Locus 5627

Sequence ID 3L_DroMel_CAF1
Location 15,446,018 – 15,446,110
Length 92
Max. P 0.873203
window8888 window8889

overview

Window 8

Location 15,446,018 – 15,446,110
Length 92
Sequences 6
Columns 93
Reading direction forward
Mean pairwise identity 80.64
Mean single sequence MFE -29.91
Consensus MFE -17.48
Energy contribution -18.03
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -2.15
Structure conservation index 0.58
SVM decision value 0.50
SVM RNA-class probability 0.760301
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15446018 92 + 23771897
GCGGAGGAGGG-UGGGAAAUCGAGGACGGUAAGGGGAUUCCCGGCCUGGCAGUAGUUAAAAUUUACUGCCCAGUUGCCAAACGCAACAGUAGC
(((..(((((.-((((((((((....)))).......)))))).)))((((((((.......))))))))......))...)))......... ( -30.81)
>DroSec_CAF1 177358 89 + 1
GCGGAGGUGGG-UGGGAAUUCGAGGAUGGUAAGGGGAUUCCCGGCCUGGCAGUAGUUAAAAUUUACUGCCCAGUUGCCAAACGC---AGUAGC
(((..(((((.-(((((((((.............))))))))).)).((((((((.......)))))))).....)))...)))---...... ( -34.42)
>DroSim_CAF1 179604 92 + 1
GCGGAGGUGGG-UGGGAAAUCCAGGAUGGUAAGGGGAUUCCCGGCCUGGCAGUAGUUAAAAUUUACUGCCCAGUUGCCAAACGCAACAGUAGC
(((..((..(.-((((....(((((.......(((....)))..)))))((((((.......)))))))))).)..))...)))......... ( -34.20)
>DroEre_CAF1 174201 69 + 1
GCGGAGGA------------------------GGGGAUUGCCGGCCUGGCAGUAGUUAAAAUUUACUGCCCAGUUGCCAAACGCAACAGUAGC
(((.....------------------------((......))(((((((((((((.......)))))).))))..)))...)))......... ( -22.40)
>DroYak_CAF1 179545 93 + 1
GCGGAGAAGGGUUGGGAAAUCGAGGAUGGUAAGGGGAUUGCCGGCCUGGCAGUAGUUAAAAUUUACUGCCCAGUUGCCAAACGCAACAGUAGC
((......(((((((..((((..............)))).)))))))((((((((.......))))))))..(((((.....)))))....)) ( -28.24)
>DroAna_CAF1 315610 84 + 1
UCA--GGGG---GGACGAAUCGGGAA----AAUAGGAUUCGUUGCCUGGCAGUAGUUAAAAUUUACUGCCCAGCUACCAAACGCAACAGUAGC
...--.(((---.((((((((.....----.....)))))))).)))((((((((.......))))))))..(((((...........))))) ( -29.40)
>consensus
GCGGAGGAGGG_UGGGAAAUCGAGGAUGGUAAGGGGAUUCCCGGCCUGGCAGUAGUUAAAAUUUACUGCCCAGUUGCCAAACGCAACAGUAGC
(((..............................((.....))(((((((((((((.......)))))).))))..)))...)))......... (-17.48 = -18.03 +   0.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,446,018 – 15,446,110
Length 92
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 80.64
Mean single sequence MFE -23.46
Consensus MFE -18.97
Energy contribution -20.19
Covariance contribution 1.22
Combinations/Pair 1.22
Mean z-score -1.82
Structure conservation index 0.81
SVM decision value 0.88
SVM RNA-class probability 0.873203
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15446018 92 - 23771897
GCUACUGUUGCGUUUGGCAACUGGGCAGUAAAUUUUAACUACUGCCAGGCCGGGAAUCCCCUUACCGUCCUCGAUUUCCCA-CCCUCCUCCGC
(((.(.(((((.....))))).)(((((((.........))))))).))).(((((...................))))).-........... ( -24.21)
>DroSec_CAF1 177358 89 - 1
GCUACU---GCGUUUGGCAACUGGGCAGUAAAUUUUAACUACUGCCAGGCCGGGAAUCCCCUUACCAUCCUCGAAUUCCCA-CCCACCUCCGC
......---(((...(((.....(((((((.........)))))))..)))((((((.................)))))).-........))) ( -23.63)
>DroSim_CAF1 179604 92 - 1
GCUACUGUUGCGUUUGGCAACUGGGCAGUAAAUUUUAACUACUGCCAGGCCGGGAAUCCCCUUACCAUCCUGGAUUUCCCA-CCCACCUCCGC
(((.(.(((((.....))))).)(((((((.........))))))).))).((((((((............))))))))..-........... ( -27.40)
>DroEre_CAF1 174201 69 - 1
GCUACUGUUGCGUUUGGCAACUGGGCAGUAAAUUUUAACUACUGCCAGGCCGGCAAUCCCC------------------------UCCUCCGC
(((.(.(((((.....))))).)(((((((.........))))))).....))).......------------------------........ ( -19.30)
>DroYak_CAF1 179545 93 - 1
GCUACUGUUGCGUUUGGCAACUGGGCAGUAAAUUUUAACUACUGCCAGGCCGGCAAUCCCCUUACCAUCCUCGAUUUCCCAACCCUUCUCCGC
(((.(.(((((.....))))).)(((((((.........))))))).))).((.((((..............)))).)).............. ( -20.14)
>DroAna_CAF1 315610 84 - 1
GCUACUGUUGCGUUUGGUAGCUGGGCAGUAAAUUUUAACUACUGCCAGGCAACGAAUCCUAUU----UUCCCGAUUCGUCC---CCCC--UGA
(((((((.......)))))))..(((((((.........))))))).((..(((((((.....----.....)))))))..---))..--... ( -26.10)
>consensus
GCUACUGUUGCGUUUGGCAACUGGGCAGUAAAUUUUAACUACUGCCAGGCCGGGAAUCCCCUUACCAUCCUCGAUUUCCCA_CCCUCCUCCGC
(((.(.(((((.....))))).)(((((((.........))))))).))).(((((((..............))))))).............. (-18.97 = -20.19 +   1.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:56 2006