Locus 541

Sequence ID 3L_DroMel_CAF1
Location 1,570,848 – 1,570,951
Length 103
Max. P 0.962118
window823 window824

overview

Window 3

Location 1,570,848 – 1,570,951
Length 103
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 92.47
Mean single sequence MFE -32.38
Consensus MFE -29.65
Energy contribution -29.27
Covariance contribution -0.37
Combinations/Pair 1.07
Mean z-score -2.08
Structure conservation index 0.92
SVM decision value 1.54
SVM RNA-class probability 0.962118
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1570848 103 + 23771897
CACACCAAACAGCUGUGCUUAAUGUUUUCACAGUUGGCU-----UGGCUUUGGCUUUGGUUUUAGCCUCAGUUUUAGCUUCGGGCCAACUUGGGUUCG------UUUUCGCUUG
..............(((...((((..((((.((((((((-----(((((..((((..(((....)))..))))..)))..))))))))))))))..))------))..)))... ( -32.00)
>DroSec_CAF1 15318 103 + 1
CACACCAAACAGCUGUGCCUAAUGUUUUCACAGUUGGCU-----UGGCUUUGGCUUUGGUUUUAGCCUCAGUUUUAGCUUCGGGCCGACUUGGGUUCG------UUUUCGCUUG
..............(((...((((..((((.((((((((-----(((((..((((..(((....)))..))))..)))..))))))))))))))..))------))..)))... ( -31.70)
>DroEre_CAF1 21554 103 + 1
CACACCAAACAGCUGUGCUUAAUGUUUUCACAGUUGGCU-----UGGCUUUAGCUUUGGUUUUAGCCUCAGUUUUAGCUGCGGGCCGACUUGGGUUCG------UUUUCGCUUG
..............(((...((((..((((.((((((((-----(((((..((((..(((....)))..))))..)))..))))))))))))))..))------))..)))... ( -31.80)
>DroYak_CAF1 15905 114 + 1
CACACCAAACAGCUGUGCUUAAUGUUUUCACAGUUGGCUUGGCUUGGCUUUGGCUUUGGUUUUAGCCUCAGUUUUAGCUUCGGGCCAACUUGGGCUCGUUUACGUUUUCGCUUG
((..((((.((((((((...........))))))))..))))..))(((..((((..(((....)))..))))..)))..((((((......))))))................ ( -34.00)
>consensus
CACACCAAACAGCUGUGCUUAAUGUUUUCACAGUUGGCU_____UGGCUUUGGCUUUGGUUUUAGCCUCAGUUUUAGCUUCGGGCCAACUUGGGUUCG______UUUUCGCUUG
.........((((((((...........))))))))((.......((((..((((..(((....)))..))))..)))).((((((......))))))...........))... (-29.65 = -29.27 +  -0.37)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 1,570,848 – 1,570,951
Length 103
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 92.47
Mean single sequence MFE -24.73
Consensus MFE -20.92
Energy contribution -21.05
Covariance contribution 0.13
Combinations/Pair 1.08
Mean z-score -1.42
Structure conservation index 0.85
SVM decision value -0.03
SVM RNA-class probability 0.516650
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1570848 103 - 23771897
CAAGCGAAAA------CGAACCCAAGUUGGCCCGAAGCUAAAACUGAGGCUAAAACCAAAGCCAAAGCCA-----AGCCAACUGUGAAAACAUUAAGCACAGCUGUUUGGUGUG
..........------......(((((((((....((......))..((((........)))).......-----.))))))).))...((((((((((....)))))))))). ( -23.30)
>DroSec_CAF1 15318 103 - 1
CAAGCGAAAA------CGAACCCAAGUCGGCCCGAAGCUAAAACUGAGGCUAAAACCAAAGCCAAAGCCA-----AGCCAACUGUGAAAACAUUAGGCACAGCUGUUUGGUGUG
..........------...(((((((.((((............((..((((........))))..))...-----.(((...(((....)))...)))...))))))))).)). ( -24.30)
>DroEre_CAF1 21554 103 - 1
CAAGCGAAAA------CGAACCCAAGUCGGCCCGCAGCUAAAACUGAGGCUAAAACCAAAGCUAAAGCCA-----AGCCAACUGUGAAAACAUUAAGCACAGCUGUUUGGUGUG
..(((.....------(((.......)))(((..(((......))).)))..........)))...((((-----(((...(((((...........)))))..)))))))... ( -23.80)
>DroYak_CAF1 15905 114 - 1
CAAGCGAAAACGUAAACGAGCCCAAGUUGGCCCGAAGCUAAAACUGAGGCUAAAACCAAAGCCAAAGCCAAGCCAAGCCAACUGUGAAAACAUUAAGCACAGCUGUUUGGUGUG
...(((....))).........(((((((((.....(((....((..((((........))))..))...)))...))))))).))...((((((((((....)))))))))). ( -27.50)
>consensus
CAAGCGAAAA______CGAACCCAAGUCGGCCCGAAGCUAAAACUGAGGCUAAAACCAAAGCCAAAGCCA_____AGCCAACUGUGAAAACAUUAAGCACAGCUGUUUGGUGUG
......................(((((((((....((......))..((((........)))).............))))))).))...((((((((((....)))))))))). (-20.92 = -21.05 +   0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:49 2006