Locus 2883

Sequence ID 2L_DroMel_CAF1
Location 8,272,577 – 8,272,717
Length 140
Max. P 0.841263
window4579 window4580 window4581

overview

Window 9

Location 8,272,577 – 8,272,687
Length 110
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 87.04
Mean single sequence MFE -27.72
Consensus MFE -18.86
Energy contribution -19.92
Covariance contribution 1.06
Combinations/Pair 1.10
Mean z-score -2.49
Structure conservation index 0.68
SVM decision value 0.71
SVM RNA-class probability 0.830952
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8272577 110 - 22407834
CUGCAAAC---AAAGCAUAAAUCAAAUGCAGAAUGU--GUUUGAUUUAUGGGGGUUUCAUGUGUGCAUACAUAUGUACGUGUGUAGUUAAAAGCAUGCCACCAAUAUUUAUACUC
........---....((((((((((((((.....))--))))))))))))..(((..(((((..((.(((((((....))))))))).....)))))..)))............. ( -30.60)
>DroSec_CAF1 50551 109 - 1
CUGCAAACAACAAAGCAUAAAUCAAAUGCAGAAUGUGUGUUUGAUUUAUGGGGGUUUCAUGUGUACAUACGU------GUGUGUACUUAAAAGCAUGCCUCCAAUAUUUAUAUUC
.(((..........)))(((((((((((((.....)))))))))))))((((((...((((((((((((...------.)))))))......)))))))))))............ ( -30.60)
>DroSim_CAF1 51440 109 - 1
CUGCAAACAACAAAGCAUAAAUCAAAUGCAGAAUGUGUGUUUGAUUUAUGGGGGUUUCGUGUGUACAUACGU------GUGUGUAGUUAAAAGCAUGCCUCCAAUAUUUAUAUUC
...............(((((((((((((((.....)))))))))))))))((((...(((((....))))).------((((((........))))))))))............. ( -27.60)
>DroEre_CAF1 52922 99 - 1
CUGCAAAC---AAAGCAUAAGUCAAAUGCAGAAUGU--GUUUGAUUUAUGGGGGUUUCAUGUGUAC--ACGA------G---GUAGUUAAAAUCAUGCCUCCAAUAUUUGUAUUC
.((((((.---....((((((((((((((.....))--))))))))))))((((...((((.....--((..------.---...))......)))).))))....))))))... ( -25.40)
>DroYak_CAF1 54397 101 - 1
CUGCACAC---AAAGCAUAAAUCAAAUGCAUAAUGU--GUUUGAUUUAUGGGGGUUUCAUGUGUUCGUACGA------G---UUAGUUAAAAGCAUGCCACCAAUAUUUAUAUUC
........---....((((((((((((((.....))--))))))))))))..(((..(((((......((..------.---...)).....)))))..)))............. ( -24.40)
>consensus
CUGCAAAC___AAAGCAUAAAUCAAAUGCAGAAUGU__GUUUGAUUUAUGGGGGUUUCAUGUGUACAUACGU______GUGUGUAGUUAAAAGCAUGCCUCCAAUAUUUAUAUUC
...............((((((((((((((.....))..))))))))))))((((...(((((.(((((((........))))))).......))))))).))............. (-18.86 = -19.92 +   1.06)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,272,613 – 8,272,717
Length 104
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 89.31
Mean single sequence MFE -19.90
Consensus MFE -15.26
Energy contribution -15.34
Covariance contribution 0.08
Combinations/Pair 1.08
Mean z-score -1.67
Structure conservation index 0.77
SVM decision value 0.32
SVM RNA-class probability 0.688216
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8272613 104 + 22407834
CGUACAUAUGUAUGCACACAUGAAACCCCCAUAAAUCAAAC--ACAUUCUGCAUUUGAUUUAUGCUUU---GUUUGCAGAACAUCAAACGUGUCUCGUUU-UUAUGGCGA
(((.((((...(((.((((..........(((((((((((.--.(.....)..)))))))))))....---(((((........)))))))))..)))..-.))))))). ( -21.60)
>DroSec_CAF1 50587 104 + 1
C------ACGUAUGUACACAUGAAACCCCCAUAAAUCAAACACACAUUCUGCAUUUGAUUUAUGCUUUGUUGUUUGCAGAACAUCAAACGUGUCUCGUUUUUUAUAGCGA
(------((((((((..............(((((((((((..((.....))..))))))))))).(((((.....)))))))))...)))))..(((((......))))) ( -21.10)
>DroSim_CAF1 51476 104 + 1
C------ACGUAUGUACACACGAAACCCCCAUAAAUCAAACACACAUUCUGCAUUUGAUUUAUGCUUUGUUGUUUGCAGAACAUCAAACGUGUCUCGUUUUUUAUAGCGA
(------((((.((((.(((((((.....(((((((((((..((.....))..))))))))))).)))).))).))))(.....)..)))))..(((((......))))) ( -21.60)
>DroEre_CAF1 52955 96 + 1
C------UCGU--GUACACAUGAAACCCCCAUAAAUCAAAC--ACAUUCUGCAUUUGACUUAUGCUUU---GUUUGCAGAACAUCAAACGUGUCUCGUUU-UUAUAGCGA
.------((((--(....)))))................((--((.....((((.......))))...---(((((........))))))))).(((((.-....))))) ( -15.90)
>DroYak_CAF1 54430 99 + 1
C------UCGUACGAACACAUGAAACCCCCAUAAAUCAAAC--ACAUUAUGCAUUUGAUUUAUGCUUU---GUGUGCAGAACAUCAAACGUGUCUCGUUUUUUAUAGUGA
.------....((((((((..........(((((((((((.--.(.....)..))))))))))).(((---((((.....))).)))).)))).))))............ ( -19.30)
>consensus
C______ACGUAUGUACACAUGAAACCCCCAUAAAUCAAAC__ACAUUCUGCAUUUGAUUUAUGCUUU___GUUUGCAGAACAUCAAACGUGUCUCGUUUUUUAUAGCGA
.............(.((((..........(((((((((((.............))))))))))).......(((((........))))))))))(((((......))))) (-15.26 = -15.34 +   0.08)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,272,613 – 8,272,717
Length 104
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 89.31
Mean single sequence MFE -27.34
Consensus MFE -19.48
Energy contribution -19.52
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -2.46
Structure conservation index 0.71
SVM decision value 0.75
SVM RNA-class probability 0.841263
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8272613 104 - 22407834
UCGCCAUAA-AAACGAGACACGUUUGAUGUUCUGCAAAC---AAAGCAUAAAUCAAAUGCAGAAUGU--GUUUGAUUUAUGGGGGUUUCAUGUGUGCAUACAUAUGUACG
.........-....(((((..(((((........)))))---....((((((((((((((.....))--))))))))))))...)))))....((((((....)))))). ( -29.90)
>DroSec_CAF1 50587 104 - 1
UCGCUAUAAAAAACGAGACACGUUUGAUGUUCUGCAAACAACAAAGCAUAAAUCAAAUGCAGAAUGUGUGUUUGAUUUAUGGGGGUUUCAUGUGUACAUACGU------G
..............(((((..(((((........))))).......(((((((((((((((.....)))))))))))))))...)))))(((((....)))))------. ( -26.10)
>DroSim_CAF1 51476 104 - 1
UCGCUAUAAAAAACGAGACACGUUUGAUGUUCUGCAAACAACAAAGCAUAAAUCAAAUGCAGAAUGUGUGUUUGAUUUAUGGGGGUUUCGUGUGUACAUACGU------G
..(.((((....(((((((..(((((........))))).......(((((((((((((((.....)))))))))))))))...))))))).)))))......------. ( -29.10)
>DroEre_CAF1 52955 96 - 1
UCGCUAUAA-AAACGAGACACGUUUGAUGUUCUGCAAAC---AAAGCAUAAGUCAAAUGCAGAAUGU--GUUUGAUUUAUGGGGGUUUCAUGUGUAC--ACGA------G
(((.((((.-....(((((..(((((........)))))---....((((((((((((((.....))--))))))))))))...)))))...)))).--.)))------. ( -25.30)
>DroYak_CAF1 54430 99 - 1
UCACUAUAAAAAACGAGACACGUUUGAUGUUCUGCACAC---AAAGCAUAAAUCAAAUGCAUAAUGU--GUUUGAUUUAUGGGGGUUUCAUGUGUUCGUACGA------G
............(((((.(((((..(((.(((.((....---...))(((((((((((((.....))--)))))))))))))).)))..))))))))))....------. ( -26.30)
>consensus
UCGCUAUAAAAAACGAGACACGUUUGAUGUUCUGCAAAC___AAAGCAUAAAUCAAAUGCAGAAUGU__GUUUGAUUUAUGGGGGUUUCAUGUGUACAUACGU______G
..............(((((..(((((........))))).......((((((((((((((.....))..))))))))))))...)))))..................... (-19.48 = -19.52 +   0.04)

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 10:38:40 2006