Locus 6562

Sequence ID 3L_DroMel_CAF1
Location 17,374,949 – 17,375,042
Length 93
Max. P 0.827846
window10682 window10683

overview

Window 2

Location 17,374,949 – 17,375,042
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.12
Mean single sequence MFE -35.40
Consensus MFE -21.83
Energy contribution -21.72
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -1.40
Structure conservation index 0.62
SVM decision value 0.06
SVM RNA-class probability 0.563500
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17374949 93 + 23771897
GAGUUGUCAUUGUGAUU------------------------GUGGUUGUUAUCGUGGCGCGGCAGAGUUGCCAUGGCGCCGGAUAUCUGGCGGUAGGUGGGCGUGG---CCGGGGGCUUG
(((((.((...(((.(.------------------------.((((....))))..))))(((...((..((.((.((((((....)))))).))))..).)...)---)))).))))). ( -36.40)
>DroSec_CAF1 1860 93 + 1
GAGUUGUCAUUGUGAUU------------------------GUGGUUGUUAUCGUGGCGCGGCAGAGUUGCCAUGGCGCCGGGUAUCUGGCGGUAGGUGGGCGUGG---CCGGGGGCUUG
(((((.((...(((.(.------------------------.((((....))))..))))(((...((..((.((.((((((....)))))).))))..).)...)---)))).))))). ( -35.50)
>DroSim_CAF1 1559 93 + 1
GAGUUGUCAUUGUGAUU------------------------GUGGUUGUUAUCGUGGCGCGGCAGAGUUGCCAUGGCGCCGGGUAUCUGGCGGUAGGUGGGCGUGG---CCGGGGGCUUG
(((((.((...(((.(.------------------------.((((....))))..))))(((...((..((.((.((((((....)))))).))))..).)...)---)))).))))). ( -35.50)
>DroEre_CAF1 1901 117 + 1
GACUUGUCAUUGUGAUUGUGAGUGUUAUUGUGGUUGUGGUUGUGGUUGUUAUCAUGACGCGGCAGAGUUGCCAUGGCGCCGGAUAUCUGGCGGUAGGUGGGCGUGG---CCGGGGGCUUG
.....(((...(..((..(((......)))..))..).((..((((....))))..)).((((...((..((.((.((((((....)))))).))))..).)...)---)))..)))... ( -38.10)
>DroYak_CAF1 2027 99 + 1
GAGUUGUCAUUGUGAUU------------------GCGGUUGUGGUUGUUAUCAUGGCGCGGCAGAGUUGCCAUGGCGCCGGAUAUCUGGCGGUAGGUGGGCGUGG---CCGGGGCCUUG
..((.(((.....))).------------------))((((.((((..(..(((((((((......).))))))))((((((....))))))..........)..)---))).))))... ( -37.20)
>DroPer_CAF1 467 76 + 1
--------------------------------------------CUCAUUGUCAUGGCGUGGCAGGGUUGCCAUGGCGCCGGAUAUCUGACGAUAGAUGGGCGUGCCGCCCAGGGGCUUG
--------------------------------------------......(((((((((.........)))))))))(((...((((....))))..((((((...))))))..)))... ( -29.70)
>consensus
GAGUUGUCAUUGUGAUU________________________GUGGUUGUUAUCAUGGCGCGGCAGAGUUGCCAUGGCGCCGGAUAUCUGGCGGUAGGUGGGCGUGG___CCGGGGGCUUG
.........................................................(.(((......((((.((.((((((....)))))).))....))))......))).)...... (-21.83 = -21.72 +  -0.11)

alignment

Postscript

secondary structure

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dotplot

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Window 3

Location 17,374,949 – 17,375,042
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.12
Mean single sequence MFE -20.24
Consensus MFE -14.03
Energy contribution -13.92
Covariance contribution -0.11
Combinations/Pair 1.15
Mean z-score -1.49
Structure conservation index 0.69
SVM decision value 0.70
SVM RNA-class probability 0.827846
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17374949 93 - 23771897
CAAGCCCCCGG---CCACGCCCACCUACCGCCAGAUAUCCGGCGCCAUGGCAACUCUGCCGCGCCACGAUAACAACCAC------------------------AAUCACAAUGACAACUC
.........((---(..............))).(.((((.(((((...((((....)))))))))..)))).)......------------------------................. ( -19.14)
>DroSec_CAF1 1860 93 - 1
CAAGCCCCCGG---CCACGCCCACCUACCGCCAGAUACCCGGCGCCAUGGCAACUCUGCCGCGCCACGAUAACAACCAC------------------------AAUCACAAUGACAACUC
.........((---(..............)))........(((((...((((....)))))))))..............------------------------................. ( -17.74)
>DroSim_CAF1 1559 93 - 1
CAAGCCCCCGG---CCACGCCCACCUACCGCCAGAUACCCGGCGCCAUGGCAACUCUGCCGCGCCACGAUAACAACCAC------------------------AAUCACAAUGACAACUC
.........((---(..............)))........(((((...((((....)))))))))..............------------------------................. ( -17.74)
>DroEre_CAF1 1901 117 - 1
CAAGCCCCCGG---CCACGCCCACCUACCGCCAGAUAUCCGGCGCCAUGGCAACUCUGCCGCGUCAUGAUAACAACCACAACCACAACCACAAUAACACUCACAAUCACAAUGACAAGUC
...(((...))---)...((........((((.(....).))))....((((....))))))(((((...........................................)))))..... ( -18.33)
>DroYak_CAF1 2027 99 - 1
CAAGGCCCCGG---CCACGCCCACCUACCGCCAGAUAUCCGGCGCCAUGGCAACUCUGCCGCGCCAUGAUAACAACCACAACCGC------------------AAUCACAAUGACAACUC
...(((....)---))..((....((......)).((((.(((((...((((....)))))))))..))))............))------------------................. ( -22.40)
>DroPer_CAF1 467 76 - 1
CAAGCCCCUGGGCGGCACGCCCAUCUAUCGUCAGAUAUCCGGCGCCAUGGCAACCCUGCCACGCCAUGACAAUGAG--------------------------------------------
...(((....)))(((.((((....((((....))))...))))...(((((....))))).)))...........-------------------------------------------- ( -26.10)
>consensus
CAAGCCCCCGG___CCACGCCCACCUACCGCCAGAUAUCCGGCGCCAUGGCAACUCUGCCGCGCCACGAUAACAACCAC________________________AAUCACAAUGACAACUC
.........((.......((.........)).......))(((((...((((....)))))))))....................................................... (-14.03 = -13.92 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:24 2006