Locus 2535

Sequence ID 3R_DroMel_CAF1
Location 6,888,003 – 6,888,109
Length 106
Max. P 0.598203
window4142 window4143

overview

Window 2

Location 6,888,003 – 6,888,109
Length 106
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 74.44
Mean single sequence MFE -31.35
Consensus MFE -21.35
Energy contribution -20.99
Covariance contribution -0.36
Combinations/Pair 1.11
Mean z-score -1.01
Structure conservation index 0.68
SVM decision value 0.13
SVM RNA-class probability 0.598203
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6888003 106 + 27905053
GAGCCUCGGAUGC--CUCGAAGGCGUGUCCGUUGCAAGGAAUUCGAACAUGUUGCAUAUGCAAUGCGGACGCUACUUUCGGC-CUCUCC-CAAUCCUUCGUGGUGUGUGU
......((.((((--(.((((((.((((((((((((.(.(((........))).)...))))..)))))))).......((.-.....)-)...)))))).))))).)). ( -34.40)
>DroPse_CAF1 58972 88 + 1
CGAAUGCGAAUGCGGCUUGAAGGCGUGUCCGUUGCAAGCA-GUCGAACAUGUUGCAUAUGCAAUGCGGACACUACUUUCGCUCCUCUCU---------------------
.((..(((((....(((....)))((((((((((((.(((-(.(......)))))...))))..))))))))....)))))...))...--------------------- ( -28.10)
>DroEre_CAF1 43053 106 + 1
GAGCCUCGGAUGC--CUCGAAGGCGUGUCCGUUGCAAGGAGUUCGAACAUGUUGCAUAUGCAAUGCGGACACUACUUUCGGU-CUCUCC-CAAUCCUUCGUGGUUUGUCU
.......((((((--(.((((((.(((((((((((((.(.((....)).).)))))........)))))))).......((.-.....)-)...)))))).)))..)))) ( -33.50)
>DroYak_CAF1 43076 107 + 1
GAGCCUCGGAUGC--CUCGAAGGCGUGUCCGUUGCAAGGAAUUCGAACAUGUUGCAUAUGCAAUGCGGACACCACUUUCGGU-CUCUCCCCCAUCCUUCGUGGUGUGACU
.........((((--(.((((((.((((((((((((.(.(((........))).)...))))..)))))))).......((.-.......))..)))))).))))).... ( -32.60)
>DroAna_CAF1 40318 83 + 1
AAGCCUGGGGUGG--CUCGAAGGCGUGUCCGUUGCACGGCAAGCGAACAUGUUGCAUAUGCAAUGCGGACACUACUUUCGUC-UU-U-----------------------
.((((......))--))((((((.((((((((((((..((((.(......)))))...))))..))))))))..))))))..-..-.----------------------- ( -31.40)
>DroPer_CAF1 59971 88 + 1
CGAAUGCGAAUGCGGCUUGAAGGCGUGUCCGUUGCAAGCA-GUCGAACAUGUUGCAUAUGCAAUGCGGACACUACUUUCGCUCCUCUCU---------------------
.((..(((((....(((....)))((((((((((((.(((-(.(......)))))...))))..))))))))....)))))...))...--------------------- ( -28.10)
>consensus
GAGCCUCGGAUGC__CUCGAAGGCGUGUCCGUUGCAAGGAAUUCGAACAUGUUGCAUAUGCAAUGCGGACACUACUUUCGGU_CUCUCC_____________________
.................((((((.((((((((..................(((((....)))))))))))))..)))))).............................. (-21.35 = -20.99 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,888,003 – 6,888,109
Length 106
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 74.44
Mean single sequence MFE -30.08
Consensus MFE -18.94
Energy contribution -19.50
Covariance contribution 0.56
Combinations/Pair 1.12
Mean z-score -1.20
Structure conservation index 0.63
SVM decision value 0.06
SVM RNA-class probability 0.564519
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6888003 106 - 27905053
ACACACACCACGAAGGAUUG-GGAGAG-GCCGAAAGUAGCGUCCGCAUUGCAUAUGCAACAUGUUCGAAUUCCUUGCAACGGACACGCCUUCGAG--GCAUCCGAGGCUC
............(((((((.-(((((.-(((....)..)).)).((((.....))))......))).)).)))))((..((((...(((.....)--)).))))..)).. ( -27.70)
>DroPse_CAF1 58972 88 - 1
---------------------AGAGAGGAGCGAAAGUAGUGUCCGCAUUGCAUAUGCAACAUGUUCGAC-UGCUUGCAACGGACACGCCUUCAAGCCGCAUUCGCAUUCG
---------------------...(((..(((((.((.(((((((..(((((...(((...........-))).))))))))))))((......)).)).))))).))). ( -28.70)
>DroEre_CAF1 43053 106 - 1
AGACAAACCACGAAGGAUUG-GGAGAG-ACCGAAAGUAGUGUCCGCAUUGCAUAUGCAACAUGUUCGAACUCCUUGCAACGGACACGCCUUCGAG--GCAUCCGAGGCUC
.......((.((((((.(((-(.....-.)))).....((((((((((.....)))).....((((((.....))).))))))))).)))))).)--)............ ( -31.50)
>DroYak_CAF1 43076 107 - 1
AGUCACACCACGAAGGAUGGGGGAGAG-ACCGAAAGUGGUGUCCGCAUUGCAUAUGCAACAUGUUCGAAUUCCUUGCAACGGACACGCCUUCGAG--GCAUCCGAGGCUC
...(((.((((....).)))((.....-.))....)))((((((((((.....)))).....((((((.....))).)))))))))(((((.((.--...)).))))).. ( -33.60)
>DroAna_CAF1 40318 83 - 1
-----------------------A-AA-GACGAAAGUAGUGUCCGCAUUGCAUAUGCAACAUGUUCGCUUGCCGUGCAACGGACACGCCUUCGAG--CCACCCCAGGCUU
-----------------------.-..-..((((.((.(((((((..((((((..(((((......).)))).))))))))))))))).))))((--((......)))). ( -30.30)
>DroPer_CAF1 59971 88 - 1
---------------------AGAGAGGAGCGAAAGUAGUGUCCGCAUUGCAUAUGCAACAUGUUCGAC-UGCUUGCAACGGACACGCCUUCAAGCCGCAUUCGCAUUCG
---------------------...(((..(((((.((.(((((((..(((((...(((...........-))).))))))))))))((......)).)).))))).))). ( -28.70)
>consensus
_____________________GGAGAG_ACCGAAAGUAGUGUCCGCAUUGCAUAUGCAACAUGUUCGAAUUCCUUGCAACGGACACGCCUUCGAG__GCAUCCGAGGCUC
..............................(....)..((((((((((.....)))).....((((((.....))).)))))))))(((((.((......)).))))).. (-18.94 = -19.50 +   0.56)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:44 2006