Locus 5062

Sequence ID 2R_DroMel_CAF1
Location 16,440,818 – 16,440,942
Length 124
Max. P 0.969913
window8090 window8091 window8092

overview

Window 0

Location 16,440,818 – 16,440,918
Length 100
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 79.72
Mean single sequence MFE -25.17
Consensus MFE -19.91
Energy contribution -20.13
Covariance contribution 0.22
Combinations/Pair 1.10
Mean z-score -3.60
Structure conservation index 0.79
SVM decision value 1.65
SVM RNA-class probability 0.969913
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16440818 100 + 20766785
CCCAUUUUUGUUUCUUUCUUUUUUUCCCUUUUUGGGU--GGAACGACACUUUGCGGCACAAGUUUUCCAAUAAAACGGCAAAACUUUGCUGCGAACAAAAUU
.....((((((((.......(((..(((.....))).--.))).........((((((.(((((((((........)).))))))))))))))))))))).. ( -27.00)
>DroPse_CAF1 146269 80 + 1
---------------------UUU-CCCAUUUUGGGGCAACAACGACACUUUGCGGCCGAAGUUUUCCAAUAAAACGGCAAAACUUUGCUGCGAACAAAAUU
---------------------..(-(((.....))))............((((((((.((((((((((........)).))))))))))))))))....... ( -23.10)
>DroSec_CAF1 116310 99 + 1
CCCAUUUUUGUUUCUUUCUUUUUU-CCCUUUUUGGGU--GGAACGACACUUUGCGGCACAAGUUUUCCAAUAAAACGGCAAAACUUUGCUGCGAACAAAAUU
.....((((((((...((.(((..-(((.....))).--.))).))......((((((.(((((((((........)).))))))))))))))))))))).. ( -28.30)
>DroEre_CAF1 116210 99 + 1
CCCAUUUUUGUUUCUUUCUUUUUU-CCUUUUUUGGGU--GGAACGACACUUUGCGGCACAAGUUUUCCAAUAAAACGGCAAAACUUUGCUGCGAACAAAAUU
.....((((((.((.((((....(-((......))).--)))).))....((((((((.(((((((((........)).))))))))))))))))))))).. ( -26.00)
>DroMoj_CAF1 193841 76 + 1
---------------------UUU-UGCUUUUUGGGC----GACGACACUUUGCGGCAGAAGUUUUCCAAUAAAAUGGCAAAACUUUGCUGCGAACAAAAUU
---------------------..(-((((.....)))----))......(((((((((((.((((((((......))).))))))))))))))))....... ( -23.50)
>DroPer_CAF1 147304 80 + 1
---------------------UUU-CCCAUUUUGGGGCAACAACGACACUUUGCGGCCGAAGUUUUCCAAUAAAACGGCAAAACUUUGCUGCGAACAAAAUU
---------------------..(-(((.....))))............((((((((.((((((((((........)).))))))))))))))))....... ( -23.10)
>consensus
_____________________UUU_CCCUUUUUGGGU__GGAACGACACUUUGCGGCACAAGUUUUCCAAUAAAACGGCAAAACUUUGCUGCGAACAAAAUU
.........................(((.....))).............(((((((((.(((((((((........)).))))))))))))))))....... (-19.91 = -20.13 +   0.22)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,440,818 – 16,440,918
Length 100
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 79.72
Mean single sequence MFE -21.73
Consensus MFE -14.85
Energy contribution -15.55
Covariance contribution 0.70
Combinations/Pair 1.04
Mean z-score -1.84
Structure conservation index 0.68
SVM decision value 0.82
SVM RNA-class probability 0.858962
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16440818 100 - 20766785
AAUUUUGUUCGCAGCAAAGUUUUGCCGUUUUAUUGGAAAACUUGUGCCGCAAAGUGUCGUUCC--ACCCAAAAAGGGAAAAAAAGAAAGAAACAAAAAUGGG
..((((((((((.((((((((((.(((......)))))))))).))).)).............--.(((.....)))...........).)))))))..... ( -23.00)
>DroPse_CAF1 146269 80 - 1
AAUUUUGUUCGCAGCAAAGUUUUGCCGUUUUAUUGGAAAACUUCGGCCGCAAAGUGUCGUUGUUGCCCCAAAAUGGG-AAA---------------------
..........(((((((((((((.(((......))))))))).(((((.....).)))))))))))(((.....)))-...--------------------- ( -21.90)
>DroSec_CAF1 116310 99 - 1
AAUUUUGUUCGCAGCAAAGUUUUGCCGUUUUAUUGGAAAACUUGUGCCGCAAAGUGUCGUUCC--ACCCAAAAAGGG-AAAAAAGAAAGAAACAAAAAUGGG
..((((((((((.((((((((((.(((......)))))))))).))).)).............--.(((.....)))-..........).)))))))..... ( -23.00)
>DroEre_CAF1 116210 99 - 1
AAUUUUGUUCGCAGCAAAGUUUUGCCGUUUUAUUGGAAAACUUGUGCCGCAAAGUGUCGUUCC--ACCCAAAAAAGG-AAAAAAGAAAGAAACAAAAAUGGG
..((((((((((.((((((((((.(((......)))))))))).))).))......((.((((--..........))-))....))..).)))))))..... ( -21.60)
>DroMoj_CAF1 193841 76 - 1
AAUUUUGUUCGCAGCAAAGUUUUGCCAUUUUAUUGGAAAACUUCUGCCGCAAAGUGUCGUC----GCCCAAAAAGCA-AAA---------------------
..(((((((.((.((((((((((.(((......)))))))))).))).))...(((....)----))......))))-)))--------------------- ( -19.00)
>DroPer_CAF1 147304 80 - 1
AAUUUUGUUCGCAGCAAAGUUUUGCCGUUUUAUUGGAAAACUUCGGCCGCAAAGUGUCGUUGUUGCCCCAAAAUGGG-AAA---------------------
..........(((((((((((((.(((......))))))))).(((((.....).)))))))))))(((.....)))-...--------------------- ( -21.90)
>consensus
AAUUUUGUUCGCAGCAAAGUUUUGCCGUUUUAUUGGAAAACUUCUGCCGCAAAGUGUCGUUCC__ACCCAAAAAGGG_AAA_____________________
.(((((((..(((...(((((((.(((......)))))))))).))).)))))))...........(((.....)))......................... (-14.85 = -15.55 +   0.70)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,440,843 – 16,440,942
Length 99
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.80
Mean single sequence MFE -24.07
Consensus MFE -18.30
Energy contribution -18.19
Covariance contribution -0.11
Combinations/Pair 1.10
Mean z-score -1.95
Structure conservation index 0.76
SVM decision value 1.08
SVM RNA-class probability 0.911851
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16440843 99 + 20766785
CCC---UUUUUGGGU--GGAACGACACUUUGCGGCACAAGUUUUCCAAUAAAACGGCAAAACUUUGCUGCGAACAAAAUUAAAGAAGACGACA-A---GG--AAAAUGG----------U
.((---((.((((((--(......))))((((((((.(((((((((........)).)))))))))))))))................))).)-)---))--.......----------. ( -27.70)
>DroVir_CAF1 167648 95 + 1
--------UUUGGGC----GACGACACUUUGCGGCAGAAGUUUUCCAAUAAAACGGCAAAACUUUGCUGCGAACAAAAUUAAAGAAGACGAC-GACAACG--ACAACGA----------C
--------(((((..----..).....(((((((((((.(((((((........)).))))))))))))))))))))...............-.......--.......----------. ( -20.40)
>DroGri_CAF1 136410 82 + 1
--------UUUGGGC----GACAACACUUUGCGGCAGAAGUUUUCCAAUAAAACGGCAAAACUUUGCUGCGAACAAAAUUAAAGAAGACGACA-A-------------------------
--------(((((..----..).....(((((((((((.(((((((........)).))))))))))))))))))))................-.------------------------- ( -20.40)
>DroWil_CAF1 265930 110 + 1
CCUCUCUUUUUGGG----CAACGACACUUUGCGGCAGAAGUUUUCCAAUAAAAUGGCAAAACUUUGCUGCGAACAAAAUUAAAGAAGACGGCA-A---GG--AAAAUGUAUCCACAAGUG
.((.(((((((.(.----...).....(((((((((((.((((((((......))).))))))))))))))))........))))))).))..-.---((--(.......)))....... ( -28.30)
>DroAna_CAF1 111560 103 + 1
CCU-UUUUAUCGGGC--GGGACGACACUUUGCGGCAGAAGUUUUCCAAUAAAACGGCAAAACUUUGCUGCGAACAAAAUUAAAGAAGACGACA-A---GGCAAAAAUGG----------U
(((-((((..(..((--((.....)..(((((((((((.(((((((........)).))))))))))))))))...............)).).-.---)..))))).))----------. ( -23.80)
>DroPer_CAF1 147307 101 + 1
CCC---AUUUUGGGGCAACAACGACACUUUGCGGCCGAAGUUUUCCAAUAAAACGGCAAAACUUUGCUGCGAACAAAAUUAAAGAAGACGACA-A---GG--AAAAUGC----------U
(((---.....)))(((..........((((((((.((((((((((........)).))))))))))))))))...............(....-.---).--....)))----------. ( -23.80)
>consensus
CC____UUUUUGGGC____AACGACACUUUGCGGCAGAAGUUUUCCAAUAAAACGGCAAAACUUUGCUGCGAACAAAAUUAAAGAAGACGACA_A___GG__AAAAUGG__________U
.........(((...............(((((((((.(((((((((........)).))))))))))))))))...............)))............................. (-18.30 = -18.19 +  -0.11)

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 11:35:32 2006