Locus 578

Sequence ID 2L_DroMel_CAF1
Location 1,769,421 – 1,769,547
Length 126
Max. P 0.965760
window951 window952 window953 window954

overview

Window 1

Location 1,769,421 – 1,769,514
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.65
Mean single sequence MFE -27.69
Consensus MFE -24.60
Energy contribution -24.10
Covariance contribution -0.50
Combinations/Pair 1.24
Mean z-score -2.53
Structure conservation index 0.89
SVM decision value 1.59
SVM RNA-class probability 0.965760
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1769421 93 + 22407834
AUCUUAGGAAUCAU---------UGUUUCAUCGAAAUUUGCAUAAUUCGCUGCGAAUUUUGUGGUCGGAAUUUAACGAGCCACACAAUUUGUCAGCGGACAA------------------
......(((((...---------.)))))................(((((((((((((.((((((((........))).))))).)))))).)))))))...------------------ ( -27.70)
>DroPse_CAF1 29773 108 + 1
AUCUUAAAGAUC------------GUUUCAUUCAAAUUUACAUAAUUCGUUGCAAGUUUUGGGGCCAACAUUUAACGAGCCCCACAAUUUGUCAGCGGACAGCGGACAAGGCAUUCCACA
............------------.....................(((((((((((((.(((((((..........).)))))).)))))).)))))))..(.(((........))).). ( -27.00)
>DroSim_CAF1 29269 93 + 1
AUCUUAGGAAUCAU---------UGUUUCAUUGAAAUUUGCAUAAUUCGCUGCGAAUUUUGUGGUCGGAAUUUAACGAGCCACACAAUUUGUCAGCGGACAA------------------
......(((((...---------.)))))................(((((((((((((.((((((((........))).))))).)))))).)))))))...------------------ ( -27.70)
>DroEre_CAF1 26241 93 + 1
GUCUUAAGAAUCAU---------UGUUUCAUUGAAAUUUGCAUAAUUCGCUGCGAAUUUUGUGGUCGGAAUUUAACGAGCCACACAAUUUGUCAGCGGACAA------------------
((((...((((...---------(((.............)))..))))((((((((((.((((((((........))).))))).)))))).))))))))..------------------ ( -28.42)
>DroYak_CAF1 35401 93 + 1
GACUUGAGAAUCAU---------UGUUUCAUUGAAAUUUGCAUAAUUCGCUGCGAAUUUUGUGGUCGCAAUUUAACGAGCCACACAAUUUGUCAGCGGACAA------------------
....(((((.....---------..)))))...............(((((((((((((.((((((((........))).))))).)))))).)))))))...------------------ ( -26.10)
>DroAna_CAF1 25744 102 + 1
AUCUGCGGGAUCGUCGUCCUGUCUGUUUCAUUGAAAUUUGCAUAAUUCGCUGGGAGUUUUGUGGCCGGAAUUUAACGAGCCAAACAAUUUGUCAGCGGACGG------------------
....(((....)))((((((((..(((((...)))))..)))......((((((((((...((((((........)).))))...))))).)))))))))).------------------ ( -29.20)
>consensus
AUCUUAAGAAUCAU_________UGUUUCAUUGAAAUUUGCAUAAUUCGCUGCGAAUUUUGUGGUCGGAAUUUAACGAGCCACACAAUUUGUCAGCGGACAA__________________
.............................................(((((((((((((.((((((((........)).)))))).)))))).)))))))..................... (-24.60 = -24.10 +  -0.50)

alignment

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secondary structure

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Window 2

Location 1,769,421 – 1,769,514
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.65
Mean single sequence MFE -22.18
Consensus MFE -16.72
Energy contribution -16.75
Covariance contribution 0.03
Combinations/Pair 1.18
Mean z-score -1.45
Structure conservation index 0.75
SVM decision value 0.41
SVM RNA-class probability 0.726712
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1769421 93 - 22407834
------------------UUGUCCGCUGACAAAUUGUGUGGCUCGUUAAAUUCCGACCACAAAAUUCGCAGCGAAUUAUGCAAAUUUCGAUGAAACA---------AUGAUUCCUAAGAU
------------------......((((.(.((((.(((((.(((........)))))))).)))).)))))(((((((.....((((...))))..---------)))))))....... ( -21.00)
>DroPse_CAF1 29773 108 - 1
UGUGGAAUGCCUUGUCCGCUGUCCGCUGACAAAUUGUGGGGCUCGUUAAAUGUUGGCCCCAAAACUUGCAACGAAUUAUGUAAAUUUGAAUGAAAC------------GAUCUUUAAGAU
.(((((..((.......))..)))))((.(((.((.((((((.((........)))))))).)).))))).((((((.....))))))........------------............ ( -23.90)
>DroSim_CAF1 29269 93 - 1
------------------UUGUCCGCUGACAAAUUGUGUGGCUCGUUAAAUUCCGACCACAAAAUUCGCAGCGAAUUAUGCAAAUUUCAAUGAAACA---------AUGAUUCCUAAGAU
------------------......((((.(.((((.(((((.(((........)))))))).)))).)))))(((((((.....((((...))))..---------)))))))....... ( -21.00)
>DroEre_CAF1 26241 93 - 1
------------------UUGUCCGCUGACAAAUUGUGUGGCUCGUUAAAUUCCGACCACAAAAUUCGCAGCGAAUUAUGCAAAUUUCAAUGAAACA---------AUGAUUCUUAAGAC
------------------..(((.((((.(.((((.(((((.(((........)))))))).)))).)))))(((((((.....((((...))))..---------)))))))....))) ( -22.40)
>DroYak_CAF1 35401 93 - 1
------------------UUGUCCGCUGACAAAUUGUGUGGCUCGUUAAAUUGCGACCACAAAAUUCGCAGCGAAUUAUGCAAAUUUCAAUGAAACA---------AUGAUUCUCAAGUC
------------------......((((.(.((((.(((((.((((......))))))))).)))).)))))(((((((.....((((...))))..---------)))))))....... ( -23.90)
>DroAna_CAF1 25744 102 - 1
------------------CCGUCCGCUGACAAAUUGUUUGGCUCGUUAAAUUCCGGCCACAAAACUCCCAGCGAAUUAUGCAAAUUUCAAUGAAACAGACAGGACGACGAUCCCGCAGAU
------------------.(((((.(((....((((..((((.((........))))))...........(((.....)))......))))....)))...))))).............. ( -20.90)
>consensus
__________________UUGUCCGCUGACAAAUUGUGUGGCUCGUUAAAUUCCGACCACAAAAUUCGCAGCGAAUUAUGCAAAUUUCAAUGAAACA_________AUGAUUCCUAAGAU
.......................(((((...((((.(((((.(((........)))))))).))))..)))))............................................... (-16.72 = -16.75 +   0.03)

alignment

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secondary structure

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Window 3

Location 1,769,452 – 1,769,547
Length 95
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 82.95
Mean single sequence MFE -33.33
Consensus MFE -27.55
Energy contribution -27.33
Covariance contribution -0.22
Combinations/Pair 1.21
Mean z-score -3.24
Structure conservation index 0.83
SVM decision value 1.52
SVM RNA-class probability 0.960656
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1769452 95 + 22407834
CAUAAUUCGCUGCGAAUUUUGUGGUCGGAAUUUAACGAGCCACACAAUUUGUCAGCGGACAA--------------------CCUCGAAUUAUUCAUGGGCAGCCAAAAAGGCAG
.(((((((((((((((((.((((((((........))).))))).)))))).))))((....--------------------))..))))))).........(((.....))).. ( -32.60)
>DroSim_CAF1 29300 95 + 1
CAUAAUUCGCUGCGAAUUUUGUGGUCGGAAUUUAACGAGCCACACAAUUUGUCAGCGGACAA--------------------CCUCGAAUUAUUCAUGGGCAGCCAAAAAGGCAG
.(((((((((((((((((.((((((((........))).))))).)))))).))))((....--------------------))..))))))).........(((.....))).. ( -32.60)
>DroEre_CAF1 26272 95 + 1
CAUAAUUCGCUGCGAAUUUUGUGGUCGGAAUUUAACGAGCCACACAAUUUGUCAGCGGACAA--------------------CCUCGAAUUAUUCAUGGGCAGCCAAAAAGGCAG
.(((((((((((((((((.((((((((........))).))))).)))))).))))((....--------------------))..))))))).........(((.....))).. ( -32.60)
>DroYak_CAF1 35432 95 + 1
CAUAAUUCGCUGCGAAUUUUGUGGUCGCAAUUUAACGAGCCACACAAUUUGUCAGCGGACAA--------------------CCUCGAAUUAUUCAUGGGCAGCCAAAAAGGCAG
.(((((((((((((((((.((((((((........))).))))).)))))).))))((....--------------------))..))))))).........(((.....))).. ( -31.30)
>DroAna_CAF1 25784 94 + 1
CAUAAUUCGCUGGGAGUUUUGUGGCCGGAAUUUAACGAGCCAAACAAUUUGUCAGCGGACGG--------------------CC-AGAAUUAUUCAUGGCCACCCCAAGGGGGAG
.....(((((((((((((...((((((........)).))))...))))).)))))))).((--------------------((-(((.....)).))))).((((...)))).. ( -36.00)
>DroPer_CAF1 28702 109 + 1
CAUAAUUCGUUGCAAGUUUUGGGGCCAACAUUUAACGAGCCCCACAAUUUGUCAGCGGACAGCGGACAAGGCAUUCCACAGUCCUCGAAUUAUUCAUGGGAA------AAGGAGG
.(((((((((((((((((.(((((((..........).)))))).)))))).))))((((.(.(((........))).).))))..))))))).........------....... ( -34.90)
>consensus
CAUAAUUCGCUGCGAAUUUUGUGGUCGGAAUUUAACGAGCCACACAAUUUGUCAGCGGACAA____________________CCUCGAAUUAUUCAUGGGCAGCCAAAAAGGCAG
.....(((((((((((((.((((((((........)).)))))).)))))).))))))).......................((..((.....))..))...(((.....))).. (-27.55 = -27.33 +  -0.22)

alignment

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secondary structure

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Window 4

Location 1,769,452 – 1,769,547
Length 95
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 82.95
Mean single sequence MFE -30.03
Consensus MFE -20.85
Energy contribution -21.16
Covariance contribution 0.31
Combinations/Pair 1.14
Mean z-score -2.30
Structure conservation index 0.69
SVM decision value 0.45
SVM RNA-class probability 0.742740
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1769452 95 - 22407834
CUGCCUUUUUGGCUGCCCAUGAAUAAUUCGAGG--------------------UUGUCCGCUGACAAAUUGUGUGGCUCGUUAAAUUCCGACCACAAAAUUCGCAGCGAAUUAUG
..(((.....))).........(((((((..((--------------------....))((((.(.((((.(((((.(((........)))))))).)))).)))))))))))). ( -28.60)
>DroSim_CAF1 29300 95 - 1
CUGCCUUUUUGGCUGCCCAUGAAUAAUUCGAGG--------------------UUGUCCGCUGACAAAUUGUGUGGCUCGUUAAAUUCCGACCACAAAAUUCGCAGCGAAUUAUG
..(((.....))).........(((((((..((--------------------....))((((.(.((((.(((((.(((........)))))))).)))).)))))))))))). ( -28.60)
>DroEre_CAF1 26272 95 - 1
CUGCCUUUUUGGCUGCCCAUGAAUAAUUCGAGG--------------------UUGUCCGCUGACAAAUUGUGUGGCUCGUUAAAUUCCGACCACAAAAUUCGCAGCGAAUUAUG
..(((.....))).........(((((((..((--------------------....))((((.(.((((.(((((.(((........)))))))).)))).)))))))))))). ( -28.60)
>DroYak_CAF1 35432 95 - 1
CUGCCUUUUUGGCUGCCCAUGAAUAAUUCGAGG--------------------UUGUCCGCUGACAAAUUGUGUGGCUCGUUAAAUUGCGACCACAAAAUUCGCAGCGAAUUAUG
..(((.....))).........(((((((..((--------------------....))((((.(.((((.(((((.((((......))))))))).)))).)))))))))))). ( -31.10)
>DroAna_CAF1 25784 94 - 1
CUCCCCCUUGGGGUGGCCAUGAAUAAUUCU-GG--------------------CCGUCCGCUGACAAAUUGUUUGGCUCGUUAAAUUCCGGCCACAAAACUCCCAGCGAAUUAUG
..((((...)))).(((((.((.....)))-))--------------------))...(((((.....((((..(((.((........)))))))))......)))))....... ( -27.60)
>DroPer_CAF1 28702 109 - 1
CCUCCUU------UUCCCAUGAAUAAUUCGAGGACUGUGGAAUGCCUUGUCCGCUGUCCGCUGACAAAUUGUGGGGCUCGUUAAAUGUUGGCCCCAAAACUUGCAACGAAUUAUG
.......------.........((((((((.((((.(((((........))))).))))..((.(((.((.((((((.((........)))))))).)).))))).)))))))). ( -35.70)
>consensus
CUGCCUUUUUGGCUGCCCAUGAAUAAUUCGAGG____________________UUGUCCGCUGACAAAUUGUGUGGCUCGUUAAAUUCCGACCACAAAAUUCGCAGCGAAUUAUG
..(((.....))).........(((((((..((........................))((((...((((.(((((.(((........)))))))).))))..))))))))))). (-20.85 = -21.16 +   0.31)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:09 2006