Locus 2754

Sequence ID 3L_DroMel_CAF1
Location 7,777,669 – 7,777,817
Length 148
Max. P 0.860569
window4304 window4305 window4306

overview

Window 4

Location 7,777,669 – 7,777,777
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.26
Mean single sequence MFE -48.28
Consensus MFE -39.52
Energy contribution -39.76
Covariance contribution 0.24
Combinations/Pair 1.21
Mean z-score -1.70
Structure conservation index 0.82
SVM decision value 0.52
SVM RNA-class probability 0.768014
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7777669 108 + 23771897
UGGCG------------AGGAUGCCUGGAUGCGAGGGAAUCGCACCUGGCAGAUGUUGCACUGCGUGAUCGUCUCACAGCAUUGCCGGCAAAAGGUGUGACCACAAUUGGUGGUCACCGG
((.((------------....((((.((.(((((.....))))))).))))......(((.(((((((.....)))).))).))))).))....(.((((((((.....))))))))).. ( -43.80)
>DroPse_CAF1 21156 120 + 1
GCCUCCGCCGCGCGGGGAGGCGUCCUGGGCGCGGGGGAACUUCACCUGGCAGAUGUUGCACUGGGUGAUCGUCUCGCAGCACUGCCGGCAGAAGGUGUGGCCGCAGUUGGUGGUCACCGG
.(((((((.((.(((((.....))))).)))))))))..((((..(((((((.((((((...(((.......))))))))))))))))..))))(.((((((((.....))))))))).. ( -61.50)
>DroSec_CAF1 18052 108 + 1
UGGCG------------AGGAUGCCUGGAUGCGAGGGAAUCGCACCUGGCAGAUGUUGCACUGCGUGAUCGUCUCACAGCAUUGCCGGCAAAAGGUGUGACCACAAUUGGUGGUCACCGG
((.((------------....((((.((.(((((.....))))))).))))......(((.(((((((.....)))).))).))))).))....(.((((((((.....))))))))).. ( -43.80)
>DroEre_CAF1 18094 108 + 1
UGGCG------------AGGAUGCCUGGAUGCGUGGGAAGCGCACCUGGCAGAUGUUGCACUGCGUGAUCGUCUCGCAGCACUGCCGGCAAAAGGUGUGGCCACAAUUGGUGGUCACCGG
...((------------....((((.((.(((((.....))))))).(((((.((((((...(((....)))...)))))))))))))))......((((((((.....)))))))))). ( -47.80)
>DroYak_CAF1 19280 108 + 1
UGGCG------------AGGAUGCCUGGAUGCGGGGGAAACGCACCUGGCAGAUGUUGCACUGCGUGAUUGUUUCGCAGCAUUGCCGGCAAAAGGUGUGGCCACAAUUGGUGGUCACCGG
.(((.------------....((((.((.((((.......)))))).))))((((((((...(((....)))...)))))))))))........(.((((((((.....))))))))).. ( -44.50)
>consensus
UGGCG____________AGGAUGCCUGGAUGCGAGGGAAUCGCACCUGGCAGAUGUUGCACUGCGUGAUCGUCUCGCAGCAUUGCCGGCAAAAGGUGUGGCCACAAUUGGUGGUCACCGG
.....................((((.((.(((((.....))))))).(((((.((((((...(((....)))...)))))))))))))))....(.((((((((.....))))))))).. (-39.52 = -39.76 +   0.24)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,777,669 – 7,777,777
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.26
Mean single sequence MFE -40.92
Consensus MFE -30.20
Energy contribution -31.04
Covariance contribution 0.84
Combinations/Pair 1.16
Mean z-score -2.12
Structure conservation index 0.74
SVM decision value 0.83
SVM RNA-class probability 0.860569
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7777669 108 - 23771897
CCGGUGACCACCAAUUGUGGUCACACCUUUUGCCGGCAAUGCUGUGAGACGAUCACGCAGUGCAACAUCUGCCAGGUGCGAUUCCCUCGCAUCCAGGCAUCCU------------CGCCA
...((((((((.....))))))))..........(((...((((((.(.....).))))))........((((.(((((((.....)))))))..))))....------------.))). ( -41.40)
>DroPse_CAF1 21156 120 - 1
CCGGUGACCACCAACUGCGGCCACACCUUCUGCCGGCAGUGCUGCGAGACGAUCACCCAGUGCAACAUCUGCCAGGUGAAGUUCCCCCGCGCCCAGGACGCCUCCCCGCGCGGCGGAGGC
..(((....))).......(((....((((.((((((((((.((((.(........)...)))).)).))))).))))))).(((.((((((...(((....)))..)))))).)))))) ( -44.80)
>DroSec_CAF1 18052 108 - 1
CCGGUGACCACCAAUUGUGGUCACACCUUUUGCCGGCAAUGCUGUGAGACGAUCACGCAGUGCAACAUCUGCCAGGUGCGAUUCCCUCGCAUCCAGGCAUCCU------------CGCCA
...((((((((.....))))))))..........(((...((((((.(.....).))))))........((((.(((((((.....)))))))..))))....------------.))). ( -41.40)
>DroEre_CAF1 18094 108 - 1
CCGGUGACCACCAAUUGUGGCCACACCUUUUGCCGGCAGUGCUGCGAGACGAUCACGCAGUGCAACAUCUGCCAGGUGCGCUUCCCACGCAUCCAGGCAUCCU------------CGCCA
..((((.((((.....))))...)))).......(((.(..(((((.(.....).)))))..)......((((.((((((.......))))))..))))....------------.))). ( -41.10)
>DroYak_CAF1 19280 108 - 1
CCGGUGACCACCAAUUGUGGCCACACCUUUUGCCGGCAAUGCUGCGAAACAAUCACGCAGUGCAACAUCUGCCAGGUGCGUUUCCCCCGCAUCCAGGCAUCCU------------CGCCA
..(((((((((.....))))..........((((((((((((((((.........))))).....))).)))).((((((.......))))))..))))...)------------)))). ( -35.90)
>consensus
CCGGUGACCACCAAUUGUGGCCACACCUUUUGCCGGCAAUGCUGCGAGACGAUCACGCAGUGCAACAUCUGCCAGGUGCGAUUCCCCCGCAUCCAGGCAUCCU____________CGCCA
..((((.((((.....))))...))))...(((((((((((.((((...((....))...)))).))).)))).(((((((.....)))))))..))))..................... (-30.20 = -31.04 +   0.84)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,777,697 – 7,777,817
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.17
Mean single sequence MFE -47.34
Consensus MFE -40.26
Energy contribution -39.98
Covariance contribution -0.28
Combinations/Pair 1.17
Mean z-score -1.24
Structure conservation index 0.85
SVM decision value 0.02
SVM RNA-class probability 0.544956
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7777697 120 + 23771897
CGCACCUGGCAGAUGUUGCACUGCGUGAUCGUCUCACAGCAUUGCCGGCAAAAGGUGUGACCACAAUUGGUGGUCACCGGACAGCGCAGGAUAUCGCUGCAAAGCGGACACAUUAGCGGA
(((.((((((...(((((((.(((((((.....)))).))).)).)))))....(.((((((((.....))))))))).....)).))))...(((((....)))))........))).. ( -45.60)
>DroPse_CAF1 21196 120 + 1
UUCACCUGGCAGAUGUUGCACUGGGUGAUCGUCUCGCAGCACUGCCGGCAGAAGGUGUGGCCGCAGUUGGUGGUCACCGGACAGCGGAGGAUGUCCCUGCAGAGCGGACAGAGCAGCGGG
.((((((.((((...))))...))))))....(((((.((.((((((((((...(.((((((((.....)))))))))(((((........)))))))))....))).))).)).))))) ( -50.80)
>DroSec_CAF1 18080 120 + 1
CGCACCUGGCAGAUGUUGCACUGCGUGAUCGUCUCACAGCAUUGCCGGCAAAAGGUGUGACCACAAUUGGUGGUCACCGGACAGCGCAGGAUAUCGCCGCAAAGCGGACACAUCAGCGGA
(((.((((((...(((((((.(((((((.....)))).))).)).)))))....(.((((((((.....))))))))).....)).)))).....(((((...)))).)......))).. ( -44.80)
>DroEre_CAF1 18122 120 + 1
CGCACCUGGCAGAUGUUGCACUGCGUGAUCGUCUCGCAGCACUGCCGGCAAAAGGUGUGGCCACAAUUGGUGGUCACCGGACAGCGCAGGAUAUCGCCGCACAGCGGACACAUCAGCGGA
(((..(((((((.((((((...(((....)))...))))))))))))).....(((((((((((.....)))))..(((....((((........).)))....))).)))))).))).. ( -47.30)
>DroYak_CAF1 19308 120 + 1
CGCACCUGGCAGAUGUUGCACUGCGUGAUUGUUUCGCAGCAUUGCCGGCAAAAGGUGUGGCCACAAUUGGUGGUCACCGGACAGCGCAGGAUGUCGCCGCACAGCGGACACAUCAGCGGA
.((..(((((((.((((((...(((....)))...)))))))))))))......(.((((((((.....))))))))).....))((..(((((..((((...))))..))))).))... ( -48.20)
>consensus
CGCACCUGGCAGAUGUUGCACUGCGUGAUCGUCUCGCAGCAUUGCCGGCAAAAGGUGUGGCCACAAUUGGUGGUCACCGGACAGCGCAGGAUAUCGCCGCAAAGCGGACACAUCAGCGGA
(((..(((((((.((((((...(((....)))...)))))))))))))......((((((((((.....)))))).(((....((((........)).))....)))))))....))).. (-40.26 = -39.98 +  -0.28)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:56 2006