Locus 3414

Sequence ID 3R_DroMel_CAF1
Location 9,270,460 – 9,270,550
Length 90
Max. P 0.996781
window5479 window5480

overview

Window 9

Location 9,270,460 – 9,270,550
Length 90
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 74.39
Mean single sequence MFE -22.92
Consensus MFE -7.48
Energy contribution -8.78
Covariance contribution 1.30
Combinations/Pair 1.00
Mean z-score -2.61
Structure conservation index 0.33
SVM decision value 2.75
SVM RNA-class probability 0.996781
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9270460 90 + 27905053
GUACUUAGAUGCAGGUA----------UUUGCCUUUGCAUCUGUAAAUACACAUGUGAGUUUCUGUAUC------------UGUGUAUGUUACUGCCUCUGUUUCUGUUUUU
......((((((((((.----------...)))..)))))))(((((((((((.(((........))).------------))))))).))))................... ( -20.10)
>DroSec_CAF1 41543 90 + 1
GUACUUAGAUGCAGGUA----------UUUGUCUUUGCAUCUGUAAAUACACAUGUGAGUAUCUGUAAC------------UGUGUAUGUUACUGCCUCUGUUUCUGUUUUU
((((.(((.((((((((----------(((......((((.(((....))).))))))))))))))).)------------)).))))........................ ( -19.00)
>DroSim_CAF1 42722 78 + 1
GUACUUAGAUGCAGGUA----------UUUGCCUUUGCAUCUGUAAAUACACAAGUGAGUAUCUGUAUC------------------------UGCCUCUGUUUCUGUUUUU
.....((((((((((((----------((..(.(((((....))))).......)..))))))))))))------------------------))................. ( -20.10)
>DroEre_CAF1 42468 102 + 1
GUACUUAGAUGCAGGUA----------UUUGCCUUCGCAUCUGUAAAUACACAUGUGAGUAUCUGUAUCUGUAUCUGUAUCUGUGUAUGUUACUGCCUCUGUUUCUGUUUUU
((((.((((((((((((----------(.(((.(((((((.(((....))).))))))).....)))...))))))))))))).))))........................ ( -27.60)
>DroAna_CAF1 41351 90 + 1
GCACUUGGAUGCAGGUACGGGUAAGCAUUUGCAUUUGCUUGGGUAUAU----------GUAUCUGUAGC------------UGAAAAUGUAAAUGUAUCUGUUUCUGUUUUG
.......((.(((((.((((((..(((((((((((((((((((((...----------.)))))).)))------------...)))))))))))))))))).))))).)). ( -27.80)
>consensus
GUACUUAGAUGCAGGUA__________UUUGCCUUUGCAUCUGUAAAUACACAUGUGAGUAUCUGUAUC____________UGUGUAUGUUACUGCCUCUGUUUCUGUUUUU
.......((((((((((................(((((....)))))(((....)))..))))))))))........................................... ( -7.48 =  -8.78 +   1.30)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 9,270,460 – 9,270,550
Length 90
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 74.39
Mean single sequence MFE -15.18
Consensus MFE -6.31
Energy contribution -7.39
Covariance contribution 1.08
Combinations/Pair 1.12
Mean z-score -1.81
Structure conservation index 0.42
SVM decision value 0.24
SVM RNA-class probability 0.647587
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9270460 90 - 27905053
AAAAACAGAAACAGAGGCAGUAACAUACACA------------GAUACAGAAACUCACAUGUGUAUUUACAGAUGCAAAGGCAAA----------UACCUGCAUCUAAGUAC
................((.((((.(((((((------------................)))))))))))(((((((..((....----------..)))))))))..)).. ( -18.29)
>DroSec_CAF1 41543 90 - 1
AAAAACAGAAACAGAGGCAGUAACAUACACA------------GUUACAGAUACUCACAUGUGUAUUUACAGAUGCAAAGACAAA----------UACCUGCAUCUAAGUAC
.............(((.(.(((((.......------------))))).)...)))......((((((..(((((((........----------....))))))))))))) ( -16.60)
>DroSim_CAF1 42722 78 - 1
AAAAACAGAAACAGAGGCA------------------------GAUACAGAUACUCACUUGUGUAUUUACAGAUGCAAAGGCAAA----------UACCUGCAUCUAAGUAC
................(((------------------------((((((.(........).)))))))..(((((((..((....----------..)))))))))..)).. ( -14.80)
>DroEre_CAF1 42468 102 - 1
AAAAACAGAAACAGAGGCAGUAACAUACACAGAUACAGAUACAGAUACAGAUACUCACAUGUGUAUUUACAGAUGCGAAGGCAAA----------UACCUGCAUCUAAGUAC
............(((.((((......................(((((((.((......)).))))))).....(((....)))..----------...)))).)))...... ( -17.90)
>DroAna_CAF1 41351 90 - 1
CAAAACAGAAACAGAUACAUUUACAUUUUCA------------GCUACAGAUAC----------AUAUACCCAAGCAAAUGCAAAUGCUUACCCGUACCUGCAUCCAAGUGC
.................(((((.........------------(((........----------.........)))..(((((..(((......)))..)))))..))))). (  -8.33)
>consensus
AAAAACAGAAACAGAGGCAGUAACAUACACA____________GAUACAGAUACUCACAUGUGUAUUUACAGAUGCAAAGGCAAA__________UACCUGCAUCUAAGUAC
.............................................(((((((((........))))))..(((((((......................)))))))..))). ( -6.31 =  -7.39 +   1.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:25 2006