Locus 1884

Sequence ID X_DroMel_CAF1
Location 5,225,278 – 5,225,376
Length 98
Max. P 0.998505
window3059 window3060

overview

Window 9

Location 5,225,278 – 5,225,376
Length 98
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 78.64
Mean single sequence MFE -27.52
Consensus MFE -15.84
Energy contribution -16.12
Covariance contribution 0.28
Combinations/Pair 1.22
Mean z-score -2.36
Structure conservation index 0.58
SVM decision value 1.54
SVM RNA-class probability 0.962781
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5225278 98 + 22224390
GCAAUAGAGAACAA--AACCCCAAUCGAUU---UGCAAAUUUUAUCGGUUGGGGCUCGUUCUUU--UG-----GAACUUAGAAA----UACGUAGACAGCAUGGGAGCAUCUAU
.(((..((((((..--..(((((((((((.---..........)))))))))))...)))))))--))-----...........----...(((((..((......)).))))) ( -26.40)
>DroSec_CAF1 1713 98 + 1
GCAAUAGAGAACAA--AACCCCAACCGAUU---UGCAAUUUUUAUCGGUUGGGGCUCGUUCUUU--UG-----GAACUUAGAAA----UACGUAGACAGCAUGGGAGCAUCUAU
.(((..((((((..--..(((((((((((.---..........)))))))))))...)))))))--))-----...........----...(((((..((......)).))))) ( -29.00)
>DroEre_CAF1 1727 98 + 1
GCAAUAGAAAACAA--AACCCCAACCGAUU---UGCAAAUUUUAUCGGUUGGGGAUCGUUCUUU--UG-----GAACUUAGAAA----UAUGUAGAUAGCAUGGGAGCAUUUAU
((............--..(((((((((((.---..........))))))))))).((((((...--..-----)))).......----(((((.....))))).))))...... ( -28.00)
>DroYak_CAF1 1781 98 + 1
GCAAUUGAAAACAA--AACCCCAACCGAUU---UGCAAAUUUGAUCGGUUGGUGCUUGUUCUUU--UG-----AAAUUUAGAAA----UACGUAGACAGCAUGGGAGCAUCUAU
(((.(((....)))--....((((((((((---.........))))))))))))).((((((..--((-----...((((....----....))))...))..))))))..... ( -23.60)
>DroAna_CAF1 3521 109 + 1
GCAAUAGAAGAGGAGGAAGCUCUGCUGAUUCUAUGCAAA-----UCCGCCGAGGAUCCUCCUCUGUUAAAAAAAAAUCUAGAGAACUGUAUGUAGAGAGCAUGGGAGCAUAUAU
((..(((.(((((((((..(((.((.((((.......))-----)).)).)))..))))))))).)))........((((.(........).))))..))(((....))).... ( -30.60)
>consensus
GCAAUAGAAAACAA__AACCCCAACCGAUU___UGCAAAUUUUAUCGGUUGGGGCUCGUUCUUU__UG_____GAACUUAGAAA____UACGUAGACAGCAUGGGAGCAUCUAU
..................(((((((((((..............))))))))))).....................................(((((..((......)).))))) (-15.84 = -16.12 +   0.28)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,225,278 – 5,225,376
Length 98
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 78.64
Mean single sequence MFE -27.12
Consensus MFE -22.20
Energy contribution -22.44
Covariance contribution 0.24
Combinations/Pair 1.31
Mean z-score -3.06
Structure conservation index 0.82
SVM decision value 3.12
SVM RNA-class probability 0.998505
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5225278 98 - 22224390
AUAGAUGCUCCCAUGCUGUCUACGUA----UUUCUAAGUUC-----CA--AAAGAACGAGCCCCAACCGAUAAAAUUUGCA---AAUCGAUUGGGGUU--UUGUUCUCUAUUGC
.(((((((......)).)))))....----...........-----..--..((((((((((((((.((((..........---.)))).)))))).)--)))))))....... ( -26.20)
>DroSec_CAF1 1713 98 - 1
AUAGAUGCUCCCAUGCUGUCUACGUA----UUUCUAAGUUC-----CA--AAAGAACGAGCCCCAACCGAUAAAAAUUGCA---AAUCGGUUGGGGUU--UUGUUCUCUAUUGC
.(((((((......)).)))))....----...........-----..--..(((((((((((((((((((..........---.))))))))))).)--)))))))....... ( -32.80)
>DroEre_CAF1 1727 98 - 1
AUAAAUGCUCCCAUGCUAUCUACAUA----UUUCUAAGUUC-----CA--AAAGAACGAUCCCCAACCGAUAAAAUUUGCA---AAUCGGUUGGGGUU--UUGUUUUCUAUUGC
......((......))..........----...........-----..--..(((((((.(((((((((((..........---.)))))))))))..--)))))))....... ( -25.00)
>DroYak_CAF1 1781 98 - 1
AUAGAUGCUCCCAUGCUGUCUACGUA----UUUCUAAAUUU-----CA--AAAGAACAAGCACCAACCGAUCAAAUUUGCA---AAUCGGUUGGGGUU--UUGUUUUCAAUUGC
.(((((((......)).)))))....----...........-----..--..(((((((((.(((((((((..........---.))))))))).).)--)))))))....... ( -23.20)
>DroAna_CAF1 3521 109 - 1
AUAUAUGCUCCCAUGCUCUCUACAUACAGUUCUCUAGAUUUUUUUUUAACAGAGGAGGAUCCUCGGCGGA-----UUUGCAUAGAAUCAGCAGAGCUUCCUCCUCUUCUAUUGC
......((......))..................................(((((((((..(((.((.((-----(((.....))))).)).)))..)))))))))........ ( -28.40)
>consensus
AUAGAUGCUCCCAUGCUGUCUACGUA____UUUCUAAGUUC_____CA__AAAGAACGAGCCCCAACCGAUAAAAUUUGCA___AAUCGGUUGGGGUU__UUGUUUUCUAUUGC
.(((((((......)).)))))..............................(((((((((((((((((((..............))))))))))))...)))))))....... (-22.20 = -22.44 +   0.24)

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 10:20:58 2006