Locus 678

Sequence ID 3R_DroMel_CAF1
Location 2,450,924 – 2,451,021
Length 97
Max. P 0.991104
window1071 window1072

overview

Window 1

Location 2,450,924 – 2,451,021
Length 97
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 90.45
Mean single sequence MFE -25.72
Consensus MFE -24.12
Energy contribution -24.15
Covariance contribution 0.03
Combinations/Pair 1.03
Mean z-score -1.25
Structure conservation index 0.94
SVM decision value 0.65
SVM RNA-class probability 0.811670
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2450924 97 + 27905053
----UUGGCGGAAAAAUGUCUUUUAAUUAGUGUUUAAUUGAAUUGCAAACUGGAAUUUUAAUCGAAAAUUGCAGCGGG-------------------UCGACUUUUCCGCCCCGUUUGGC
----..(((((((((.(((..(((((((((...)))))))))..)))..(((.((((((.....)))))).)))....-------------------.....)))))))))......... ( -25.50)
>DroSec_CAF1 9924 97 + 1
----UUGGCUGAAAAAUGUCUUUUAAUUAGUGUUUAAUUGAAUUGCAAACUGGAAUUUUAAUCGAAAAUUGCAGCGGG-------------------UCGACUUUUCCGCCCCGUUUGGC
----...((..((...(((..(((((((((...)))))))))..)))..(((.((((((.....)))))).)))((((-------------------.((.......)).))))))..)) ( -22.10)
>DroSim_CAF1 6663 97 + 1
----UUGGCGGAAAAAUGUCUUUUAAUUAGUGUUUAAUUGAAUUGCAAACUGGAAUUUUAAUCGAAAAUUGCAGCGGG-------------------UCGACUUUUCCGCCCCGUUUGGC
----..(((((((((.(((..(((((((((...)))))))))..)))..(((.((((((.....)))))).)))....-------------------.....)))))))))......... ( -25.50)
>DroEre_CAF1 10975 97 + 1
----UUGGCGGAAAAAUGUCUUUUAAUUAGUGUUUAAUUGAAUUGCAAACUGGAAUUUUAAUCGAAAAUUGCAGCGGG-------------------UCGACUUUUCCGCCCCGUUUGGC
----..(((((((((.(((..(((((((((...)))))))))..)))..(((.((((((.....)))))).)))....-------------------.....)))))))))......... ( -25.50)
>DroYak_CAF1 11083 97 + 1
----UUGGCGGAAAAAUGUCUUUUAAUUAGUGUUUAAUUGAAUUGCAAACUGGAAUUUUAAUCGAAAAUUGCAGCGGG-------------------UCGACUUUUCCGUCCCGUUUGGC
----..(((((((((.(((..(((((((((...)))))))))..)))..(((.((((((.....)))))).)))....-------------------.....)))))))))......... ( -22.80)
>DroAna_CAF1 10511 120 + 1
GGCUUCGGCGGAAAAAUGUCUUUUAAUUAGUGUUUAAUUGAAUUGCAAACUGGAAUUUUAAUCGAAAAUUGCAGCUGGUGGGAGGCCGGGCUAGUUCUCGACUUUUCCGCCCCGUUAGAA
((....(((((((((..(((....(((((((..................(((.((((((.....)))))).)))(((((.....))))))))))))...))))))))))))))....... ( -32.90)
>consensus
____UUGGCGGAAAAAUGUCUUUUAAUUAGUGUUUAAUUGAAUUGCAAACUGGAAUUUUAAUCGAAAAUUGCAGCGGG___________________UCGACUUUUCCGCCCCGUUUGGC
......(((((((((.(((..(((((((((...)))))))))..)))..(((.((((((.....)))))).)))............................)))))))))......... (-24.12 = -24.15 +   0.03)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,450,924 – 2,451,021
Length 97
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.45
Mean single sequence MFE -21.75
Consensus MFE -20.29
Energy contribution -20.48
Covariance contribution 0.19
Combinations/Pair 1.03
Mean z-score -1.97
Structure conservation index 0.93
SVM decision value 2.25
SVM RNA-class probability 0.991104
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2450924 97 - 27905053
GCCAAACGGGGCGGAAAAGUCGA-------------------CCCGCUGCAAUUUUCGAUUAAAAUUCCAGUUUGCAAUUCAAUUAAACACUAAUUAAAAGACAUUUUUCCGCCAA----
.((....))((((((((((((..-------------------...((((.((((((.....)))))).)))).........(((((.....)))))....)))..)))))))))..---- ( -22.70)
>DroSec_CAF1 9924 97 - 1
GCCAAACGGGGCGGAAAAGUCGA-------------------CCCGCUGCAAUUUUCGAUUAAAAUUCCAGUUUGCAAUUCAAUUAAACACUAAUUAAAAGACAUUUUUCAGCCAA----
.((....))((((((((((((..-------------------...((((.((((((.....)))))).)))).........(((((.....)))))....))).)))))).)))..---- ( -17.60)
>DroSim_CAF1 6663 97 - 1
GCCAAACGGGGCGGAAAAGUCGA-------------------CCCGCUGCAAUUUUCGAUUAAAAUUCCAGUUUGCAAUUCAAUUAAACACUAAUUAAAAGACAUUUUUCCGCCAA----
.((....))((((((((((((..-------------------...((((.((((((.....)))))).)))).........(((((.....)))))....)))..)))))))))..---- ( -22.70)
>DroEre_CAF1 10975 97 - 1
GCCAAACGGGGCGGAAAAGUCGA-------------------CCCGCUGCAAUUUUCGAUUAAAAUUCCAGUUUGCAAUUCAAUUAAACACUAAUUAAAAGACAUUUUUCCGCCAA----
.((....))((((((((((((..-------------------...((((.((((((.....)))))).)))).........(((((.....)))))....)))..)))))))))..---- ( -22.70)
>DroYak_CAF1 11083 97 - 1
GCCAAACGGGACGGAAAAGUCGA-------------------CCCGCUGCAAUUUUCGAUUAAAAUUCCAGUUUGCAAUUCAAUUAAACACUAAUUAAAAGACAUUUUUCCGCCAA----
........((.((((((((((..-------------------...((((.((((((.....)))))).)))).........(((((.....)))))....)))..)))))))))..---- ( -18.20)
>DroAna_CAF1 10511 120 - 1
UUCUAACGGGGCGGAAAAGUCGAGAACUAGCCCGGCCUCCCACCAGCUGCAAUUUUCGAUUAAAAUUCCAGUUUGCAAUUCAAUUAAACACUAAUUAAAAGACAUUUUUCCGCCGAAGCC
.........(((((((((((((((((.((((..((.......)).))))...))))))))).........(((((.........))))).................))))))))...... ( -26.60)
>consensus
GCCAAACGGGGCGGAAAAGUCGA___________________CCCGCUGCAAUUUUCGAUUAAAAUUCCAGUUUGCAAUUCAAUUAAACACUAAUUAAAAGACAUUUUUCCGCCAA____
.((....))((((((((((((........................((((.((((((.....)))))).)))).........(((((.....)))))....)))..)))))))))...... (-20.29 = -20.48 +   0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:04 2006