Locus 7969

Sequence ID 3L_DroMel_CAF1
Location 21,098,646 – 21,098,806
Length 160
Max. P 0.989145
window13005 window13006 window13007 window13008

overview

Window 5

Location 21,098,646 – 21,098,766
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.96
Mean single sequence MFE -33.24
Consensus MFE -25.26
Energy contribution -27.54
Covariance contribution 2.28
Combinations/Pair 1.14
Mean z-score -2.97
Structure conservation index 0.76
SVM decision value 1.98
SVM RNA-class probability 0.984488
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21098646 120 + 23771897
CUGCUAAUCAUGACAUUUGCUCGUUUACAUUAUGUGGUCGGUUUUCAGUUUUUGCAGCUUGCGCAUGUAAUUUUUGAUGCAUGCAUUAGCUGCAGCUGCAUAUUGCAUGGCUCUCUCUUA
.......(((((.((..((((((.((((.....)))).))).....(((...(((((((...(((((((........)))))))...)))))))))))))...))))))).......... ( -32.50)
>DroSec_CAF1 148832 119 + 1
CUGCUAAUCAUGGCAUUUGCUCGUUUACAUUAUGUGGUCGGUUUUCAGUUUUU-CAGCUUGCGCAUGUAAUUUUUGUUGCAUGCAUUAGCUGCAGCUGCAUAUUGCAUGACUCUCUCUUA
.......(((((.((..((((((.((((.....)))).))).....((((...-(((((...(((((((((....)))))))))...))))).)))))))...))))))).......... ( -32.10)
>DroSim_CAF1 56361 120 + 1
CUGCUAAUCAUGGCAUUUGCUCGUUUACAUUAUGUGGUCGGUUUUCAGUUUUUGCAGCUUGCGCGUGUAAUUUUUGUUGCAUGCAUUAGCUGCAGCUGCAUAUUGCAUGACUCUCUCUUA
.......(((((.((..((((((.((((.....)))).))).....(((...(((((((...(((((((((....)))))))))...)))))))))))))...))))))).......... ( -35.80)
>DroEre_CAF1 71196 115 + 1
CUGCUAAUCAUGGCAUUUGCUCGUUUACAUUAUGUGGUCGGUUUUCAGUUUUUGCAGCUUGUGC-----AUUUUUGUUGCAUGCAUCAGCCACGGCUGCAUAUUGCAUGACUUUCCCUUG
.......(((((((....)).......((.((((..((((.......((....)).(((.((((-----((.........)))))).)))..))))..)))).))))))).......... ( -28.20)
>DroYak_CAF1 43072 115 + 1
UUGCUAAUCAUGGCAUUUGCUCGUUCACAUUAUGUGGUUGCAGCUCAGUUUUUGCAGCUUGUUC-----AUUUUUGUUGCAUGCAUCAGCUGCAGCUGCAUAUUGCAUGACUUUCCCUUA
.......(((((((....)).......((.((((..(((((((((..((...((((((..(...-----...)..)))))).))...)))))))))..)))).))))))).......... ( -37.60)
>consensus
CUGCUAAUCAUGGCAUUUGCUCGUUUACAUUAUGUGGUCGGUUUUCAGUUUUUGCAGCUUGCGC_UGUAAUUUUUGUUGCAUGCAUUAGCUGCAGCUGCAUAUUGCAUGACUCUCUCUUA
.......(((((.((..(((.((.((((.....)))).))......(((...(((((((...(((((((((....)))))))))...)))))))))))))...))))))).......... (-25.26 = -27.54 +   2.28)

alignment

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secondary structure

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Window 6

Location 21,098,646 – 21,098,766
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.96
Mean single sequence MFE -26.63
Consensus MFE -19.56
Energy contribution -19.84
Covariance contribution 0.28
Combinations/Pair 1.08
Mean z-score -2.15
Structure conservation index 0.73
SVM decision value 0.64
SVM RNA-class probability 0.807966
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21098646 120 - 23771897
UAAGAGAGAGCCAUGCAAUAUGCAGCUGCAGCUAAUGCAUGCAUCAAAAAUUACAUGCGCAAGCUGCAAAAACUGAAAACCGACCACAUAAUGUAAACGAGCAAAUGUCAUGAUUAGCAG
.....(..(..((((((...(((...(((((((..((((((............))))))..)))))))............((...((.....))...)).)))..)).))))..)..).. ( -25.00)
>DroSec_CAF1 148832 119 - 1
UAAGAGAGAGUCAUGCAAUAUGCAGCUGCAGCUAAUGCAUGCAACAAAAAUUACAUGCGCAAGCUG-AAAAACUGAAAACCGACCACAUAAUGUAAACGAGCAAAUGCCAUGAUUAGCAG
.....(..(((((((((...(((.((((((.....)))).))........((((((((....))(.-...)...................))))))....)))..)).)))))))..).. ( -25.40)
>DroSim_CAF1 56361 120 - 1
UAAGAGAGAGUCAUGCAAUAUGCAGCUGCAGCUAAUGCAUGCAACAAAAAUUACACGCGCAAGCUGCAAAAACUGAAAACCGACCACAUAAUGUAAACGAGCAAAUGCCAUGAUUAGCAG
.....(..(((((((((...(((((((((.((....))..((..............)))).))))))).......................(((......)))..)).)))))))..).. ( -26.24)
>DroEre_CAF1 71196 115 - 1
CAAGGGAAAGUCAUGCAAUAUGCAGCCGUGGCUGAUGCAUGCAACAAAAAU-----GCACAAGCUGCAAAAACUGAAAACCGACCACAUAAUGUAAACGAGCAAAUGCCAUGAUUAGCAG
.....(..(((((((((...(((....(..(((..(((((.........))-----)))..)))..).............((...((.....))...)).)))..)).)))))))..).. ( -25.10)
>DroYak_CAF1 43072 115 - 1
UAAGGGAAAGUCAUGCAAUAUGCAGCUGCAGCUGAUGCAUGCAACAAAAAU-----GAACAAGCUGCAAAAACUGAGCUGCAACCACAUAAUGUGAACGAGCAAAUGCCAUGAUUAGCAA
.....(..(((((((((...(((((((((((((....(((.........))-----)....))))))........)))))))..(((.....)))..........)).)))))))..).. ( -31.40)
>consensus
UAAGAGAGAGUCAUGCAAUAUGCAGCUGCAGCUAAUGCAUGCAACAAAAAUUACA_GCGCAAGCUGCAAAAACUGAAAACCGACCACAUAAUGUAAACGAGCAAAUGCCAUGAUUAGCAG
.....(..(((((((((...((((((((((((....)).)))...................))))))).......................(((......)))..)).)))))))..).. (-19.56 = -19.84 +   0.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 21,098,686 – 21,098,806
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.29
Mean single sequence MFE -29.99
Consensus MFE -22.80
Energy contribution -24.60
Covariance contribution 1.80
Combinations/Pair 1.15
Mean z-score -2.69
Structure conservation index 0.76
SVM decision value 1.73
SVM RNA-class probability 0.974387
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21098686 120 + 23771897
GUUUUCAGUUUUUGCAGCUUGCGCAUGUAAUUUUUGAUGCAUGCAUUAGCUGCAGCUGCAUAUUGCAUGGCUCUCUCUUAGAAUUGCUUUCACCGCUGCACUUUUGGGAUUUAACAUUUU
............(((((((...(((((((........)))))))...)))))))(((((.....))..)))....((((((((.(((..........))).))))))))........... ( -32.10)
>DroSec_CAF1 148872 119 + 1
GUUUUCAGUUUUU-CAGCUUGCGCAUGUAAUUUUUGUUGCAUGCAUUAGCUGCAGCUGCAUAUUGCAUGACUCUCUCUUAGAAAUGCUUUCAUCGCUGCACUUUUGGGAUUUAACAUUUU
..(..(((.....-.((((...(((((((((....)))))))))...))))(((((........((((...(((.....))).)))).......)))))....)))..)........... ( -30.46)
>DroSim_CAF1 56401 120 + 1
GUUUUCAGUUUUUGCAGCUUGCGCGUGUAAUUUUUGUUGCAUGCAUUAGCUGCAGCUGCAUAUUGCAUGACUCUCUCUUAGAAAUGCUUUCACCGCUGCACUUUUGGGAUUUAACAUUUU
.......((..((((((((...(((((((((....)))))))))...))))))))..))................((((((((.(((..........))).))))))))........... ( -34.20)
>DroEre_CAF1 71236 115 + 1
GUUUUCAGUUUUUGCAGCUUGUGC-----AUUUUUGUUGCAUGCAUCAGCCACGGCUGCAUAUUGCAUGACUUUCCCUUGGAAAUGCUUUCACCACUGCACUUUUGGGAUUUUACAUUUU
..(..(((....(((((..((.((-----((((..(..(((((((.((((....)))).....)))))).).......)..))))))...))...)))))...)))..)........... ( -27.70)
>DroYak_CAF1 43112 115 + 1
CAGCUCAGUUUUUGCAGCUUGUUC-----AUUUUUGUUGCAUGCAUCAGCUGCAGCUGCAUAUUGCAUGACUUUCCCUUAGAAAUGUUUUCACCACUGCACUUUUGGGAUUUUACAUUUU
...(((((....(((((..((..(-----((((((((((((.((....))))))))(((.....)))............)))))))....))...)))))...)))))............ ( -25.50)
>consensus
GUUUUCAGUUUUUGCAGCUUGCGC_UGUAAUUUUUGUUGCAUGCAUUAGCUGCAGCUGCAUAUUGCAUGACUCUCUCUUAGAAAUGCUUUCACCGCUGCACUUUUGGGAUUUAACAUUUU
......((((..(((((..((((((((((((....)))))))))...(((....))))))..))))).))))....(((((((.(((..........))).)))))))............ (-22.80 = -24.60 +   1.80)

alignment

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secondary structure

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dotplot

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Window 8

Location 21,098,686 – 21,098,806
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.29
Mean single sequence MFE -26.20
Consensus MFE -21.86
Energy contribution -21.26
Covariance contribution -0.60
Combinations/Pair 1.24
Mean z-score -2.28
Structure conservation index 0.83
SVM decision value 2.15
SVM RNA-class probability 0.989145
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21098686 120 - 23771897
AAAAUGUUAAAUCCCAAAAGUGCAGCGGUGAAAGCAAUUCUAAGAGAGAGCCAUGCAAUAUGCAGCUGCAGCUAAUGCAUGCAUCAAAAAUUACAUGCGCAAGCUGCAAAAACUGAAAAC
....................((((((.((....))..............((((((.((((((((..((((.....))))))))).....))).)))).))..))))))............ ( -26.30)
>DroSec_CAF1 148872 119 - 1
AAAAUGUUAAAUCCCAAAAGUGCAGCGAUGAAAGCAUUUCUAAGAGAGAGUCAUGCAAUAUGCAGCUGCAGCUAAUGCAUGCAACAAAAAUUACAUGCGCAAGCUG-AAAAACUGAAAAC
..................((((((((.((((.....((((.....)))).))))((.....)).)))))((((..((((((.((......)).))))))..)))).-....)))...... ( -25.60)
>DroSim_CAF1 56401 120 - 1
AAAAUGUUAAAUCCCAAAAGUGCAGCGGUGAAAGCAUUUCUAAGAGAGAGUCAUGCAAUAUGCAGCUGCAGCUAAUGCAUGCAACAAAAAUUACACGCGCAAGCUGCAAAAACUGAAAAC
....................((((((..((...((.((((.....))))(.((((((...(((....))).....)))))))..............)).)).))))))............ ( -26.20)
>DroEre_CAF1 71236 115 - 1
AAAAUGUAAAAUCCCAAAAGUGCAGUGGUGAAAGCAUUUCCAAGGGAAAGUCAUGCAAUAUGCAGCCGUGGCUGAUGCAUGCAACAAAAAU-----GCACAAGCUGCAAAAACUGAAAAC
....................((((((..((...((((((((...)))))(.((((((.....((((....)))).)))))))........)-----)).)).))))))............ ( -27.50)
>DroYak_CAF1 43112 115 - 1
AAAAUGUAAAAUCCCAAAAGUGCAGUGGUGAAAACAUUUCUAAGGGAAAGUCAUGCAAUAUGCAGCUGCAGCUGAUGCAUGCAACAAAAAU-----GAACAAGCUGCAAAAACUGAGCUG
..................(((.((((.((((.....((((.....)))).))))......((((((((((((....)).)))..((....)-----)....)))))))...)))).))). ( -25.40)
>consensus
AAAAUGUUAAAUCCCAAAAGUGCAGCGGUGAAAGCAUUUCUAAGAGAGAGUCAUGCAAUAUGCAGCUGCAGCUAAUGCAUGCAACAAAAAUUACA_GCGCAAGCUGCAAAAACUGAAAAC
....................((((((..((...((.(((((...)))))(.((((((...(((....))).....)))))))..............)).)).))))))............ (-21.86 = -21.26 +  -0.60)

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 13:02:28 2006