Locus 5825

Sequence ID 2R_DroMel_CAF1
Location 18,459,711 – 18,459,820
Length 109
Max. P 0.993363
window9330 window9331

overview

Window 0

Location 18,459,711 – 18,459,820
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 71.11
Mean single sequence MFE -22.53
Consensus MFE -14.27
Energy contribution -14.77
Covariance contribution 0.50
Combinations/Pair 1.14
Mean z-score -2.04
Structure conservation index 0.63
SVM decision value 2.04
SVM RNA-class probability 0.986521
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18459711 109 + 20766785
GCCUUGACUGGACUAAAUUGAUGCCUUGUCUUUCUUG-UUUUUGAAAGUUGCAUCUGUUGCACAAAUUGGUGC-UGCAGUUGCAGCUAAAUAUUGGUCUAAUUUU---------UUUUUC
........((((((((...............(((...-.....)))(((((((.((((.((((......))))-.)))).))))))).....)))))))).....---------...... ( -29.90)
>DroSec_CAF1 21757 85 + 1
G----------------------CCUUGUCUUUCUCG-UUUU-AAAAG-UGCAUCUGUUGCACAAAUUGGUGC-UGCAGUUGCAGCUAAAUAUUGGUCUUAUUUU---------UUUUUU
(----------------------((............-....-....(-((((.....)))))..(((...((-(((....)))))..)))...)))........---------...... ( -17.70)
>DroSim_CAF1 21958 106 + 1
GCCUUGACUGGAAUAAAUUGAUGCCUUGUCUUUCUCG-UUUU-AAAAGUUGCAUCUGUUGCACAAAUUGGUGC-UGCAGUUGCAGCUAAAUAUUGGUCUUAUUUU-----------UUUU
.....(((..(........(((.....))).......-....-...(((((((.((((.((((......))))-.)))).))))))).....)..))).......-----------.... ( -27.00)
>DroEre_CAF1 21666 117 + 1
UUUUUGCUUUGACUUAAUUGAUGCCUAUGCUUUCUUG-UUAU-AAAAGUUGCAUCUGUUGCACAAAUUGGUGU-UGCAGUUGCAGCUAAAUAUUGUUAUUAUUUUAACUGCAUAUUUUUU
.....((.(..(.....)..).)).(((((.......-....-...(((((((.((((.((((......))))-.)))).))))))).......((((......)))).)))))...... ( -26.60)
>DroYak_CAF1 22408 116 + 1
GUUUUGCUUUGACUAAAUUGUUGCCCUUUCUUUCUUG-UUAU-AAAAGUUGCAUCUGUUGCACAAAUUGGUGU-UGCAGUUCCAGCUAAAUAUUGUUAUUAUUUUAACUG-AUUUUUUUU
.....((...(((......))))).............-....-...(((((...((((.((((......))))-.))))...)))))((((...((((......))))..-))))..... ( -16.50)
>DroAna_CAF1 19836 105 + 1
UGUUUGA---GAGCGA------GUUCUAUCUCUCUUUUUUAG-CAAACUUGCAACUGUUGCACAAAAUAGUGCCUUCUACUGCAACUAAAUAUUGUUAUUUUC---CCUUCAC--UUUUU
((((.((---(((.((------(......))).)))))..))-))...(((((...(..((((......))))...)...)))))..................---.......--..... ( -17.50)
>consensus
GCUUUGA_U_GACUAAAUUGAUGCCUUGUCUUUCUUG_UUAU_AAAAGUUGCAUCUGUUGCACAAAUUGGUGC_UGCAGUUGCAGCUAAAUAUUGGUAUUAUUUU_________UUUUUU
..............................................(((((((.(((..((((......))))...))).)))))))................................. (-14.27 = -14.77 +   0.50)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,459,711 – 18,459,820
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 71.11
Mean single sequence MFE -19.67
Consensus MFE -9.39
Energy contribution -9.75
Covariance contribution 0.36
Combinations/Pair 1.28
Mean z-score -2.49
Structure conservation index 0.48
SVM decision value 2.39
SVM RNA-class probability 0.993363
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18459711 109 - 20766785
GAAAAA---------AAAAUUAGACCAAUAUUUAGCUGCAACUGCA-GCACCAAUUUGUGCAACAGAUGCAACUUUCAAAAA-CAAGAAAGACAAGGCAUCAAUUUAGUCCAGUCAAGGC
......---------.......(((.........(((((....)))-))................(((((..(((((.....-...))))).....)))))...........)))..... ( -22.50)
>DroSec_CAF1 21757 85 - 1
AAAAAA---------AAAAUAAGACCAAUAUUUAGCUGCAACUGCA-GCACCAAUUUGUGCAACAGAUGCA-CUUUU-AAAA-CGAGAAAGACAAGG----------------------C
......---------.........((........(((((....)))-))........(((((.....))))-)....-....-............))----------------------. ( -16.30)
>DroSim_CAF1 21958 106 - 1
AAAA-----------AAAAUAAGACCAAUAUUUAGCUGCAACUGCA-GCACCAAUUUGUGCAACAGAUGCAACUUUU-AAAA-CGAGAAAGACAAGGCAUCAAUUUAUUCCAGUCAAGGC
....-----------.......(((.........(((((....)))-))................(((((..(((((-....-...))))).....)))))...........)))..... ( -20.10)
>DroEre_CAF1 21666 117 - 1
AAAAAAUAUGCAGUUAAAAUAAUAACAAUAUUUAGCUGCAACUGCA-ACACCAAUUUGUGCAACAGAUGCAACUUUU-AUAA-CAAGAAAGCAUAGGCAUCAAUUAAGUCAAAGCAAAAA
........((((((((((............))))))))))..(((.-.(((......))).....(((((..(((((-....-...))))).....)))))............))).... ( -22.00)
>DroYak_CAF1 22408 116 - 1
AAAAAAAAU-CAGUUAAAAUAAUAACAAUAUUUAGCUGGAACUGCA-ACACCAAUUUGUGCAACAGAUGCAACUUUU-AUAA-CAAGAAAGAAAGGGCAACAAUUUAGUCAAAGCAAAAC
........(-((((((((............)))))))))..(((..-.(((......)))...))).(((..(((((-....-...)))))....(....)............))).... ( -15.40)
>DroAna_CAF1 19836 105 - 1
AAAAA--GUGAAGG---GAAAAUAACAAUAUUUAGUUGCAGUAGAAGGCACUAUUUUGUGCAACAGUUGCAAGUUUG-CUAAAAAAGAGAGAUAGAAC------UCGCUC---UCAAACA
....(--(..((..---..(((((....)))))..((((((..(...((((......))))..)..)))))).))..-))......(((((...(...------.).)))---))..... ( -21.70)
>consensus
AAAAAA_________AAAAUAAGAACAAUAUUUAGCUGCAACUGCA_GCACCAAUUUGUGCAACAGAUGCAACUUUU_AAAA_CAAGAAAGACAAGGCAUCAAUUUAGUC_A_UCAAAAC
..................................((((((.(((...((((......))))..))).)))..(((((.........)))))....)))...................... ( -9.39 =  -9.75 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:23 2006