Locus 3464

Sequence ID 2R_DroMel_CAF1
Location 11,629,981 – 11,630,124
Length 143
Max. P 0.992546
window5652 window5653 window5654 window5655

overview

Window 2

Location 11,629,981 – 11,630,089
Length 108
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 76.50
Mean single sequence MFE -35.46
Consensus MFE -24.03
Energy contribution -24.34
Covariance contribution 0.31
Combinations/Pair 1.33
Mean z-score -2.93
Structure conservation index 0.68
SVM decision value 2.30
SVM RNA-class probability 0.992038
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11629981 108 + 20766785
CGCUCAUUUCAAGAGACCCAUAUAUGAUUGGGAUGAACCCACGACCAGUUACUCCAAGAACUACACACCCACUUGGAGUAAACUUUGAUCGCGGGCUCAUCCUUGGAA
......(((((((.((((((........)))).(((.(((.(((.(((((((((((((.............))))))))))...))).))).))).)))))))))))) ( -36.62)
>DroPse_CAF1 1388 101 + 1
CCCUCUUGUCAAA----GCUU-UUCAAUUGGGCGCAACCAAAGGCGGCCUCCUCCAGCCA-GACACACCCACUGG-AGGGGUCCUCCUCGAUGGGAUGUUCCCCUGAA
.............----....-((((...(((.(((.(((.(((.((.(((((((((...-..........))))-))))).)).)))...)))..))).))).)))) ( -32.82)
>DroSec_CAF1 2512 106 + 1
CGCUCUUUUCAGGAGACACAU--AUGGUUUGGAUGAACCCACGACCACUUACUCCAAAAACUACACACCCACUUGGAGGAAACUUUGGUCGCGGGCUCAUCCUUGGAA
.(((((.....)))).)....--.......((((((.(((.((((((....((((((...............)))))).......)))))).))).))))))...... ( -34.66)
>DroSim_CAF1 2528 106 + 1
CGCUCUUAUCAGGAGACGCAU--AUUGUUGGGAUGAACCCACGACCAGUUACUCCAAAAACUACACACCCACUUGGAGGAAACUUUGGUCGCGGGCUCAUCCUUGGAU
.((((((.....)))).))..--......(((((((.(((.(((((((((.((((((...............))))))..)))..)))))).))).)))))))..... ( -38.36)
>DroEre_CAF1 2488 106 + 1
CGCUCUUUUCAGGAGAUGUAU--AUGGUUGGGAUGAACCCACGACGAGCUACUCCAAAAUUUACACACCCACUAGGAGGAAGCUUUGGUCGCGGGCUCAUCCUUAGAA
..((((.....))))......--......(((((((.(((.(((((((((.((((...................))))..)))))..)))).))).)))))))..... ( -34.91)
>DroYak_CAF1 2516 106 + 1
CGCUCUUUUCAGGAAAUGCAU--UUGACUGGGAUGAACCCACGAUCAGCUACUCCAAAAACUACACACCCACCAGGAGGUAGCUUUGGUCGCGGGCUCAUCCUUGGAA
.((..(((....)))..))..--....(.(((((((.(((.((((((((((((((...................))).)))))..)))))).))).))))))).)... ( -35.41)
>consensus
CGCUCUUUUCAGGAGACGCAU__AUGAUUGGGAUGAACCCACGACCAGCUACUCCAAAAACUACACACCCACUUGGAGGAAACUUUGGUCGCGGGCUCAUCCUUGGAA
.............................(((((((.(((.(((((((...((((...................))))......))))))).))).)))))))..... (-24.03 = -24.34 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 11,629,981 – 11,630,089
Length 108
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 76.50
Mean single sequence MFE -41.58
Consensus MFE -28.60
Energy contribution -28.99
Covariance contribution 0.39
Combinations/Pair 1.29
Mean z-score -3.28
Structure conservation index 0.69
SVM decision value 2.34
SVM RNA-class probability 0.992546
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11629981 108 - 20766785
UUCCAAGGAUGAGCCCGCGAUCAAAGUUUACUCCAAGUGGGUGUGUAGUUCUUGGAGUAACUGGUCGUGGGUUCAUCCCAAUCAUAUAUGGGUCUCUUGAAAUGAGCG
......(((((((((((((((((....((((((((((.............)))))))))).))))))))))))))))).............(.(((.......)))). ( -44.92)
>DroPse_CAF1 1388 101 - 1
UUCAGGGGAACAUCCCAUCGAGGAGGACCCCU-CCAGUGGGUGUGUC-UGGCUGGAGGAGGCCGCCUUUGGUUGCGCCCAAUUGAA-AAGC----UUUGACAAGAGGG
((((.(((..((..(((..((((.((.(((((-(((((.((.....)-).)))))))).)))).))))))).))..)))...))))-...(----(((....)))).. ( -41.30)
>DroSec_CAF1 2512 106 - 1
UUCCAAGGAUGAGCCCGCGACCAAAGUUUCCUCCAAGUGGGUGUGUAGUUUUUGGAGUAAGUGGUCGUGGGUUCAUCCAAACCAU--AUGUGUCUCCUGAAAAGAGCG
......(((((((((((((((((.......(((((((.............)))))))....))))))))))))))))).......--....(.(((.(....))))). ( -42.62)
>DroSim_CAF1 2528 106 - 1
AUCCAAGGAUGAGCCCGCGACCAAAGUUUCCUCCAAGUGGGUGUGUAGUUUUUGGAGUAACUGGUCGUGGGUUCAUCCCAACAAU--AUGCGUCUCCUGAUAAGAGCG
......(((((((((((((((((..(((..(((((((.............))))))).)))))))))))))))))))).......--..((.(((.......))))). ( -43.52)
>DroEre_CAF1 2488 106 - 1
UUCUAAGGAUGAGCCCGCGACCAAAGCUUCCUCCUAGUGGGUGUGUAAAUUUUGGAGUAGCUCGUCGUGGGUUCAUCCCAACCAU--AUACAUCUCCUGAAAAGAGCG
......(((((((((((((((...((((..((((....((((......)))).)))).)))).))))))))))))))).......--.........((....)).... ( -39.00)
>DroYak_CAF1 2516 106 - 1
UUCCAAGGAUGAGCCCGCGACCAAAGCUACCUCCUGGUGGGUGUGUAGUUUUUGGAGUAGCUGAUCGUGGGUUCAUCCCAGUCAA--AUGCAUUUCCUGAAAAGAGCG
......((((((((((((((....((((((.(((...................)))))))))..)))))))))))))).......--.........((....)).... ( -38.11)
>consensus
UUCCAAGGAUGAGCCCGCGACCAAAGUUUCCUCCAAGUGGGUGUGUAGUUUUUGGAGUAACUGGUCGUGGGUUCAUCCCAACCAU__AUGCGUCUCCUGAAAAGAGCG
......(((((((((((((((((.......((((...................))))....))))))))))))))))).............................. (-28.60 = -28.99 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 11,630,012 – 11,630,124
Length 112
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 79.82
Mean single sequence MFE -32.94
Consensus MFE -19.72
Energy contribution -19.98
Covariance contribution 0.26
Combinations/Pair 1.32
Mean z-score -2.23
Structure conservation index 0.60
SVM decision value 0.88
SVM RNA-class probability 0.872293
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11630012 112 + 20766785
GAUGAACCCACGACCAGUUACUCCAAGAACUACACACCCACUUGGAGUAAACUUUGAUCGCGGGCUCAUCCUUGGAACUCCUUU--CAACAGCGUUUCA-AUUCUUGAGAGAAUG
(((((.(((.(((.(((((((((((((.............))))))))))...))).))).))).)))))..((((((..((..--....)).))))))-(((((....))))). ( -33.82)
>DroPse_CAF1 1414 113 + 1
GCGCAACCAAAGGCGGCCUCCUCCAGCCA-GACACACCCACUGG-AGGGGUCCUCCUCGAUGGGAUGUUCCCCUGAAGUCCUCUGAAAAUUGUGUUUCCUCUUCUAAUGAGCUUC
((((((.....((.((.(((((((((...-..........))))-))))).)).))(((..(((((.(((....)))))))).)))...))))))...(((.......))).... ( -31.82)
>DroSec_CAF1 2541 112 + 1
GAUGAACCCACGACCACUUACUCCAAAAACUACACACCCACUUGGAGGAAACUUUGGUCGCGGGCUCAUCCUUGGAACUCCUGU--CAACUGCGUUUCA-AUUCUUGAGAGAAUG
(((((.(((.((((((....((((((...............)))))).......)))))).))).)))))..((((((.(..(.--...).).))))))-(((((....))))). ( -33.16)
>DroSim_CAF1 2557 112 + 1
GAUGAACCCACGACCAGUUACUCCAAAAACUACACACCCACUUGGAGGAAACUUUGGUCGCGGGCUCAUCCUUGGAUCUCCUGU--CAACUGCGUUUCA-AUUCUUGAGAGAAUG
(((((.(((.(((((((((.((((((...............))))))..)))..)))))).))).)))))...((....))...--.............-(((((....))))). ( -32.36)
>DroEre_CAF1 2517 112 + 1
GAUGAACCCACGACGAGCUACUCCAAAAUUUACACACCCACUAGGAGGAAGCUUUGGUCGCGGGCUCAUCCUUAGAACUCCUGU--CAACUGCGUUUCA-AUUCUUGAGAGAAUG
(((((.(((.(((((((((.((((...................))))..)))))..)))).))).)))))..........((.(--(((..........-....)))).)).... ( -30.25)
>DroYak_CAF1 2545 112 + 1
GAUGAACCCACGAUCAGCUACUCCAAAAACUACACACCCACCAGGAGGUAGCUUUGGUCGCGGGCUCAUCCUUGGAACUCCUGU--CAACAGCGUUUCA-AUACUUAAGAGAAUG
(((((.(((.((((((((((((((...................))).)))))..)))))).))).))))).(((((((..(((.--...))).))))))-).............. ( -36.21)
>consensus
GAUGAACCCACGACCAGCUACUCCAAAAACUACACACCCACUUGGAGGAAACUUUGGUCGCGGGCUCAUCCUUGGAACUCCUGU__CAACUGCGUUUCA_AUUCUUGAGAGAAUG
(((((.(((.(((((((...((((...................))))......))))))).))).)))))............................................. (-19.72 = -19.98 +   0.26)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 11,630,012 – 11,630,124
Length 112
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 79.82
Mean single sequence MFE -41.06
Consensus MFE -24.44
Energy contribution -24.89
Covariance contribution 0.45
Combinations/Pair 1.32
Mean z-score -2.67
Structure conservation index 0.60
SVM decision value 1.31
SVM RNA-class probability 0.941015
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11630012 112 - 20766785
CAUUCUCUCAAGAAU-UGAAACGCUGUUG--AAAGGAGUUCCAAGGAUGAGCCCGCGAUCAAAGUUUACUCCAAGUGGGUGUGUAGUUCUUGGAGUAACUGGUCGUGGGUUCAUC
..((((.((((.(..-........).)))--).))))........((((((((((((((((....((((((((((.............)))))))))).)))))))))))))))) ( -42.32)
>DroPse_CAF1 1414 113 - 1
GAAGCUCAUUAGAAGAGGAAACACAAUUUUCAGAGGACUUCAGGGGAACAUCCCAUCGAGGAGGACCCCU-CCAGUGGGUGUGUC-UGGCUGGAGGAGGCCGCCUUUGGUUGCGC
...((...........(....).......(((((((.((((..(((.....)))...)))).((.(((((-(((((.((.....)-).)))))))).)))).)))))))..)).. ( -43.90)
>DroSec_CAF1 2541 112 - 1
CAUUCUCUCAAGAAU-UGAAACGCAGUUG--ACAGGAGUUCCAAGGAUGAGCCCGCGACCAAAGUUUCCUCCAAGUGGGUGUGUAGUUUUUGGAGUAAGUGGUCGUGGGUUCAUC
....((((....(((-((.....))))).--...)))).......((((((((((((((((.......(((((((.............)))))))....)))))))))))))))) ( -40.32)
>DroSim_CAF1 2557 112 - 1
CAUUCUCUCAAGAAU-UGAAACGCAGUUG--ACAGGAGAUCCAAGGAUGAGCCCGCGACCAAAGUUUCCUCCAAGUGGGUGUGUAGUUUUUGGAGUAACUGGUCGUGGGUUCAUC
...(((((....(((-((.....))))).--...)))))......((((((((((((((((..(((..(((((((.............))))))).))))))))))))))))))) ( -43.32)
>DroEre_CAF1 2517 112 - 1
CAUUCUCUCAAGAAU-UGAAACGCAGUUG--ACAGGAGUUCUAAGGAUGAGCCCGCGACCAAAGCUUCCUCCUAGUGGGUGUGUAAAUUUUGGAGUAGCUCGUCGUGGGUUCAUC
....((((....(((-((.....))))).--...)))).......((((((((((((((...((((..((((....((((......)))).)))).)))).)))))))))))))) ( -38.20)
>DroYak_CAF1 2545 112 - 1
CAUUCUCUUAAGUAU-UGAAACGCUGUUG--ACAGGAGUUCCAAGGAUGAGCCCGCGACCAAAGCUACCUCCUGGUGGGUGUGUAGUUUUUGGAGUAGCUGAUCGUGGGUUCAUC
..............(-((.(((.(((...--.)))..))).))).(((((((((((((....((((((.(((...................)))))))))..))))))))))))) ( -38.31)
>consensus
CAUUCUCUCAAGAAU_UGAAACGCAGUUG__ACAGGAGUUCCAAGGAUGAGCCCGCGACCAAAGUUUCCUCCAAGUGGGUGUGUAGUUUUUGGAGUAACUGGUCGUGGGUUCAUC
..................................((....))...((((((((((((((((.......((((...................))))....)))))))))))))))) (-24.44 = -24.89 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:14 2006