Locus 2955

Sequence ID 3R_DroMel_CAF1
Location 7,901,077 – 7,901,184
Length 107
Max. P 0.984741
window4752 window4753

overview

Window 2

Location 7,901,077 – 7,901,184
Length 107
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 73.69
Mean single sequence MFE -26.72
Consensus MFE -17.64
Energy contribution -17.78
Covariance contribution 0.14
Combinations/Pair 1.10
Mean z-score -1.37
Structure conservation index 0.66
SVM decision value 0.80
SVM RNA-class probability 0.854181
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7901077 107 + 27905053
UAUUGGUGGUCGGAUAGUACAUCUCCUCAUCCCAGUUGAUGAGGAACGACUGUACAAAGCGUAUAACCUGUACGGA---AU-AUUGGUGUUUGUUUCUCAGAAUGGA--AUUU
(((..(((.((.....(((((((((((((((......))))))))..)).)))))....(((((.....)))))))---.)-))..)))((..(((....)))..))--.... ( -27.70)
>DroGri_CAF1 20377 104 + 1
UUUGGGUGCGUGCAUAGUACAUCUCCUCAUCCCAGUUGAUGAGGAACGAUUGAACAAAUCGUAUAACCUGCAGCAU---AUAU---AUACAUAU---UGAGAUGUAUACACAG
.....((((.((((.........((((((((......))))))))((((((.....))))))......))))))))---...(---((((((..---....)))))))..... ( -30.50)
>DroSec_CAF1 32501 104 + 1
UAUUGGUGGUCGGAUAGUACAUCUCCUCAUCCCAGUUGAUGAGGAACGACUGUACGAAGCGUAUAACCUGCACGGU---AU-U---AUAUUUGUUUCUCAGAAAGGC--AUUU
........(((.....(((((((((((((((......))))))))..)).)))))(((((((((((((.....)))---..-)---))))..))))).......)))--.... ( -27.50)
>DroSim_CAF1 33459 104 + 1
UAUUGGUGGUCGGAUAGUACAUCUCCUCAUCCCAGUUGAUGAGGAACGACUGUACGAAGCGUAUAACCUGCACGGU---AU-U---AUAUUUGUUUCUCAGAAAGGC--AUUU
........(((.....(((((((((((((((......))))))))..)).)))))(((((((((((((.....)))---..-)---))))..))))).......)))--.... ( -27.50)
>DroWil_CAF1 8917 99 + 1
UAUUGGUGCGUGCAUAAUACAUUUCCUCAUCCCAAUUGAUGAGGAACGACUGUACAAAGCGUAUUACCUGCCAUGAAAGAU-G---AUAUAUAUAGU----AAUG------GU
...((((((((......((((.(((((((((......)))))))))....))))....))))))))...(((((.....((-(---.....)))...----.)))------)) ( -23.60)
>DroAna_CAF1 29194 95 + 1
UAUUGGUGGUCGCAUAGUACAUCUCCUCAUCCCAGUUAAUGAGGAACGAUUGUACAAAGCGGAUGACCUGGGGAA----AU-C---AUUAGCA--UC------GGGU--AUUG
..((((((..(((...((((((((((((((........)))))))..)).)))))...)))(((..((...))..----))-)---.....))--))------))..--.... ( -23.50)
>consensus
UAUUGGUGGUCGCAUAGUACAUCUCCUCAUCCCAGUUGAUGAGGAACGACUGUACAAAGCGUAUAACCUGCACGGU___AU_U___AUAUUUAUUUCUCAGAAAGGC__AUUU
....(((...((....(((((((((((((((......))))))))..)).)))))....))....)))............................................. (-17.64 = -17.78 +   0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 7,901,077 – 7,901,184
Length 107
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 73.69
Mean single sequence MFE -24.59
Consensus MFE -19.81
Energy contribution -19.56
Covariance contribution -0.25
Combinations/Pair 1.18
Mean z-score -1.81
Structure conservation index 0.81
SVM decision value 1.98
SVM RNA-class probability 0.984741
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7901077 107 - 27905053
AAAU--UCCAUUCUGAGAAACAAACACCAAU-AU---UCCGUACAGGUUAUACGCUUUGUACAGUCGUUCCUCAUCAACUGGGAUGAGGAGAUGUACUAUCCGACCACCAAUA
....--.........................-..---........(((....((....(((((....(((((((((......))))))))).)))))....))...))).... ( -22.50)
>DroGri_CAF1 20377 104 - 1
CUGUGUAUACAUCUCA---AUAUGUAU---AUAU---AUGCUGCAGGUUAUACGAUUUGUUCAAUCGUUCCUCAUCAACUGGGAUGAGGAGAUGUACUAUGCACGCACCCAAA
.(((((((((((....---..))))))---))))---)(((((((...(((((((((.....)))))(((((((((......))))))))).))))...)))).)))...... ( -32.80)
>DroSec_CAF1 32501 104 - 1
AAAU--GCCUUUCUGAGAAACAAAUAU---A-AU---ACCGUGCAGGUUAUACGCUUCGUACAGUCGUUCCUCAUCAACUGGGAUGAGGAGAUGUACUAUCCGACCACCAAUA
....--.....((.(((((.(...(((---(-..---(((.....))))))).).)))(((((....(((((((((......))))))))).)))))..)).))......... ( -22.50)
>DroSim_CAF1 33459 104 - 1
AAAU--GCCUUUCUGAGAAACAAAUAU---A-AU---ACCGUGCAGGUUAUACGCUUCGUACAGUCGUUCCUCAUCAACUGGGAUGAGGAGAUGUACUAUCCGACCACCAAUA
....--.....((.(((((.(...(((---(-..---(((.....))))))).).)))(((((....(((((((((......))))))))).)))))..)).))......... ( -22.50)
>DroWil_CAF1 8917 99 - 1
AC------CAUU----ACUAUAUAUAU---C-AUCUUUCAUGGCAGGUAAUACGCUUUGUACAGUCGUUCCUCAUCAAUUGGGAUGAGGAAAUGUAUUAUGCACGCACCAAUA
.(------(((.----...........---.-.......))))..(((.....((...(((((....(((((((((......))))))))).)))))...))....))).... ( -23.35)
>DroAna_CAF1 29194 95 - 1
CAAU--ACCC------GA--UGCUAAU---G-AU----UUCCCCAGGUCAUCCGCUUUGUACAAUCGUUCCUCAUUAACUGGGAUGAGGAGAUGUACUAUGCGACCACCAAUA
....--....------..--.....((---(-((----(......)))))).(((...(((((....(((((((((......))))))))).)))))...))).......... ( -23.90)
>consensus
AAAU__ACCAUUCUGAGAAACAAAUAU___A_AU___ACCGUGCAGGUUAUACGCUUUGUACAGUCGUUCCUCAUCAACUGGGAUGAGGAGAUGUACUAUCCGACCACCAAUA
.............................................(((..........(((((....(((((((((......))))))))).))))).........))).... (-19.81 = -19.56 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:38 2006