Locus 6773

Sequence ID 3R_DroMel_CAF1
Location 17,867,331 – 17,867,427
Length 96
Max. P 0.942159
window10998 window10999

overview

Window 8

Location 17,867,331 – 17,867,427
Length 96
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 76.49
Mean single sequence MFE -29.23
Consensus MFE -14.21
Energy contribution -15.77
Covariance contribution 1.56
Combinations/Pair 1.11
Mean z-score -2.04
Structure conservation index 0.49
SVM decision value 0.55
SVM RNA-class probability 0.779701
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17867331 96 + 27905053
GCCAACGCGCCAAAUUGUGGCCCACCCAGCUACC--AGGUGGCAACGCUGAAUGUUGUUAG---UCA---AUUAAUGCAUUAACUAGCCUCCAUUUGGAAGAAU
((....))((((..(.(((((.......))))).--)..))))....(..((((..(((((---(.(---((......))).))))))...))))..)...... ( -23.90)
>DroVir_CAF1 8676 98 + 1
GCCAACGCGCCAAAUA-UGCCUAAACAAGCGAGUGCAAGCGG----GAUGGCUGCUGUUAACAGCGCAUGAUUGACAGGCUUAGA-GCUGCCACCUAACAGAAA
((((.(.(((...((.-(((........))).))....))).----).)))).((((....))))............(((.....-...)))............ ( -24.60)
>DroSec_CAF1 8982 96 + 1
GCCAACGCGCCAAAUUGUGGCCCACCCAGCGACC--UGGUGGCAACGCUGAAUAUUGUUAG---UCA---AUUAAUGCAUUAACUAGGCUCCAUUUGGCAGAAU
((....))(((((((.(..(((....(((((.((--....))...)))))......(((((---(((---.....)).))))))..)))..))))))))..... ( -28.50)
>DroSim_CAF1 10519 96 + 1
GCCAACGCGCCAAAUUGUGGCCCACCAAGCGACC--AGGUGGCAACGCUAAAUGUUGUUAG---UCA---AUUAAUGCAUUAACUGGGCUUCAUUUGGCAAAAU
((....))(((((((.(.(((((....((((((.--.((((....))))....))))))((---(.(---((......))).)))))))).))))))))..... ( -30.30)
>DroEre_CAF1 9607 96 + 1
GCCAACGCGCCAAAUGGUGGCCCACCAAGCGACC--AGGUGGCAACGCUGAAUGUUGUUAG---UCA---AUUAAUUAACUAACUAGGCACUAUUUGGCCGAAU
.....((.(((((((((((.((.....((((...--.((((....))))...))))(((((---(.(---(....)).))))))..)))))))))))))))... ( -33.00)
>DroYak_CAF1 9699 96 + 1
GCCAACGCGCCAAAUGGUGGCCCACCUAGCGACU--AGGUGGCAACGCUGAAUGUUGUUAG---UCA---AUUAAUGUACUAACUAGACACUAUUUGGCCAAAA
((....))((((((((((((((.((((((...))--))))))).............(((((---(((---.....)).))))))....)))))))))))..... ( -35.10)
>consensus
GCCAACGCGCCAAAUUGUGGCCCACCAAGCGACC__AGGUGGCAACGCUGAAUGUUGUUAG___UCA___AUUAAUGCACUAACUAGGCUCCAUUUGGCAGAAU
(((((...((((.....))))......((((((....((((....))))....))))))...................................)))))..... (-14.21 = -15.77 +   1.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,867,331 – 17,867,427
Length 96
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 76.49
Mean single sequence MFE -33.13
Consensus MFE -14.35
Energy contribution -14.97
Covariance contribution 0.61
Combinations/Pair 1.25
Mean z-score -2.56
Structure conservation index 0.43
SVM decision value 1.32
SVM RNA-class probability 0.942159
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17867331 96 - 27905053
AUUCUUCCAAAUGGAGGCUAGUUAAUGCAUUAAU---UGA---CUAACAACAUUCAGCGUUGCCACCU--GGUAGCUGGGUGGGCCACAAUUUGGCGCGUUGGC
...(((((....))))).((((((((......))---)))---))).......(((((((..(((((.--.(...)..)))))((((.....))))))))))). ( -34.50)
>DroVir_CAF1 8676 98 - 1
UUUCUGUUAGGUGGCAGC-UCUAAGCCUGUCAAUCAUGCGCUGUUAACAGCAGCCAUC----CCGCUUGCACUCGCUUGUUUAGGCA-UAUUUGGCGCGUUGGC
.........(((((((((-.....).))))).)))((((((((....)))).((((..----..(((((.((......)).))))).-....)))))))).... ( -28.40)
>DroSec_CAF1 8982 96 - 1
AUUCUGCCAAAUGGAGCCUAGUUAAUGCAUUAAU---UGA---CUAACAAUAUUCAGCGUUGCCACCA--GGUCGCUGGGUGGGCCACAAUUUGGCGCGUUGGC
.....((((((((..(((((((((((......))---)))---)))....(((((((((..(((....--)))))))))))))))..).)))))))........ ( -35.40)
>DroSim_CAF1 10519 96 - 1
AUUUUGCCAAAUGAAGCCCAGUUAAUGCAUUAAU---UGA---CUAACAACAUUUAGCGUUGCCACCU--GGUCGCUUGGUGGGCCACAAUUUGGCGCGUUGGC
.....(((((((...(((((((((((......))---)))---))......((..((((..(((....--)))))))..))))))....)))))))........ ( -30.90)
>DroEre_CAF1 9607 96 - 1
AUUCGGCCAAAUAGUGCCUAGUUAGUUAAUUAAU---UGA---CUAACAACAUUCAGCGUUGCCACCU--GGUCGCUUGGUGGGCCACCAUUUGGCGCGUUGGC
...(((((((((.(((((..(((((((((....)---)))---)))))..(((..((((..(((....--)))))))..))))).))).))))))).))..... ( -36.40)
>DroYak_CAF1 9699 96 - 1
UUUUGGCCAAAUAGUGUCUAGUUAGUACAUUAAU---UGA---CUAACAACAUUCAGCGUUGCCACCU--AGUCGCUAGGUGGGCCACCAUUUGGCGCGUUGGC
.....(((((..(((((...((((((.((.....---)))---))))).)))))..((....((((((--((...))))))))((((.....)))))).))))) ( -33.20)
>consensus
AUUCUGCCAAAUGGAGCCUAGUUAAUGCAUUAAU___UGA___CUAACAACAUUCAGCGUUGCCACCU__GGUCGCUUGGUGGGCCACAAUUUGGCGCGUUGGC
.....................................................(((((((..(((((...........)))))((((.....))))))))))). (-14.35 = -14.97 +   0.61)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:29:37 2006