Locus 5184

Sequence ID 3L_DroMel_CAF1
Location 14,267,266 – 14,267,439
Length 173
Max. P 0.927402
window8205 window8206 window8207 window8208

overview

Window 5

Location 14,267,266 – 14,267,363
Length 97
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 92.36
Mean single sequence MFE -30.68
Consensus MFE -24.36
Energy contribution -24.56
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.79
Structure conservation index 0.79
SVM decision value 0.76
SVM RNA-class probability 0.842562
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14267266 97 + 23771897
UAG---------CCACUAUAGUGACUCUUGCAGGGCAGUUUAGUCGCUGUCCGGUUCGUGUUUUACUGUUUCCACAGCUUUUAGCCGCUGCUGACGGUCGGAUGCU
.((---------((...(((((((((.((((...))))...)))))))))..)))).(((((..((((((....((((........))))..))))))..))))). ( -29.90)
>DroSec_CAF1 97271 97 + 1
UAG---------UCACUAUAGUGACUCUUGCAGGGCAGUUUAGUCGCUGUCCGGUUCUUGUUUUACUGUUUCCACAGCUUUUAGCCGCUGCUGACGGUCGGAUGCU
.((---------((((....))))))...((.(((((((......))))))).......(((..((((((....((((........))))..))))))..))))). ( -31.20)
>DroSim_CAF1 97340 97 + 1
UAG---------UCACUAUAGUGACUCUUGCAGGGCAGUUUAGUCGCUGUCCGGUUCUUGUUUUACUGUUUCCACAGCUUUUAGCCGCUGCUGACGUUCGGAUGCU
.((---------((((....))))))...((((((((((......))))))).............(((....((((((........)))).)).....))).))). ( -27.00)
>DroEre_CAF1 96827 102 + 1
UAGUCACUA----CACUAUAGUGACUCUUGCAGGGCAGUUUAGUCGCUGUCCGGUUCUUGUUUUACUGUUUCCACAGCUUUUAGCUGCUGCUGAUGGUCGGAUGCU
.((((((((----.....))))))))...((.(((((((......))))))).......(((..((((((..((((((.....)))).))..))))))..))))). ( -33.30)
>DroYak_CAF1 100525 105 + 1
UAA-GACUAUAGUCACUAUAGUGACUCUUGCAGGGCAGUUUAGUCGCUGUCCGGUUCUUGUUUUACUGUUUCCACAGCUUUUAGCUGCUGCUGAUGGUCGGAUGCU
.((-((((..((((((....))))))......(((((((......))))))))).))))(((..((((((..((((((.....)))).))..))))))..)))... ( -32.00)
>consensus
UAG_________UCACUAUAGUGACUCUUGCAGGGCAGUUUAGUCGCUGUCCGGUUCUUGUUUUACUGUUUCCACAGCUUUUAGCCGCUGCUGACGGUCGGAUGCU
.................(((((((..(..((.(((((((......))))))).))....)..))))))).(((...(((.(((((....))))).))).))).... (-24.36 = -24.56 +   0.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,267,266 – 14,267,363
Length 97
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 92.36
Mean single sequence MFE -27.28
Consensus MFE -21.04
Energy contribution -21.04
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.29
Structure conservation index 0.77
SVM decision value 1.18
SVM RNA-class probability 0.927402
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14267266 97 - 23771897
AGCAUCCGACCGUCAGCAGCGGCUAAAAGCUGUGGAAACAGUAAAACACGAACCGGACAGCGACUAAACUGCCCUGCAAGAGUCACUAUAGUGG---------CUA
.(((((((.((((.....))))......(((((....)))))...........))))(((........)))...)))...((((((....))))---------)). ( -26.30)
>DroSec_CAF1 97271 97 - 1
AGCAUCCGACCGUCAGCAGCGGCUAAAAGCUGUGGAAACAGUAAAACAAGAACCGGACAGCGACUAAACUGCCCUGCAAGAGUCACUAUAGUGA---------CUA
.(((((((.((((.....))))......(((((....)))))...........))))(((........)))...)))...((((((....))))---------)). ( -26.90)
>DroSim_CAF1 97340 97 - 1
AGCAUCCGAACGUCAGCAGCGGCUAAAAGCUGUGGAAACAGUAAAACAAGAACCGGACAGCGACUAAACUGCCCUGCAAGAGUCACUAUAGUGA---------CUA
...............((((.(((.....(((((....)))))...........((.....))........)))))))...((((((....))))---------)). ( -26.30)
>DroEre_CAF1 96827 102 - 1
AGCAUCCGACCAUCAGCAGCAGCUAAAAGCUGUGGAAACAGUAAAACAAGAACCGGACAGCGACUAAACUGCCCUGCAAGAGUCACUAUAGUG----UAGUGACUA
.(((((((......(((....)))....(((((....)))))...........))))(((........)))...)))...(((((((((...)----)))))))). ( -27.60)
>DroYak_CAF1 100525 105 - 1
AGCAUCCGACCAUCAGCAGCAGCUAAAAGCUGUGGAAACAGUAAAACAAGAACCGGACAGCGACUAAACUGCCCUGCAAGAGUCACUAUAGUGACUAUAGUC-UUA
.((.((((......(((....)))....(((((....)))))...........))))..))(((((...(((...)))..((((((....)))))).)))))-... ( -29.30)
>consensus
AGCAUCCGACCGUCAGCAGCGGCUAAAAGCUGUGGAAACAGUAAAACAAGAACCGGACAGCGACUAAACUGCCCUGCAAGAGUCACUAUAGUGA_________CUA
.((.((((......(((....)))....(((((....)))))...........))))..))((((....(((...)))..))))...................... (-21.04 = -21.04 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,267,294 – 14,267,399
Length 105
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 90.63
Mean single sequence MFE -35.62
Consensus MFE -31.42
Energy contribution -32.03
Covariance contribution 0.61
Combinations/Pair 1.03
Mean z-score -1.61
Structure conservation index 0.88
SVM decision value 0.63
SVM RNA-class probability 0.804179
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14267294 105 + 23771897
GUUUAGUCGC-UGUCCGGUUCGUGUUUUACUGUUUCCACAGCUUUUAGCCGCUGCUGACGGUCGGAUGCUCACGCGGCCGGCAUGAAAACUUAUGUCGGCGGCCUU
.....(((((-((.(((((..(((((..((((((....((((........))))..))))))..)))))..)).))).)(((((((....)))))))))))))... ( -35.60)
>DroSec_CAF1 97299 105 + 1
GUUUAGUCGC-UGUCCGGUUCUUGUUUUACUGUUUCCACAGCUUUUAGCCGCUGCUGACGGUCGGAUGCUCACGCGGCCGGCAUGAAAACUUAUGUCGGCGGCCUU
........((-.(((((...........((((((....((((........))))..)))))))))))))....((.((((((((((....)))))))))).))... ( -35.50)
>DroSim_CAF1 97368 105 + 1
GUUUAGUCGC-UGUCCGGUUCUUGUUUUACUGUUUCCACAGCUUUUAGCCGCUGCUGACGUUCGGAUGCUCACGCGGCCGGCAUGAAAACUUAUGUCGGCGGCCUU
........((-.((((((...........((((....))))...(((((....)))))...))))))))....((.((((((((((....)))))))))).))... ( -33.60)
>DroEre_CAF1 96860 105 + 1
GUUUAGUCGC-UGUCCGGUUCUUGUUUUACUGUUUCCACAGCUUUUAGCUGCUGCUGAUGGUCGGAUGCUCACGCGGCCGGCAUGAAAACUUAUGUCGGCGGCCUU
........((-.((((((...........((((....))))((.(((((....))))).))))))))))....((.((((((((((....)))))))))).))... ( -35.80)
>DroYak_CAF1 100561 105 + 1
GUUUAGUCGC-UGUCCGGUUCUUGUUUUACUGUUUCCACAGCUUUUAGCUGCUGCUGAUGGUCGGAUGCUCACGCGGCCGGCAUGAAAACUUAUGUCGGCGGCCUU
........((-.((((((...........((((....))))((.(((((....))))).))))))))))....((.((((((((((....)))))))))).))... ( -35.80)
>DroAna_CAF1 92692 89 + 1
GUUUAGACGCCUGUCCGACUUU-----------------GGCUUUUCGCUGCUGCUGAUGGUCGGAUGCUCACGCGGCCGGCAUGAAAACUUAUGUCGGCGGCCUU
.....((.((..(((((((((.-----------------.((...........))..).))))))))))))..((.((((((((((....)))))))))).))... ( -37.40)
>consensus
GUUUAGUCGC_UGUCCGGUUCUUGUUUUACUGUUUCCACAGCUUUUAGCCGCUGCUGACGGUCGGAUGCUCACGCGGCCGGCAUGAAAACUUAUGUCGGCGGCCUU
........((..((((((...........((((....))))((.(((((....))))).))))))))))....((.((((((((((....)))))))))).))... (-31.42 = -32.03 +   0.61)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,267,329 – 14,267,439
Length 110
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 84.00
Mean single sequence MFE -32.07
Consensus MFE -26.55
Energy contribution -26.05
Covariance contribution -0.50
Combinations/Pair 1.10
Mean z-score -1.61
Structure conservation index 0.83
SVM decision value 0.21
SVM RNA-class probability 0.634587
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14267329 110 + 23771897
CACAGCUUUUAGCCGCUG---CUGAC---GGUCGGAUGCUCACGCGGCCGGCAUGAAAACUUAUGUCGGCGGCCUUUGGGCGCAAUUAUUUAUACAUGCCUCAUAAAAAUCGCAAG
...(((.((..(((((..---..).)---)))..)).)))...(((((((((((((....)))))))))).(((....))).............................)))... ( -34.70)
>DroVir_CAF1 109384 100 + 1
-----GUUUUAGUUGUUG---CUGUU---GUUC----GUCCACGCGGCCGGCAUGAAAACUUAUGUCGGCGGCCUUUGGGCGCAAUUAUUUAUACAUGCCUCAUAAAAAUCG-AAA
-----.(((((..((..(---((((.---((((----(((((.((.((((((((((....)))))))))).))...)))))).))).......))).))..)))))))....-... ( -30.90)
>DroPse_CAF1 93833 97 + 1
-------------UGCUG---CUCCU---GGUCGGAUGCUCACGCGGCCGGCAUGAAAACUUAUGUCGGCGGCCUUUGGGCGCAAUUAUUUAUACAUGCCUCAUAAAAAUCGCAAG
-------------(((((---((((.---....))).(((((.((.((((((((((....)))))))))).))...))))))))....(((((.........)))))....))).. ( -31.60)
>DroGri_CAF1 119798 106 + 1
-----AUUUUAGUUGUUGUUGCUGCCGUUGUUC----GUCCACGCGGCCGGCAUGAAAACUUAUGUCGGCGGCCUUUGGGCGCAAUUAUUUAUACAUGCCUCAUAAAAAUCG-AAA
-----.((((((..(((((.......((((..(----(((((.((.((((((((((....)))))))))).))...)))))))))).......))).))..).)))))....-... ( -31.04)
>DroMoj_CAF1 131422 103 + 1
-----GUUUUAGUUGUUG---CUGUUGGUGUUC----GUCCACGCGGCCGGCAUGAAAACUUAUGUCGGCGGCCUUUGGGCGCAAUUAUUUAUACAUGCCUCAUAAAAAUCG-AAA
-----.(((((..((..(---((((.(((((((----(((((.((.((((((((((....)))))))))).))...)))))).)).))))...))).))..)))))))....-... ( -32.60)
>DroPer_CAF1 105854 97 + 1
-------------UGCUG---CUCCU---GGUCGGAUGCUCACGCGGCCGGCAUGAAAACUUAUGUCGGCGGCCUUUGGGCGCAAUUAUUUAUACAUGCCUCAUAAAAAUCGCAAG
-------------(((((---((((.---....))).(((((.((.((((((((((....)))))))))).))...))))))))....(((((.........)))))....))).. ( -31.60)
>consensus
______UUUUAGUUGCUG___CUGCU___GGUC____GCCCACGCGGCCGGCAUGAAAACUUAUGUCGGCGGCCUUUGGGCGCAAUUAUUUAUACAUGCCUCAUAAAAAUCG_AAA
.....................................(((((.((.((((((((((....)))))))))).))...)))))(((............)))................. (-26.55 = -26.05 +  -0.50)

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 11:44:01 2006