Locus 4496

Sequence ID 2L_DroMel_CAF1
Location 12,885,272 – 12,885,412
Length 140
Max. P 0.919741
window7070 window7071 window7072

overview

Window 0

Location 12,885,272 – 12,885,379
Length 107
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 89.74
Mean single sequence MFE -24.59
Consensus MFE -20.92
Energy contribution -20.80
Covariance contribution -0.12
Combinations/Pair 1.10
Mean z-score -1.53
Structure conservation index 0.85
SVM decision value 0.64
SVM RNA-class probability 0.808399
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12885272 107 + 22407834
UUUGUUUGUCUCACUAUCAGACGAACAUCCGCUGACGCCGAGACUUCCUCUUCCUCUUCGCCCGUGUUCCUUAUUCCUUAUUCCCGGUCCCACAGACGCGGAACUGU
..(((((((((.......)))))))))(((((....((.((((...........)))).))..(((..((...............))...)))....)))))..... ( -23.36)
>DroSec_CAF1 64419 102 + 1
UUUGUUUGUCUCACUAUCAGACGAACAUCCGCUGACGCCGGGACUUCCUCUAC-----CGCCCGCAUUCCUUAUUCCUUAUUCCCGGUCCCACAGACGCGGAACUGU
..(((((((((.......)))))))))(((((((..(((((((..........-----.......................)))))))..)).....)))))..... ( -26.61)
>DroSim_CAF1 67224 102 + 1
UUUGUUUGUCUCACUAUCAGACGAACAUCCGCUGACGCCGAGACUUCCUCUAC-----CGCCCGCAUUCCUUAUUCCUUAUUCCCGGUCCCACAGACGCGGAACUGU
..(((((((((.......)))))))))(((((.......(((.....)))...-----............................(((.....))))))))..... ( -21.70)
>DroEre_CAF1 70139 95 + 1
UUUGUUUGUCUCACUAUCAGACGAACAUCCGCUGACGCCGAGGCUUCCUCCAC-----CGCCCG-------UAUUCCUUGUUGCCGGUCCCACAGACGCGGAACUGU
..(((((((((.......)))))))))(((((.......((((...))))...-----.(((.(-------((........))).))).........)))))..... ( -25.60)
>DroYak_CAF1 66561 95 + 1
UUUGUUUGUCUCACUAUCAGACGAGCAUCCGCUGACGCCGAGACUUCCUCUAC-----CGCCCA-------UAUUCCCUAUUCCCGGGCCCACAGACGCGGAACUGU
..(((((((((.......)))))))))(((((.......(((.....)))...-----.((((.-------..............))))........)))))..... ( -25.66)
>consensus
UUUGUUUGUCUCACUAUCAGACGAACAUCCGCUGACGCCGAGACUUCCUCUAC_____CGCCCG__UUCCUUAUUCCUUAUUCCCGGUCCCACAGACGCGGAACUGU
..(((((((((.......)))))))))(((((.......(((.....)))....................................(((.....))))))))..... (-20.92 = -20.80 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,885,303 – 12,885,412
Length 109
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 88.98
Mean single sequence MFE -25.20
Consensus MFE -19.22
Energy contribution -19.50
Covariance contribution 0.28
Combinations/Pair 1.11
Mean z-score -1.83
Structure conservation index 0.76
SVM decision value 0.54
SVM RNA-class probability 0.776274
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12885303 109 + 22407834
CUGACGCCGAGACUUCCUCUUCCUCUUCGCCCGUGUUCCUUAUUCCUUAUUCCCGGUCCCACAGACGCGGAACUGUAUCCUCGUCUAUUCCCAAGCUGCAUUUGCAGCU
..((((..(((.....)))...........(((((((.......((........)).......)))))))...........))))........((((((....)))))) ( -25.84)
>DroSec_CAF1 64450 104 + 1
CUGACGCCGGGACUUCCUCUAC-----CGCCCGCAUUCCUUAUUCCUUAUUCCCGGUCCCACAGACGCGGAACUGUAUCCUCGUCUAUUCCCAAGCUGCAUUUGCAGCU
.((..(((((((..........-----.......................)))))))..)).(((((.(((......))).))))).......((((((....)))))) ( -29.31)
>DroSim_CAF1 67255 104 + 1
CUGACGCCGAGACUUCCUCUAC-----CGCCCGCAUUCCUUAUUCCUUAUUCCCGGUCCCACAGACGCGGAACUGUAUCCUCGUCUAUUCCCAAGCUGCAUUUGCAGCU
.((..((((((.....)))...-----.(....)....................)))..)).(((((.(((......))).))))).......((((((....)))))) ( -23.60)
>DroEre_CAF1 70170 97 + 1
CUGACGCCGAGGCUUCCUCCAC-----CGCCCG-------UAUUCCUUGUUGCCGGUCCCACAGACGCGGAACUGUAUCCUCAACUAUUCCCAGGCUGCAUUUGCAGCU
(((..((.((((...))))...-----.(((.(-------((........))).))).........))((((..((.......))..)))))))(((((....))))). ( -23.70)
>DroYak_CAF1 66592 97 + 1
CUGACGCCGAGACUUCCUCUAC-----CGCCCA-------UAUUCCCUAUUCCCGGGCCCACAGACGCGGAACUGUAUCCUCGACUAUUCCCAAGCUGCAUUUGCAGCU
(((.....(((.....)))...-----.((((.-------..............))))...))).((.(((......))).))..........((((((....)))))) ( -23.56)
>consensus
CUGACGCCGAGACUUCCUCUAC_____CGCCCG__UUCCUUAUUCCUUAUUCCCGGUCCCACAGACGCGGAACUGUAUCCUCGUCUAUUCCCAAGCUGCAUUUGCAGCU
........(((.....)))...................................((......(((((.(((......))).)))))....)).((((((....)))))) (-19.22 = -19.50 +   0.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,885,303 – 12,885,412
Length 109
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 88.98
Mean single sequence MFE -35.04
Consensus MFE -26.76
Energy contribution -26.52
Covariance contribution -0.24
Combinations/Pair 1.17
Mean z-score -2.20
Structure conservation index 0.76
SVM decision value 1.13
SVM RNA-class probability 0.919741
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12885303 109 - 22407834
AGCUGCAAAUGCAGCUUGGGAAUAGACGAGGAUACAGUUCCGCGUCUGUGGGACCGGGAAUAAGGAAUAAGGAACACGGGCGAAGAGGAAGAGGAAGUCUCGGCGUCAG
((((((....))))))........((((.((((.(..((((.((((((((...((...............))..))))))))....))))..)...))))...)))).. ( -34.86)
>DroSec_CAF1 64450 104 - 1
AGCUGCAAAUGCAGCUUGGGAAUAGACGAGGAUACAGUUCCGCGUCUGUGGGACCGGGAAUAAGGAAUAAGGAAUGCGGGCG-----GUAGAGGAAGUCCCGGCGUCAG
((((((....)))))).....(((((((.(((......))).)))))))((..((((((...............(((.....-----))).......))))))..)).. ( -33.05)
>DroSim_CAF1 67255 104 - 1
AGCUGCAAAUGCAGCUUGGGAAUAGACGAGGAUACAGUUCCGCGUCUGUGGGACCGGGAAUAAGGAAUAAGGAAUGCGGGCG-----GUAGAGGAAGUCUCGGCGUCAG
.(((((....)))))((((..(((((((.(((......))).)))))))....)))).....................((((-----...(((.....)))..)))).. ( -32.70)
>DroEre_CAF1 70170 97 - 1
AGCUGCAAAUGCAGCCUGGGAAUAGUUGAGGAUACAGUUCCGCGUCUGUGGGACCGGCAACAAGGAAUA-------CGGGCG-----GUGGAGGAAGCCUCGGCGUCAG
.(((((....)))))....((...(((((((......(((((((((((((...((........))..))-------))))).-----))))))....))))))).)).. ( -37.70)
>DroYak_CAF1 66592 97 - 1
AGCUGCAAAUGCAGCUUGGGAAUAGUCGAGGAUACAGUUCCGCGUCUGUGGGCCCGGGAAUAGGGAAUA-------UGGGCG-----GUAGAGGAAGUCUCGGCGUCAG
((((((....))))))...((...(((((((......((((.((((((((..(((.......)))..))-------))))))-----.....)))).))))))).)).. ( -36.90)
>consensus
AGCUGCAAAUGCAGCUUGGGAAUAGACGAGGAUACAGUUCCGCGUCUGUGGGACCGGGAAUAAGGAAUAAGGAA__CGGGCG_____GUAGAGGAAGUCUCGGCGUCAG
.(((((....)))))((((..(((((((.(((......))).)))))))....))))...................(((((...............))).))....... (-26.76 = -26.52 +  -0.24)

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 11:19:12 2006