Locus 8143

Sequence ID 3L_DroMel_CAF1
Location 21,473,824 – 21,474,014
Length 190
Max. P 0.956661
window13302 window13303 window13304

overview

Window 2

Location 21,473,824 – 21,473,944
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 91.65
Mean single sequence MFE -38.42
Consensus MFE -34.75
Energy contribution -34.25
Covariance contribution -0.50
Combinations/Pair 1.19
Mean z-score -1.78
Structure conservation index 0.90
SVM decision value 1.47
SVM RNA-class probability 0.956661
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21473824 120 + 23771897
CAAAAUGGUAUCCGAGUGGGUGGCACCAAUCGUUAUCACCAGCAUUUGGGCCUUCAUUGGCAUCAUCUGCCCCUUCUUCGCCCGAGGACCCAACAGGGGGUAAGCUAAUCUGUUUACCCA
...........((...(((((((((((((..(((......)))..))))(((......)))......))))....((((....)))))))))...))((((((((......)))))))). ( -41.10)
>DroSec_CAF1 10724 120 + 1
CAAAAUGGUAUCCGAGUGGGUGGCACCAAUUGUAAUCACCAGCAUUUGGGCCUUCAUUGGCAUCAUCUGCCCCUUUUUCGCCCGAGGACCCAACAGGGGGUAAGCAAAUCUGUUUACCCA
...........((...(((((((((((((.(((........))).))))(((......)))......))))((((........)))))))))...))(((((((((....))))))))). ( -43.00)
>DroSim_CAF1 9235 120 + 1
CAAAAUGGUAUCCGAGUGGGUGGCACCAAUUGUAAUCACCAGCAUUUGGGCCUUUAUUGGCAUCAUCUGCCCCUUUUUCGCCCGAGGACCCAACAGGGGGUAAGCAAAUCUGUUUACCCA
...........((...(((((((((((((.(((........))).))))(((......)))......))))((((........)))))))))...))(((((((((....))))))))). ( -43.00)
>DroEre_CAF1 10831 115 + 1
CAAAAUGGUUUCCGAGUGGGUGGCACCAAUCGUAAUCACCAGCAUUUGGGCCUUCAUUGGCAUCAUCUGCCCCUUCUUCGCCCGAGGGCCCAACAGAGGGUAAGC-----UGUUUACCCA
.....((((((.(((.(((......))).))).))..))))....((((((((((...((((.....)))).(......)...))))))))))....(((((((.-----..))))))). ( -37.00)
>DroYak_CAF1 19750 115 + 1
CAAAAUGGUUUCCGAGUGGGUGGCACCAAUCGUAAUCACCAGCAUUUGGGCCUUCAUUGGCAUCAUCUGCCCCUUCUUCGCCCGAGGUCCCAACAGGGGGUAAGC-----UGUUUACCCA
.....(((...((...((((((((.((((..((........))..)))))))......((((.....))))........))))).))..))).....(((((((.-----..))))))). ( -34.10)
>DroAna_CAF1 9542 114 + 1
CAAAAUGGUUUCCGAGUGGGUGCCACCGAUCGUUAUCACCAGCAUUUGGGCCUUUAUUGGCAUCAUCUGUCCCUUCUUCGCUCGAGGUCCCAACAAGGGGUAGG------UGUUUACUUA
.....((((.(((....))).))))((((..(((......)))..))))(((......)))..(((((..(((((((((....)))).......)))))..)))------))........ ( -32.31)
>consensus
CAAAAUGGUAUCCGAGUGGGUGGCACCAAUCGUAAUCACCAGCAUUUGGGCCUUCAUUGGCAUCAUCUGCCCCUUCUUCGCCCGAGGACCCAACAGGGGGUAAGC_____UGUUUACCCA
.....(((...((...((((((((.((((..((........))..)))))))......((((.....))))........))))).))..))).....((((((((......)))))))). (-34.75 = -34.25 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,473,864 – 21,473,979
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.41
Mean single sequence MFE -29.41
Consensus MFE -24.43
Energy contribution -24.08
Covariance contribution -0.36
Combinations/Pair 1.24
Mean z-score -1.75
Structure conservation index 0.83
SVM decision value 0.72
SVM RNA-class probability 0.831142
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21473864 115 + 23771897
AGCAUUUGGGCCUUCAUUGGCAUCAUCUGCCCCUUCUUCGCCCGAGGACCCAACAGGGGGUAAGCUAAUCUGUUUACCCAACUUCAGUCUUGAGUAGCUUUGCAACCC-----ACAAAUG
.(((..(((((.......((((.....))))........)))))(((((((....))((((((((......)))))))).......))))).........))).....-----....... ( -32.56)
>DroSec_CAF1 10764 115 + 1
AGCAUUUGGGCCUUCAUUGGCAUCAUCUGCCCCUUUUUCGCCCGAGGACCCAACAGGGGGUAAGCAAAUCUGUUUACCCAACUUUAGUCUUGAGUAGCUUUGCAACCA-----ACUAAUU
.(((..(((((.......((((.....))))........)))))(((((((....))(((((((((....))))))))).......))))).........))).....-----....... ( -32.96)
>DroSim_CAF1 9275 115 + 1
AGCAUUUGGGCCUUUAUUGGCAUCAUCUGCCCCUUUUUCGCCCGAGGACCCAACAGGGGGUAAGCAAAUCUGUUUACCCAACUUUAGUCUUGAGUAGCUUUGCAACCA-----ACUAAUU
.(((..(((((.......((((.....))))........)))))(((((((....))(((((((((....))))))))).......))))).........))).....-----....... ( -32.96)
>DroEre_CAF1 10871 103 + 1
AGCAUUUGGGCCUUCAUUGGCAUCAUCUGCCCCUUCUUCGCCCGAGGGCCCAACAGAGGGUAAGC-----UGUUUACCCAACUUUAG-------UAGCUGUAGAACCA-----ACUAAUU
(((..((((((((((...((((.....)))).(......)...))))))))))....(((((((.-----..)))))))........-------..))).........-----....... ( -30.30)
>DroYak_CAF1 19790 108 + 1
AGCAUUUGGGCCUUCAUUGGCAUCAUCUGCCCCUUCUUCGCCCGAGGUCCCAACAGGGGGUAAGC-----UGUUUACCCAACUUUAG-------UUCCCUUACAACUAACUUAACUAAUU
.((.(((((((.......((((.....))))........))))))))).((....))(((((((.-----..)))))))....((((-------((.......))))))........... ( -23.76)
>DroAna_CAF1 9582 99 + 1
AGCAUUUGGGCCUUUAUUGGCAUCAUCUGUCCCUUCUUCGCUCGAGGUCCCAACAAGGGGUAGG------UGUUUACUUAAUAU---------GUUGCUU-AAACCCU-----CCCACUU
((((.....(((......)))..(((((..(((((((((....)))).......)))))..)))------))............---------..)))).-.......-----....... ( -23.91)
>consensus
AGCAUUUGGGCCUUCAUUGGCAUCAUCUGCCCCUUCUUCGCCCGAGGACCCAACAGGGGGUAAGC_____UGUUUACCCAACUUUAG______GUAGCUUUACAACCA_____ACUAAUU
.((.(((((((.......((((.....))))........)))))))...........((((((((......)))))))).................))...................... (-24.43 = -24.08 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,473,904 – 21,474,014
Length 110
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.85
Mean single sequence MFE -29.81
Consensus MFE -16.85
Energy contribution -17.11
Covariance contribution 0.25
Combinations/Pair 1.35
Mean z-score -2.21
Structure conservation index 0.57
SVM decision value 1.14
SVM RNA-class probability 0.921811
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21473904 110 + 23771897
CCCGAGGACCCAACAGGGGGUAAGCUAAUCUGUUUACCCAACUUCAGUCUUGAGUAGCUUUGCAACCC-----ACAAAUGAAACUAUU-----UUGCAGGGUGACUCAAUGCUGCCUGAU
.............((((((((((((......)))))))).....((((.((((((.(((((((((...-----...............-----))))))))).)))))).)))))))).. ( -39.17)
>DroSec_CAF1 10804 110 + 1
CCCGAGGACCCAACAGGGGGUAAGCAAAUCUGUUUACCCAACUUUAGUCUUGAGUAGCUUUGCAACCA-----ACUAAUUAAACUAUU-----UUGCAGGGUGACUCAAUGCUGCCUGAU
.............(((((((((((((....))))))))).....((((.((((((.(((((((((...-----...............-----))))))))).)))))).)))))))).. ( -38.17)
>DroSim_CAF1 9315 110 + 1
CCCGAGGACCCAACAGGGGGUAAGCAAAUCUGUUUACCCAACUUUAGUCUUGAGUAGCUUUGCAACCA-----ACUAAUUAAACUAUU-----UUGCAGGGUGACUCAAUGCUGCCUGAU
.............(((((((((((((....))))))))).....((((.((((((.(((((((((...-----...............-----))))))))).)))))).)))))))).. ( -38.17)
>DroEre_CAF1 10911 98 + 1
CCCGAGGGCCCAACAGAGGGUAAGC-----UGUUUACCCAACUUUAG-------UAGCUGUAGAACCA-----ACUAAUUUAACUAUU-----UUGCAGAGUGACUCAAUGCUGCCUGAU
((....)).....(((.(((((((.-----..))))))).......(-------(((((((((((...-----.............))-----)))))(((...)))...)))))))).. ( -20.09)
>DroYak_CAF1 19830 103 + 1
CCCGAGGUCCCAACAGGGGGUAAGC-----UGUUUACCCAACUUUAG-------UUCCCUUACAACUAACUUAACUAAUUUAAAAAUU-----UUGCAGGGUGACUCAAUGCUGCCUGAU
.............((((.((((...-----.(((.((((....((((-------((.......)))))).((((.....)))).....-----.....)))))))....)))).)))).. ( -20.10)
>DroAna_CAF1 9622 99 + 1
CUCGAGGUCCCAACAAGGGGUAGG------UGUUUACUUAAUAU---------GUUGCUU-AAACCCU-----CCCACUUAAUAUAUUCCCGAUUUUAGGGUGACUCAAUGCUGCCUUAU
.(((.((.......((((((.(((------.(((((..(((...---------.)))..)-)))))))-----))).)))........)))))...((((((..(.....)..)))))). ( -23.16)
>consensus
CCCGAGGACCCAACAGGGGGUAAGC_____UGUUUACCCAACUUUAG______GUAGCUUUACAACCA_____ACUAAUUAAACUAUU_____UUGCAGGGUGACUCAAUGCUGCCUGAU
...(((...........((((((((......)))))))).................(((((((((............................)))))))))..)))............. (-16.85 = -17.11 +   0.25)

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 13:07:22 2006