Locus 4798

Sequence ID 3L_DroMel_CAF1
Location 13,429,215 – 13,429,448
Length 233
Max. P 0.864932
window7554 window7555 window7556

overview

Window 4

Location 13,429,215 – 13,429,335
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.33
Mean single sequence MFE -31.46
Consensus MFE -26.10
Energy contribution -27.10
Covariance contribution 1.00
Combinations/Pair 1.11
Mean z-score -1.64
Structure conservation index 0.83
SVM decision value 0.84
SVM RNA-class probability 0.864932
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13429215 120 - 23771897
CGAAAUGCACUCGAUAGCAGUCCAAAAAGCACCCACCGCCCAGAAAAAUCGCACCCUGGUGUGUGCGUGUCACUUGAAAGUCGCGCUAAAGGAAAACUGUCACAAAUUGCAUUUAAAUGC
..(((((((...(((((...(((.....((((.(((((....((....))......))))).))))((((.(((....))).))))....)))...)))))......)))))))...... ( -32.10)
>DroSec_CAF1 26338 120 - 1
CGAAAUGCACUGGAUGGCAGUCCAAAAAGCACCCACCACCCAGAAAAAUCGCACCCUGGUGUGUGCGUGUCACUUGAAAGUCGCGCUAAAGGAAAACUGUCACAAAUUGCAUUUAAAUGC
..(((((((...(.(((((((((.....((((.(((((....((....))......))))).))))((((.(((....))).))))....)))...)))))))....)))))))...... ( -34.80)
>DroSim_CAF1 28206 120 - 1
CGAAAUGCACUGGAUAGCAGUCCAAAAAGCACCCACCACCCAGAAAAAUCGCACCCUGGUGUGUGCGUGUCACUUGAAAGUCGCGCUAAAGGAAAACUGUCACAAAUUGCAUUUAAAUGC
..(((((((.(((((((...(((.....((((.(((((....((....))......))))).))))((((.(((....))).))))....)))...))))).))...)))))))...... ( -34.90)
>DroEre_CAF1 27362 119 - 1
CCAAAUGCACUGGAAAGCAUUU-GGGCUGCACCCACCACCCAGAAAAAUCGCACCCAGCUGUGUGCGUGUCACUUGAAAGUCGCGCUAAAGGAAAACUGUCACAAAUUGCAUUUAAAUGC
..(((((((((((...((...(-(((.((.......))))))((....))))..)))).((((.(((((.(........).)))))...((.....))..))))...)))))))...... ( -26.80)
>DroYak_CAF1 26590 120 - 1
CCAAAUGCAGUGGAUAGCAGCCCAAAAAGCACCCGCCACCCAGAAAAAUCGCACCCUGCUGUGUGCGUGUCAGUUGAAAGUCGCGCUAAAGGAAAACUGUCACAAAUUGCAUUUAAAUGC
..((((((((((.(((((((........((....))......((....)).....))))))).)))(((.(((((.....((.(......))).))))).)))....)))))))...... ( -28.70)
>consensus
CGAAAUGCACUGGAUAGCAGUCCAAAAAGCACCCACCACCCAGAAAAAUCGCACCCUGGUGUGUGCGUGUCACUUGAAAGUCGCGCUAAAGGAAAACUGUCACAAAUUGCAUUUAAAUGC
..(((((((.(((((((...(((.....((((.(((((....((....))......))))).))))((((.(((....))).))))....)))...))))).))...)))))))...... (-26.10 = -27.10 +   1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,429,295 – 13,429,410
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.25
Mean single sequence MFE -39.56
Consensus MFE -30.14
Energy contribution -30.30
Covariance contribution 0.16
Combinations/Pair 1.30
Mean z-score -1.64
Structure conservation index 0.76
SVM decision value 0.22
SVM RNA-class probability 0.638743
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13429295 115 + 23771897
GGCGGUGGGUGCUUUUUGGACUGCUAUCGAGUGCAUUUCGAGGAGUAAUAUGGGGGUGGC-----CACCCGGUUUGGAAAAAAGUUAAGGCAUGCCGUCGCACAAAGGAAUUUUCCUAUA
.(((..((((((((((..(((((((.(((((.....)))))..))).......((((...-----.))))))))..))).........))))).))..)))....((((....))))... ( -36.20)
>DroSec_CAF1 26418 115 + 1
GGUGGUGGGUGCUUUUUGGACUGCCAUCCAGUGCAUUUCGAGGAGCCAUAUGGGGGUGGC-----CACCCGGUUUGGAAAGAAGUUAAGGCAUGCCAUCGCACAAAGGAAUUUUCCUAUA
.((((((((((((((...((((....(((((......(((.((.(((((......)))))-----..))))).)))))....))))))))))).)))))))....((((....))))... ( -37.60)
>DroSim_CAF1 28286 115 + 1
GGUGGUGGGUGCUUUUUGGACUGCUAUCCAGUGCAUUUCGAGGAGCAAUAUGGGGGUGGC-----CACCCGGUUUGGAAAAAAGUUAAGGCAUGCCGUCGCACAAAGGAAUUUUCCUAUA
.(((..((.(((((((((((.(((........))).))))))))))).((((.((((...-----.))))..(((....)))........))))))..)))....((((....))))... ( -34.50)
>DroEre_CAF1 27442 118 + 1
GGUGGUGGGUGCAGCCC-AAAUGCUUUCCAGUGCAUUUGGAGGAGCAAUGUGGGGUUGGGGCCACCACCCAGUAUGGAUA-AAGUUAAGGCAUGCCGUCGCACAAAGGAAUUUUCCUAUA
((((((((.(.((((((-.(.((((((((((.....))))).))))).)...)))))).).))))))))..((((((...-..((....))...)))).))....((((....))))... ( -45.80)
>DroYak_CAF1 26670 114 + 1
GGUGGCGGGUGCUUUUUGGGCUGCUAUCCACUGCAUUUGGAGGAGCAAUGUGGGGAUGGG-----CGCCCACUAUGGAAA-AAGUUAAGGCAUGCCGUCGCACAAAGGAAUUUUCCUAUA
.((((((((((((((..((((..((((((.(..((((.(......)))))..))))))).-----.))))(((.(....)-.))).))))))).)))))))....((((....))))... ( -43.70)
>consensus
GGUGGUGGGUGCUUUUUGGACUGCUAUCCAGUGCAUUUCGAGGAGCAAUAUGGGGGUGGC_____CACCCGGUUUGGAAA_AAGUUAAGGCAUGCCGUCGCACAAAGGAAUUUUCCUAUA
.(((((((.(((((((((((.(((........))).)))))))))))......(((((.......)))))........................)))))))....((((....))))... (-30.14 = -30.30 +   0.16)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,429,335 – 13,429,448
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.71
Mean single sequence MFE -32.83
Consensus MFE -24.30
Energy contribution -25.42
Covariance contribution 1.12
Combinations/Pair 1.07
Mean z-score -1.83
Structure conservation index 0.74
SVM decision value 0.32
SVM RNA-class probability 0.685548
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13429335 113 - 23771897
CCAAAAUGGUAGUUGUUGCGCAUAU--UUCCGUGCAAUAUUAUAGGAAAAUUCCUUUGUGCGACGGCAUGCCUUAACUUUUUUCCAAACCGGGUG-----GCCACCCCCAUAUUACUCCU
.......(((((((((((((((..(--((((.............))))).......))))))))))).))))..................(((.(-----(...)))))........... ( -28.02)
>DroSec_CAF1 26458 113 - 1
CCGGAAUGGUAGUUGUUGCGCAUAU--UUCCGUGCAAUAUUAUAGGAAAAUUCCUUUGUGCGAUGGCAUGCCUUAACUUCUUUCCAAACCGGGUG-----GCCACCCCCAUAUGGCUCCU
((((..(((.((..((((.((((.(--(..((..(((......((((....)))))))..))..)).))))..))))..))..)))..))))(..-----((((........))))..). ( -32.10)
>DroSim_CAF1 28326 113 - 1
CCGGAAUGGUAGUUGUUGCGCAUAU--UUCCGUGCAAUAUUAUAGGAAAAUUCCUUUGUGCGACGGCAUGCCUUAACUUUUUUCCAAACCGGGUG-----GCCACCCCCAUAUUGCUCCU
..(((..(((((((((((((((..(--((((.............))))).......))))))))))).))))..................(((.(-----(...))))).......))). ( -31.02)
>DroEre_CAF1 27481 119 - 1
CCGGCAUGGUAGUUGUUGGGCAUAUUUUUCCGUGCAAUGUUAUAGGAAAAUUCCUUUGUGCGACGGCAUGCCUUAACUU-UAUCCAUACUGGGUGGUGGCCCCAACCCCACAUUGCUCCU
((((.((((.(((((..((((((......(((((((.......((((....))))...))).)))).))))))))))).-...)))).))))((((.((......))))))......... ( -37.80)
>DroYak_CAF1 26710 112 - 1
CUGGAAUGGAAGUUGUUGCGCAUAU--UUCCGUGCAAUAUUAUAGGAAAAUUCCUUUGUGCGACGGCAUGCCUUAACUU-UUUCCAUAGUGGGCG-----CCCAUCCCCACAUUGCUCCU
..((((((((((..((((.((((..--..(((((((.......((((....))))...))).)))).))))..))))..-))))))).(((((..-----......))))).....))). ( -35.20)
>consensus
CCGGAAUGGUAGUUGUUGCGCAUAU__UUCCGUGCAAUAUUAUAGGAAAAUUCCUUUGUGCGACGGCAUGCCUUAACUU_UUUCCAAACCGGGUG_____GCCACCCCCAUAUUGCUCCU
..(((..(((((((((((((((.....((((.............))))........))))))))))).))))..................(((((.......))))).........))). (-24.30 = -25.42 +   1.12)

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 11:33:35 2006