Locus 2064

Sequence ID 2L_DroMel_CAF1
Location 5,574,431 – 5,574,625
Length 194
Max. P 0.995642
window3325 window3326 window3327 window3328

overview

Window 5

Location 5,574,431 – 5,574,545
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.82
Mean single sequence MFE -53.07
Consensus MFE -38.30
Energy contribution -41.18
Covariance contribution 2.88
Combinations/Pair 1.08
Mean z-score -4.95
Structure conservation index 0.72
SVM decision value 2.60
SVM RNA-class probability 0.995642
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5574431 114 + 22407834
GGCCGUCAGGGGCAUGAUAAAUGUCCUCAAUUGCAGAUCCUGCCUAUCUGCGGCAUGAAUCUCCUACGCAGUUGCAGU------UGCAAUUGCAACUGCAGUUGCAUGCAGGAUGGCCUG
(((((((.(((((((.....)))))))...(((((((((.((((.......)))).).)))......(((..((((((------(((....)))))))))..))).)))))))))))).. ( -55.40)
>DroSec_CAF1 18516 108 + 1
GGCCGUCAGGGGCAUGAUAAAUGUCCUCAAUUGCAGAUCCUGCCUAUCUGCGGCAUGAAUCUCCUACGCAGUUGCAAC------UG------CAACUGCAGUUGCAUGCAGGAUGGCCUG
((((....(((((((.....))))))).........(((((((....(((((..............))))).((((((------((------(....))))))))).))))))))))).. ( -48.84)
>DroSim_CAF1 20166 114 + 1
GGCCGUCAGGGGCAUGAUAAAUGUCCUCAAUUGCAGAUCCUGCCUAUCUGCGGCAUGAAUCUCCUACGCAGUUGCAAC------UGCAACUGCAACUGCAGUUGCAUGCAGGAUGGCCUG
(((((((.(((((((.....)))))))(((((((((.((.((((.......)))).)).........((((((((...------.))))))))..))))))))).......))))))).. ( -54.60)
>DroEre_CAF1 18433 120 + 1
GCCCGUCAGGGGCAUGAUAAAUGUCCUCAAUUGCAGAUCCUGCCUAUCUGCGGGAUGCAUCUCCUACGCAGUUGCAGCUGCAGUUGCAGUUGCAGCUACAGUUGCAUGCAGGAUGGCCUG
(((.....(((((((.....))))))).........(((((((....((((((((......)))..))))).((((((((.((((((....)))))).)))))))).))))))))))... ( -52.70)
>DroYak_CAF1 18276 111 + 1
GGCCGUCAGGGGCAUGAUAAAUGUCCUCAAUUGCAGAUCCUGCCUAUCUGCAGGAUGAAUCUCCUACGA---------CGCAGUUGCAGCUGCAGCUGCAGUUGCAUGCAGGAUGGCCUG
(((((((.(((((((.....)))))))...(((((.(((((((......)))))))..........(((---------(((((((((....)))))))).))))..)))))))))))).. ( -53.80)
>consensus
GGCCGUCAGGGGCAUGAUAAAUGUCCUCAAUUGCAGAUCCUGCCUAUCUGCGGCAUGAAUCUCCUACGCAGUUGCAAC______UGCAACUGCAACUGCAGUUGCAUGCAGGAUGGCCUG
(((((((.(((((((.....)))))))(((((((((...((((......))))..............(((((((((........)))))))))..))))))))).......))))))).. (-38.30 = -41.18 +   2.88)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,574,431 – 5,574,545
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.82
Mean single sequence MFE -45.68
Consensus MFE -28.16
Energy contribution -29.56
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -3.34
Structure conservation index 0.62
SVM decision value 0.56
SVM RNA-class probability 0.780767
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5574431 114 - 22407834
CAGGCCAUCCUGCAUGCAACUGCAGUUGCAAUUGCA------ACUGCAACUGCGUAGGAGAUUCAUGCCGCAGAUAGGCAGGAUCUGCAAUUGAGGACAUUUAUCAUGCCCCUGACGGCC
..((((.((((((..(((..(((((((((....)))------))))))..)))))))))(((((.((((.......)))))))))........(((.(((.....)))..)))...)))) ( -46.90)
>DroSec_CAF1 18516 108 - 1
CAGGCCAUCCUGCAUGCAACUGCAGUUG------CA------GUUGCAACUGCGUAGGAGAUUCAUGCCGCAGAUAGGCAGGAUCUGCAAUUGAGGACAUUUAUCAUGCCCCUGACGGCC
..((((.((((((((((((((((....)------))------))))))..)))...(.((((((.((((.......)))))))))).).....))))......(((......))).)))) ( -44.00)
>DroSim_CAF1 20166 114 - 1
CAGGCCAUCCUGCAUGCAACUGCAGUUGCAGUUGCA------GUUGCAACUGCGUAGGAGAUUCAUGCCGCAGAUAGGCAGGAUCUGCAAUUGAGGACAUUUAUCAUGCCCCUGACGGCC
..((((.((((((.(((....)))...((((((((.------...))))))))))))))(((((.((((.......)))))))))........(((.(((.....)))..)))...)))) ( -46.00)
>DroEre_CAF1 18433 120 - 1
CAGGCCAUCCUGCAUGCAACUGUAGCUGCAACUGCAACUGCAGCUGCAACUGCGUAGGAGAUGCAUCCCGCAGAUAGGCAGGAUCUGCAAUUGAGGACAUUUAUCAUGCCCCUGACGGGC
...((.(((((((.((((.((((((.(((....))).)))))).)))).(((((..(((......))))))))....)))))))..))...................((((.....)))) ( -46.60)
>DroYak_CAF1 18276 111 - 1
CAGGCCAUCCUGCAUGCAACUGCAGCUGCAGCUGCAACUGCG---------UCGUAGGAGAUUCAUCCUGCAGAUAGGCAGGAUCUGCAAUUGAGGACAUUUAUCAUGCCCCUGACGGCC
..((((((((((((((((..((((((....))))))..))))---------).((((((......))))))......))))))).........(((.(((.....)))..)))...)))) ( -44.90)
>consensus
CAGGCCAUCCUGCAUGCAACUGCAGUUGCAACUGCA______GCUGCAACUGCGUAGGAGAUUCAUGCCGCAGAUAGGCAGGAUCUGCAAUUGAGGACAUUUAUCAUGCCCCUGACGGCC
..((((.((((((.((((((....))))))...............((....))))))))..........((((((.......)))))).....(((.(((.....)))..)))...)))) (-28.16 = -29.56 +   1.40)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,574,471 – 5,574,585
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.63
Mean single sequence MFE -43.08
Consensus MFE -26.09
Energy contribution -26.90
Covariance contribution 0.81
Combinations/Pair 1.17
Mean z-score -3.29
Structure conservation index 0.61
SVM decision value 0.79
SVM RNA-class probability 0.851124
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5574471 114 - 22407834
AGGCAAAGUCGACGGCAUUUACAUAAACUUCGUGGACACUCAGGCCAUCCUGCAUGCAACUGCAGUUGCAAUUGCA------ACUGCAACUGCGUAGGAGAUUCAUGCCGCAGAUAGGCA
.(((...(((.((((..(((....)))..)))).)))......))).((((((..(((..(((((((((....)))------))))))..)))))))))......((((.......)))) ( -43.50)
>DroSec_CAF1 18556 107 - 1
G-GCAAAGUCGGCGGCAUUUACAUAAACUUCGUGGACACUCAGGCCAUCCUGCAUGCAACUGCAGUUG------CA------GUUGCAACUGCGUAGGAGAUUCAUGCCGCAGAUAGGCA
.-((...(((.(((((((.........((.((..(.....((((....))))..(((((((((....)------))------)))))).)..)).)).......))))))).)))..)). ( -41.49)
>DroSim_CAF1 20206 114 - 1
GGGCAAAGUCGACGGCAUUUACAUAAACUUCGUGGACACUCAGGCCAUCCUGCAUGCAACUGCAGUUGCAGUUGCA------GUUGCAACUGCGUAGGAGAUUCAUGCCGCAGAUAGGCA
.(((...(((.((((..(((....)))..)))).)))......))).((((((.(((....)))...((((((((.------...))))))))))))))......((((.......)))) ( -42.40)
>DroEre_CAF1 18473 120 - 1
AGGCAAAGUCGACGGCAUUUACAUAAACUUCGUGGACACUCAGGCCAUCCUGCAUGCAACUGUAGCUGCAACUGCAACUGCAGCUGCAACUGCGUAGGAGAUGCAUCCCGCAGAUAGGCA
.......(((.((((..(((....)))..)))).)))......((((((.((((((((..((((((((((........))))))))))..))))).(((......))).)))))).))). ( -43.90)
>DroYak_CAF1 18316 111 - 1
GGCCAAAGUCGACGGCAUUUACAUAAACUUCGUGGACACUCAGGCCAUCCUGCAUGCAACUGCAGCUGCAGCUGCAACUGCG---------UCGUAGGAGAUUCAUCCUGCAGAUAGGCA
.(((...(((.((((..(((....)))..)))).))).((((((...(((((((((((..((((((....))))))..))))---------).)))))).......)))).))...))). ( -44.10)
>consensus
GGGCAAAGUCGACGGCAUUUACAUAAACUUCGUGGACACUCAGGCCAUCCUGCAUGCAACUGCAGUUGCAACUGCA______GCUGCAACUGCGUAGGAGAUUCAUGCCGCAGAUAGGCA
.......(((.((((..(((....)))..)))).)))......((((((.((((((((..(((((((((....)))......))))))..))))).((.........)))))))).))). (-26.09 = -26.90 +   0.81)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,574,509 – 5,574,625
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.42
Mean single sequence MFE -37.68
Consensus MFE -31.82
Energy contribution -32.30
Covariance contribution 0.48
Combinations/Pair 1.12
Mean z-score -1.78
Structure conservation index 0.84
SVM decision value 1.41
SVM RNA-class probability 0.950893
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5574509 116 - 22407834
CUAAAGUAGGCAGCAAGCAGGAAUCAGGACGACGUCAUCGAGGCAAAGUCGACGGCAUUUACAUAAACUUCGUGGACACUCAGGCCAUCCUGCAUGCAACUGCAGUUGCAAUUGCA----
............((((((((((.......(((.....))).(((...(((.((((..(((....)))..)))).)))......))).)))))).((((((....)))))).)))).---- ( -35.80)
>DroSec_CAF1 18594 109 - 1
CUAAAGUAGGCAGCAAGCAGGAAUCAGGACGACGUCAUCGG-GCAAAGUCGGCGGCAUUUACAUAAACUUCGUGGACACUCAGGCCAUCCUGCAUGCAACUGCAGUUG------CA----
.........(((((..((((((.......(((.....)))(-((...(((.((((..(((....)))..)))).)))......))).)))))).(((....)))))))------).---- ( -34.30)
>DroSim_CAF1 20244 116 - 1
CUAAAGUAGGCAGCAAGCAGGAAUCAGGACGACGUCAUCGGGGCAAAGUCGACGGCAUUUACAUAAACUUCGUGGACACUCAGGCCAUCCUGCAUGCAACUGCAGUUGCAGUUGCA----
.........(((((..((((((.......(((.....))).(((...(((.((((..(((....)))..)))).)))......))).)))))).((((((....))))))))))).---- ( -39.10)
>DroEre_CAF1 18513 120 - 1
CUAAAGUAGGCAGCAGGCAGGAAUCAGGACGACGUCAUCGAGGCAAAGUCGACGGCAUUUACAUAAACUUCGUGGACACUCAGGCCAUCCUGCAUGCAACUGUAGCUGCAACUGCAACUG
.....(((((((((..((((((.......(((.....))).(((...(((.((((..(((....)))..)))).)))......))).)))))).(((....))))))))..))))..... ( -37.20)
>DroYak_CAF1 18347 120 - 1
CUAAAGUAGGCAGCAGGCAGGAAUCAGGACGACGUCAUCGGGCCAAAGUCGACGGCAUUUACAUAAACUUCGUGGACACUCAGGCCAUCCUGCAUGCAACUGCAGCUGCAGCUGCAACUG
.....(((((((((..((((((.......(((.....)))((((...(((.((((..(((....)))..)))).))).....)))).)))))).(((....))))))))..))))..... ( -42.00)
>consensus
CUAAAGUAGGCAGCAAGCAGGAAUCAGGACGACGUCAUCGGGGCAAAGUCGACGGCAUUUACAUAAACUUCGUGGACACUCAGGCCAUCCUGCAUGCAACUGCAGUUGCAACUGCA____
.....(((((((((..((((((.......(((.....))).(((...(((.((((..(((....)))..)))).)))......))).)))))).(((....))))))))..))))..... (-31.82 = -32.30 +   0.48)

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 10:18:31 2006