGGCCAA-ACGGA-----AAAACGAGGCAGCCGAAAUAGAAAUACUCGCAGAAU--------------AAUGGGAG
......(((((.(((((((.((((...)))).)))))))...-.(((.-----............))).........))))).......--------------........ ( -19.12)
>consensus
AAAGCGGAGUAAGCCAAAAGCAAUUAUAUUGGUUUUGGCCAA_ACGCAAAG__AAAGCAAGGCAGCCGAAAAAGAAAUACGCCGAGAACGAAGUGCUGUCCUCAAUGGGGA
...(((......(((((((.((((...)))).))))))).....))).............((((((............................))))))........... (-13.86 = -15.86 +   2.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,521,267 – 20,521,375
Length 108
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 81.30
Mean single sequence MFE -21.75
Consensus MFE -15.00
Energy contribution -16.75
Covariance contribution 1.75
Combinations/Pair 1.12
Mean z-score -1.62
Structure conservation index 0.69
SVM decision value 0.13
SVM RNA-class probability 0.595791
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20521267 108 - 23771897
UCCCCAUUGAGGACAGCACUUUAUUCUCGGCGUAUUUCUCUUUCGGCUGCCUUGCUUU--UUUUGCGC-UCGGCCAAAACCAAUAUAAUUGCUUUUGGCUUACUACGCUUU
........(((((..........)))))((((((..........(((......)))..--........-..((((((((.((((...)))).))))))))...)))))).. ( -21.80)
>DroSec_CAF1 63836 111 - 1
UCCCCAUUGAGGACAGCACAUCGUUCUCGGCGUAUUUCUUUUUCGGCUGCCUUGCUCUUUCUUUGCGUUUUGGCCAAAACCAAUAUAAUUGCUUUUGGCUUACUCCGCUUU
........((((.((((((..((....))..))....(......)))))))))...........(((....((((((((.((((...)))).)))))))).....)))... ( -24.90)
>DroSim_CAF1 63991 111 - 1
UCCCCAUUGAGGACAGCACUUCGUUUUCGGCGUAUUUCUUUUUCGGCUGCCUUGCUCUUUCUUUGCGUUUUGGCCAAAACCAAUAUAAUUGCUUUUGGCUUACUCCGCUUU
........((((.((((...(((....)))((...........))))))))))...........(((....((((((((.((((...)))).)))))))).....)))... ( -24.70)
>DroEre_CAF1 66329 91 - 1
CUCCCAUU--------------AUUCUGCGAGUAUUUCUAUUUCGGCUGCCUCGUUUU-----UCCGU-UUGGCCAAAACCAAUAUAAUUGCUUUUGGCUUACUCUGUUUU
........--------------.......(((((.........(((..((...))...-----.))).-..((((((((.((((...)))).)))))))))))))...... ( -15.60)
>consensus
UCCCCAUUGAGGACAGCACUUCAUUCUCGGCGUAUUUCUUUUUCGGCUGCCUUGCUCU__CUUUGCGU_UUGGCCAAAACCAAUAUAAUUGCUUUUGGCUUACUCCGCUUU
......((((((((........))))))))..............(((......)))........(((....((((((((.((((...)))).)))))))).....)))... (-15.00 = -16.75 +   1.75)

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 12:52:02 2006