Locus 7947

Sequence ID 3L_DroMel_CAF1
Location 21,077,860 – 21,077,973
Length 113
Max. P 0.998541
window12963 window12964

overview

Window 3

Location 21,077,860 – 21,077,973
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.77
Mean single sequence MFE -22.95
Consensus MFE -9.68
Energy contribution -12.64
Covariance contribution 2.96
Combinations/Pair 1.21
Mean z-score -3.40
Structure conservation index 0.42
SVM decision value 3.14
SVM RNA-class probability 0.998541
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21077860 113 + 23771897
AUUU-CACCCUAUUGCCCUCAAAAGUAUGCUACACCUUUAAUGGAUUUUCCAUUUGCUCGCUAUACC-UUUUGUUUG-----UUUAAAUCAUUUAAAUAAAAUUUUGAGGGCCACACUUC
....-.........((((((((((((((((.........(((((.....))))).....)).)))).-.....((((-----(((((.....))))))))).))))))))))........ ( -25.84)
>DroSec_CAF1 133135 113 + 1
AUUU-CAACCC-UUGCCCUCAAAAGUAUGCUACACCUUUAAUGGAUUUUCCAUUUGCUUGCUGUACCAUUUUGUUUG-----UUUAAAUCAUUUAAAUAACAUUUUGAGGGCCACACUUC
....-......-..((((((((((..(((.((((.(...(((((.....))))).....).)))).)))..((((.(-----(((((.....))))))))))))))))))))........ ( -26.60)
>DroSim_CAF1 39422 113 + 1
AUUU-CAACCC-UUGCCCUCAAAAGUAUGCUACACCUUUAAUGGAUUUUCCAUUGGCUUGCUGUACCUUUUUGUUUG-----UUUAAAUCAUUUAAAUAACAUUUUGAGGGCCACACUUC
....-......-..((((((((((((((((....((...(((((.....)))))))...)).)))).....((((.(-----(((((.....))))))))))))))))))))........ ( -27.30)
>DroEre_CAF1 55678 115 + 1
CAUUUAAACC--CCGCCCUCAAAAGUAUGCUACAGCUUAAAUGGUUUC-CC-GCUCUUUGCUGCACCACUUUGCUUGCUUAACUUAAAUCAUUUAAAUAACAU-GUUGGGGCCACACUUC
..........--..((((.(((..((..((....))(((((((((((.-..-((.....)).(((......)))...........)))))))))))...))..-.)))))))........ ( -20.80)
>DroYak_CAF1 27118 109 + 1
AUUUCCAACC--CAGCCUUCC--AGUGUGCUACACCUUAAAUGCCCUCACC-UCUUUUCAUUGCACCAUUUUGCUU------UUUAAAUUAUUUAAAUAACUUUGUGAGGACCACACUUU
..........--.........--((((((......(......).((((((.-..........(((......)))..------(((((.....))))).......))))))..)))))).. ( -14.20)
>consensus
AUUU_CAACC__UUGCCCUCAAAAGUAUGCUACACCUUUAAUGGAUUUUCCAUUUGCUUGCUGUACCAUUUUGUUUG_____UUUAAAUCAUUUAAAUAACAUUUUGAGGGCCACACUUC
..............((((((((((((((((.......(((((((.....)))))))...)).))))................(((((.....))))).....))))))))))........ ( -9.68 = -12.64 +   2.96)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 21,077,860 – 21,077,973
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.77
Mean single sequence MFE -27.84
Consensus MFE -14.90
Energy contribution -16.38
Covariance contribution 1.48
Combinations/Pair 1.23
Mean z-score -2.82
Structure conservation index 0.54
SVM decision value 2.38
SVM RNA-class probability 0.993232
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21077860 113 - 23771897
GAAGUGUGGCCCUCAAAAUUUUAUUUAAAUGAUUUAAA-----CAAACAAAA-GGUAUAGCGAGCAAAUGGAAAAUCCAUUAAAGGUGUAGCAUACUUUUGAGGGCAAUAGGGUG-AAAU
....(((.((((((.(((((..........)))))...-----......(((-(((((.((..((.(((((.....)))))....))...)))))))))))))))).))).....-.... ( -26.40)
>DroSec_CAF1 133135 113 - 1
GAAGUGUGGCCCUCAAAAUGUUAUUUAAAUGAUUUAAA-----CAAACAAAAUGGUACAGCAAGCAAAUGGAAAAUCCAUUAAAGGUGUAGCAUACUUUUGAGGGCAA-GGGUUG-AAAU
........((((((((((((((.(((((.....)))))-----..))))..(((.((((.(.....(((((.....)))))...).)))).)))..))))))))))..-......-.... ( -28.70)
>DroSim_CAF1 39422 113 - 1
GAAGUGUGGCCCUCAAAAUGUUAUUUAAAUGAUUUAAA-----CAAACAAAAAGGUACAGCAAGCCAAUGGAAAAUCCAUUAAAGGUGUAGCAUACUUUUGAGGGCAA-GGGUUG-AAAU
........((((((....((((.(((((.....)))))-----..)))).(((((((..((..((((((((.....)))))...)))...)).)))))))))))))..-......-.... ( -27.30)
>DroEre_CAF1 55678 115 - 1
GAAGUGUGGCCCCAAC-AUGUUAUUUAAAUGAUUUAAGUUAAGCAAGCAAAGUGGUGCAGCAAAGAGC-GG-GAAACCAUUUAAGCUGUAGCAUACUUUUGAGGGCGG--GGUUUAAAUG
...((..(((((((((-..(((((....)))))....)))..((...(((((((.((((((..(((..-((-....)).)))..)))))).)))...))))...))))--))))...)). ( -32.80)
>DroYak_CAF1 27118 109 - 1
AAAGUGUGGUCCUCACAAAGUUAUUUAAAUAAUUUAAA------AAGCAAAAUGGUGCAAUGAAAAGA-GGUGAGGGCAUUUAAGGUGUAGCACACU--GGAAGGCUG--GGUUGGAAAU
..((((((..((((((.(((((((....)))))))...------..(((......)))..........-.))))))((((.....))))..))))))--.........--.......... ( -24.00)
>consensus
GAAGUGUGGCCCUCAAAAUGUUAUUUAAAUGAUUUAAA_____CAAACAAAAUGGUACAGCAAGCAAAUGGAAAAUCCAUUAAAGGUGUAGCAUACUUUUGAGGGCAA__GGUUG_AAAU
........((((((((((.(((((....)))))....................(.((((.(.....(((((.....)))))...).)))).)....)))))))))).............. (-14.90 = -16.38 +   1.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:01:44 2006