Locus 6977

Sequence ID 3R_DroMel_CAF1
Location 18,403,797 – 18,403,946
Length 149
Max. P 0.786562
window11312 window11313

overview

Window 2

Location 18,403,797 – 18,403,913
Length 116
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 88.76
Mean single sequence MFE -27.94
Consensus MFE -19.24
Energy contribution -19.12
Covariance contribution -0.12
Combinations/Pair 1.10
Mean z-score -2.20
Structure conservation index 0.69
SVM decision value 0.27
SVM RNA-class probability 0.659970
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18403797 116 + 27905053
AGACGUG-UAAAACAAUUUAUAAUUCUCCAGAAGCAGCUCACACUCAAUAAGAGCGACUAUUAUGAGGAAGCUGGCCAUUCGACCUGCCGGACUUCCCAUAAAACCCAG-CAUAGAUA
(((..((-((((....))))))..)))......((.((((...........)))).....(((((.((((((((((..........))))).))))))))))......)-)....... ( -27.70)
>DroSec_CAF1 23297 115 + 1
AGACAUU-UAAAACCAUUU-CAAUUCUCCAGAAGCAGUUUACACUCAAUAAUAGCGACUUUUAUGAGGAAGCUGGCCAUUCGACCUGCCGGACUUCCCAUAAAACCCAG-CAUACAUA
.......-..((((..(((-(.........))))..)))).............((...(((((((.((((((((((..........))))).))))))))))))....)-)....... ( -24.30)
>DroSim_CAF1 25390 115 + 1
AGACGUU-UAAAACAAUUU-CAAUUCUCCAGAAGCAGUUUACACUCAAUAAUAGCGACUUUUAUGAGGAAGCUGGCCAUUCGACCUGCCGGACUUCCCAUAAAACCCAG-CAUAGAUA
....(((-((((((..(((-(.........))))..)))).............((...(((((((.((((((((((..........))))).))))))))))))....)-).))))). ( -25.30)
>DroEre_CAF1 26475 116 + 1
AAACGUUUUAAAACAGUUU-CGAUUCUACAGAAGCAGUUUACCCUCAAUAAUAGCGACUUUUAUGAGGAAGCUGGCCAUUGGACCUGCCGGACUUCCCAUAAAACCCAA-CGUUGCUA
..........((((.((((-(.........))))).))))...........((((((((((((((.((((((((((..........))))).)))))))))))).....-.))))))) ( -31.70)
>DroYak_CAF1 24572 117 + 1
AAACGUUUUUAAACAGUUU-CGAUUCCACAGAAGCAGUUUGCACUCGAUAAUGGCGACUUUUAUGAGGAAGCUGGCCAUUGGACCUGCCGGACUUCCCAUAAAACCAACCCAUAGAUG
...((....(((((.((((-(.........))))).)))))....))...((((....(((((((.((((((((((..........))))).)))))))))))).....))))..... ( -30.70)
>consensus
AGACGUU_UAAAACAAUUU_CAAUUCUCCAGAAGCAGUUUACACUCAAUAAUAGCGACUUUUAUGAGGAAGCUGGCCAUUCGACCUGCCGGACUUCCCAUAAAACCCAG_CAUAGAUA
..............................((((..(((.............)))..))))((((.((((((((((..........))))).)))))))))................. (-19.24 = -19.12 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,403,836 – 18,403,946
Length 110
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 91.79
Mean single sequence MFE -26.87
Consensus MFE -19.20
Energy contribution -19.60
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.63
Structure conservation index 0.71
SVM decision value 0.57
SVM RNA-class probability 0.786562
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18403836 110 + 27905053
ACACUCAAUAAGAGCGACUAUUAUGAGGAAGCUGGCCAUUCGACCUGCCGGACUUCCCAUAAAACCCAG-CAUAGAUAUUGCCCCACUUCCAUCCAUCAAUU-UGAGGCCCA
...(((((...((..((...(((((.((((((((((..........))))).))))))))))......(-((.......)))..........))..))...)-))))..... ( -25.80)
>DroSec_CAF1 23335 110 + 1
ACACUCAAUAAUAGCGACUUUUAUGAGGAAGCUGGCCAUUCGACCUGCCGGACUUCCCAUAAAACCCAG-CAUACAUAUUGCCCCACUUCCAUCCAUCAAUU-UGAAGCCCA
.............(((..(((((((.((((((((((..........))))).))))))))))))..).(-((.......)))....................-....))... ( -23.40)
>DroSim_CAF1 25428 110 + 1
ACACUCAAUAAUAGCGACUUUUAUGAGGAAGCUGGCCAUUCGACCUGCCGGACUUCCCAUAAAACCCAG-CAUAGAUAUUGCCCCACUUCCAUCCAUCAAUU-UGAAGCCCA
.....(((((.((((...(((((((.((((((((((..........))))).))))))))))))....)-).))..))))).....((((............-.)))).... ( -23.92)
>DroEre_CAF1 26514 110 + 1
ACCCUCAAUAAUAGCGACUUUUAUGAGGAAGCUGGCCAUUGGACCUGCCGGACUUCCCAUAAAACCCAA-CGUUGCUAUUGCCCCACUUCCAUCAAUCAUUU-UGAGGCCCA
..(((((((((((((((((((((((.((((((((((..........))))).)))))))))))).....-.))))))))))....................)-))))).... ( -34.15)
>DroYak_CAF1 24611 112 + 1
GCACUCGAUAAUGGCGACUUUUAUGAGGAAGCUGGCCAUUGGACCUGCCGGACUUCCCAUAAAACCAACCCAUAGAUGUUGCCCCACUUCCAUCAAUCAUUUUUUAGGCCCA
((.((.((.(((((....(((((((.((((((((((..........))))).))))))))))))..........((((..(......)..))))..))))).)).))))... ( -27.10)
>consensus
ACACUCAAUAAUAGCGACUUUUAUGAGGAAGCUGGCCAUUCGACCUGCCGGACUUCCCAUAAAACCCAG_CAUAGAUAUUGCCCCACUUCCAUCCAUCAAUU_UGAGGCCCA
.............((...(((((((.((((((((((..........))))).))))))))))))................................(((....))).))... (-19.20 = -19.60 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:38 2006