Locus 1072

Sequence ID 2R_DroMel_CAF1
Location 4,365,056 – 4,365,312
Length 256
Max. P 0.985894
window1889 window1890 window1891 window1892 window1893

overview

Window 9

Location 4,365,056 – 4,365,165
Length 109
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 86.03
Mean single sequence MFE -41.10
Consensus MFE -30.85
Energy contribution -31.23
Covariance contribution 0.37
Combinations/Pair 1.03
Mean z-score -2.36
Structure conservation index 0.75
SVM decision value 1.27
SVM RNA-class probability 0.938822
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4365056 109 + 20766785
CAUCCCCAUCUCCAU------C-CCAGAUCAAGAUCCCGAGAAGCGAGUGCUAGAUUUGCCACCUCCCCUAAAAUGGGGCAGAUGGAAAAUCUGGGAGUGGAAUGGGUUGCUGGUU
....(((((.(((((------(-((((((.....(((......((((((.....))))))...((((((......)))).))..)))..)))))))).)))))))))......... ( -39.20)
>DroSec_CAF1 35604 109 + 1
CAUCCCCAUCUCCAU------C-ACAGAUCUAGAUCCUGAGAAGGGAGUGCUAGAUUCGCCACCUCCCCUCAAAUGGGGCAGAUGGAAAAUCUGGGAGUGGAAUGGGCUGCUGGUU
....(((((.(((((------.-.(((((((((.((((.....))))...)))))....(((.((((((......)))).)).)))....))))...))))))))))......... ( -40.20)
>DroSim_CAF1 35811 115 + 1
CAUCCCCAUCUCCAUCUCUAUC-CCAGAUCAAGAUCCCGAGAAGCGAGUGCUAGAUUCGCCACCUCCCCUCAAAUGGGGCAGAUGGAAAAUCUGGGAGUGGAAUGGGUUGCUGGUU
....(((((.(((((.....((-((((((.....(((......((((((.....))))))...((((((......)))).))..)))..))))))))))))))))))......... ( -40.40)
>DroYak_CAF1 33649 115 + 1
CUUCACAAUACCCAUCCCCAUCCCCAGAUCCAGAUCCCGAGAUGCGAGUGCUAGAUUCGCCACCUCCCCUCAAAUGGGGCAGAUGGAAAAUCUGAGCGUGGGAUGGGA-ACGGGGC
..........(((...(((((((((.(((....))).............((((((((..(((.((((((......)))).)).)))..))))).)))).)))))))).-..))).. ( -44.60)
>consensus
CAUCCCCAUCUCCAU______C_CCAGAUCAAGAUCCCGAGAAGCGAGUGCUAGAUUCGCCACCUCCCCUCAAAUGGGGCAGAUGGAAAAUCUGGGAGUGGAAUGGGUUGCUGGUU
....(((((.(((((...........(((....)))..............(((((((..(((.((((((......)))).)).)))..)))))))..))))))))))......... (-30.85 = -31.23 +   0.37)

alignment

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secondary structure

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Window 0

Location 4,365,056 – 4,365,165
Length 109
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 86.03
Mean single sequence MFE -46.92
Consensus MFE -33.91
Energy contribution -33.85
Covariance contribution -0.06
Combinations/Pair 1.07
Mean z-score -3.41
Structure conservation index 0.72
SVM decision value 2.02
SVM RNA-class probability 0.985894
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4365056 109 - 20766785
AACCAGCAACCCAUUCCACUCCCAGAUUUUCCAUCUGCCCCAUUUUAGGGGAGGUGGCAAAUCUAGCACUCGCUUCUCGGGAUCUUGAUCUGG-G------AUGGAGAUGGGGAUG
.........(((((((((.(((((((((..((((((.((((......))))))))))...........((((.....)))).....)))))))-)------))))).))))).... ( -45.00)
>DroSec_CAF1 35604 109 - 1
AACCAGCAGCCCAUUCCACUCCCAGAUUUUCCAUCUGCCCCAUUUGAGGGGAGGUGGCGAAUCUAGCACUCCCUUCUCAGGAUCUAGAUCUGU-G------AUGGAGAUGGGGAUG
.........(((((((((.((.(((((((.((((((.((((......)))))))))).)))(((((...(((.......))).))))))))).-)------))))).))))).... ( -40.00)
>DroSim_CAF1 35811 115 - 1
AACCAGCAACCCAUUCCACUCCCAGAUUUUCCAUCUGCCCCAUUUGAGGGGAGGUGGCGAAUCUAGCACUCGCUUCUCGGGAUCUUGAUCUGG-GAUAGAGAUGGAGAUGGGGAUG
.........(((((((((.((((((((((.((((((.((((......)))))))))).))))))(((....)))....))))((((.(((...-))).)))))))).))))).... ( -44.50)
>DroYak_CAF1 33649 115 - 1
GCCCCGU-UCCCAUCCCACGCUCAGAUUUUCCAUCUGCCCCAUUUGAGGGGAGGUGGCGAAUCUAGCACUCGCAUCUCGGGAUCUGGAUCUGGGGAUGGGGAUGGGUAUUGUGAAG
..(((((-(((((((((..(((.((((((.((((((.((((......)))))))))).))))))))).((((.....))))...........)))))))))))))).......... ( -58.20)
>consensus
AACCAGCAACCCAUUCCACUCCCAGAUUUUCCAUCUGCCCCAUUUGAGGGGAGGUGGCGAAUCUAGCACUCGCUUCUCGGGAUCUUGAUCUGG_G______AUGGAGAUGGGGAUG
.........(((((((((.....((((((.((((((.((((......)))))))))).))))))...............((((....))))...........)))).))))).... (-33.91 = -33.85 +  -0.06)

alignment

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secondary structure

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Window 1

Location 4,365,089 – 4,365,205
Length 116
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 88.99
Mean single sequence MFE -43.28
Consensus MFE -31.84
Energy contribution -34.56
Covariance contribution 2.72
Combinations/Pair 1.09
Mean z-score -2.32
Structure conservation index 0.74
SVM decision value 0.94
SVM RNA-class probability 0.886351
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4365089 116 + 20766785
GAAGCGAGUGCUAGAUUUGCCACCUCCCCUAAAAUGGGGCAGAUGGAAAAUCUGGGAGUGGAAUGGGUUGCUGGUUGCUGUGUCGCAACCACAGUGGAGCCUACUUAACUCAAACC
..........((((((((.(((.((((((......)))).)).))).))))))))((((.((.((((((.((((((((......)))))))....).)))))).)).))))..... ( -45.10)
>DroSec_CAF1 35637 116 + 1
GAAGGGAGUGCUAGAUUCGCCACCUCCCCUCAAAUGGGGCAGAUGGAAAAUCUGGGAGUGGAAUGGGCUGCUGGUUGCUGUGUCGCAACCACAGUGGAGCCUACUUAACUCAAACC
.....((((.(((((((..(((.((((((......)))).)).)))..)))))))((((((..(..((((.(((((((......)))))))))))..)..)))))).))))..... ( -48.90)
>DroSim_CAF1 35850 116 + 1
GAAGCGAGUGCUAGAUUCGCCACCUCCCCUCAAAUGGGGCAGAUGGAAAAUCUGGGAGUGGAAUGGGUUGCUGGUUGCUGUGUCGCAACCACAGUGGAGCCUACUUAACUCAAACC
..........(((((((..(((.((((((......)))).)).)))..)))))))((((.((.((((((.((((((((......)))))))....).)))))).)).))))..... ( -45.00)
>DroEre_CAF1 32467 109 + 1
GAUGCGAGUGCUAGAUUCGCCACCUCCCCUCAAAUGAGGCAGAUGGAAAAUCUGAGCGUGGGAUGGGA-GCUGGGAGCUGUGUGGCAACCACAGUGGAGCCUACUUAACU------
...((((((.....))))))...(((((.((..(((...(((((.....)))))..)))..)).))))-).((((.((((((.(....)))))))....)))).......------ ( -39.90)
>DroYak_CAF1 33689 109 + 1
GAUGCGAGUGCUAGAUUCGCCACCUCCCCUCAAAUGGGGCAGAUGGAAAAUCUGAGCGUGGGAUGGGA-ACGGGGCGCAGUGUCGCUACCACAGUGGAGCCUACUUAAUU------
(((((..(((((...(((.((((((((((......))))(((((.....))))).....))).)))))-)...))))).)))))(((.((.....)))))..........------ ( -37.50)
>consensus
GAAGCGAGUGCUAGAUUCGCCACCUCCCCUCAAAUGGGGCAGAUGGAAAAUCUGGGAGUGGAAUGGGAUGCUGGUUGCUGUGUCGCAACCACAGUGGAGCCUACUUAACUCAAACC
..........(((((((..(((.((((((......)))).)).)))..)))))))((((..(.((((((.((((((((......)))))))....).)))))).)..))))..... (-31.84 = -34.56 +   2.72)

alignment

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secondary structure

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Window 2

Location 4,365,089 – 4,365,205
Length 116
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 88.99
Mean single sequence MFE -38.72
Consensus MFE -31.68
Energy contribution -32.56
Covariance contribution 0.88
Combinations/Pair 1.07
Mean z-score -2.25
Structure conservation index 0.82
SVM decision value 1.86
SVM RNA-class probability 0.980496
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4365089 116 - 20766785
GGUUUGAGUUAAGUAGGCUCCACUGUGGUUGCGACACAGCAACCAGCAACCCAUUCCACUCCCAGAUUUUCCAUCUGCCCCAUUUUAGGGGAGGUGGCAAAUCUAGCACUCGCUUC
((..((.(((.(((.(....)))).(((((((......)))))))..))).))..))......((((((.((((((.((((......)))))))))).))))))(((....))).. ( -40.50)
>DroSec_CAF1 35637 116 - 1
GGUUUGAGUUAAGUAGGCUCCACUGUGGUUGCGACACAGCAACCAGCAGCCCAUUCCACUCCCAGAUUUUCCAUCUGCCCCAUUUGAGGGGAGGUGGCGAAUCUAGCACUCCCUUC
((...((((..(((.((((.(....(((((((......)))))))).)))).)))..))))))((((((.((((((.((((......)))))))))).))))))............ ( -43.70)
>DroSim_CAF1 35850 116 - 1
GGUUUGAGUUAAGUAGGCUCCACUGUGGUUGCGACACAGCAACCAGCAACCCAUUCCACUCCCAGAUUUUCCAUCUGCCCCAUUUGAGGGGAGGUGGCGAAUCUAGCACUCGCUUC
((..((.(((.(((.(....)))).(((((((......)))))))..))).))..))......((((((.((((((.((((......)))))))))).))))))(((....))).. ( -40.90)
>DroEre_CAF1 32467 109 - 1
------AGUUAAGUAGGCUCCACUGUGGUUGCCACACAGCUCCCAGC-UCCCAUCCCACGCUCAGAUUUUCCAUCUGCCUCAUUUGAGGGGAGGUGGCGAAUCUAGCACUCGCAUC
------......(..((((...(((((.......))))).....)))-)..).......(((.((((((.((((((.((((......)))))))))).)))))))))......... ( -33.80)
>DroYak_CAF1 33689 109 - 1
------AAUUAAGUAGGCUCCACUGUGGUAGCGACACUGCGCCCCGU-UCCCAUCCCACGCUCAGAUUUUCCAUCUGCCCCAUUUGAGGGGAGGUGGCGAAUCUAGCACUCGCAUC
------......((..(((((.....)).))).))..((((....((-.........))(((.((((((.((((((.((((......)))))))))).)))))))))...)))).. ( -34.70)
>consensus
GGUUUGAGUUAAGUAGGCUCCACUGUGGUUGCGACACAGCAACCAGCAACCCAUUCCACUCCCAGAUUUUCCAUCUGCCCCAUUUGAGGGGAGGUGGCGAAUCUAGCACUCGCUUC
............(((((((......(((((((......)))))))..................((((((.((((((.((((......)))))))))).))))))))).)).))... (-31.68 = -32.56 +   0.88)

alignment

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secondary structure

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Window 3

Location 4,365,205 – 4,365,312
Length 107
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 87.17
Mean single sequence MFE -18.44
Consensus MFE -14.08
Energy contribution -13.92
Covariance contribution -0.16
Combinations/Pair 1.19
Mean z-score -1.62
Structure conservation index 0.76
SVM decision value 0.19
SVM RNA-class probability 0.628019
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4365205 107 - 20766785
CAAAUAUUUAAAGGAAAGCCAAACCCCAUUUGGCGCAAUAAGAAAUGUAAUAAACCCACAUUUAUGCAAUUAAAAUUUCCCGCACCUAAAGUGUUUAAUUGUCGAGU
...(((.((((.(((((((((((.....))))))(((.....((((((.........)))))).)))........))))).((((.....)))))))).)))..... ( -18.00)
>DroSec_CAF1 35753 107 - 1
CAAAUAUUUAAGGGAAAGCCAAACCCCAUUUGGCGCAAUAAGAAAUGUAAUAAACCCACAUUUAUGCAAUUAAAAUUUCCCGCUCCUCAAGUGUUUAAUUAUCGAGU
.((((((((..((((((((((((.....))))))(((.....((((((.........)))))).)))........)))))).......))))))))........... ( -21.20)
>DroSim_CAF1 35966 107 - 1
CAAAUAUUUAAGGGAAAGCCAAACCCCAUUUGGCGCAAUAAGAAAUGUAAUAAACCCACAUUUAUGCAAUUAAAAUUUCCCGCUCCUCAAGUGUUUAAUUGUCGAGU
...........((((((((((((.....))))))(((.....((((((.........)))))).)))........))))))((((..(((........)))..)))) ( -25.40)
>DroEre_CAF1 32576 96 - 1
CAGAUAUUUAAAGGUAAGCCAAACCCCAUUUGGUGCAAUAAGAAAUGUAAUAAACCCACAUUUAUGCAAUUAAACUCUC-CGCUCCGAAAGUGUUUA----------
.((((((((...((...((((((.....))))))(((.....((((((.........)))))).)))............-....))..)))))))).---------- ( -13.90)
>DroYak_CAF1 33798 97 - 1
CGAAUAUUUAAAGGGAAACUAAACCCUAUUUGGCGCAAUAAGCAAUGUAAUAAACCCACAUUUAUGCAAUUAAACUGUCCCGCACCUAAAGUGUUUA----------
.((((((((..((((........)))).....((((.....))..((((.((((......)))))))).............)).....)))))))).---------- ( -13.70)
>consensus
CAAAUAUUUAAAGGAAAGCCAAACCCCAUUUGGCGCAAUAAGAAAUGUAAUAAACCCACAUUUAUGCAAUUAAAAUUUCCCGCUCCUAAAGUGUUUAAUU_UCGAGU
.((((((((..(((...((((((.....))))))(((.....((((((.........)))))).))).................))).))))))))........... (-14.08 = -13.92 +  -0.16)

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 09:55:42 2006