Locus 655

Sequence ID 2R_DroMel_CAF1
Location 3,264,931 – 3,265,062
Length 131
Max. P 0.984985
window1161 window1162 window1163

overview

Window 1

Location 3,264,931 – 3,265,023
Length 92
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 85.33
Mean single sequence MFE -30.60
Consensus MFE -22.82
Energy contribution -23.66
Covariance contribution 0.84
Combinations/Pair 1.17
Mean z-score -2.34
Structure conservation index 0.75
SVM decision value 1.26
SVM RNA-class probability 0.937155
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3264931 92 - 20766785
CCAGCCGCAAAAGCGAAGAUGAAAUUUCUGCUUGCU--------UGCUGCGGCUUUGGUUGCAGUUUCAUCAGUGUGCCUCCUCUGCGGCUUUCACACAA
..(((((((...(((..((((((((....((.....--------.))((((((....))))))))))))))..)))........)))))))......... ( -28.50)
>DroSec_CAF1 34022 86 - 1
UCAGCCGCAAAAGCGAAGAUGAAAUUUCUGCCUGCUG------------CGGCUUUGGUUGCAAUUUCAUCAGU--GCCUCGUCUGCGGCUUUCACACAA
..(((((((.(.(((..(((((((((.(.(((.((..------------..))...))).).)))))))))..)--))....).)))))))......... ( -29.70)
>DroSim_CAF1 43393 98 - 1
CCAGCCGCAAAAGCGAAGAUGAAAUUUCUACCUGCUGCGGCUGCGGCUGCGGCUUUGGUUGCAGUUUCAUCAGU--GCCUCGUCUGCGGCUUUCACACAA
..(((((((.(.(((..(((((((((.(.(((.((((((((....))))))))...))).).)))))))))..)--))....).)))))))......... ( -43.20)
>DroEre_CAF1 33228 88 - 1
CCAGCCGCAAAAGCGAAGAUGAAAUUUCUGUUUGCUG------------UGGCUUUGGUUGCAGUUUCAUCAGUGCGCCUCCUCUGCGGCUUUCACACAA
..(((((((...(((..((((((..........((((------------..((....))..))))))))))....)))......)))))))......... ( -28.20)
>DroYak_CAF1 33300 88 - 1
CCAUCCGCAAAAGCGAAGAUGAAAUUUCUGUUUGCUG------------UGGCUUUGGUUGCAGUUUCAUCAGUGACGCCUGUCUGCGGCUUUUACACAA
......(.((((((...((((((..........((((------------..((....))..)))))))))).....(((......))))))))).).... ( -23.40)
>consensus
CCAGCCGCAAAAGCGAAGAUGAAAUUUCUGCUUGCUG____________CGGCUUUGGUUGCAGUUUCAUCAGUG_GCCUCGUCUGCGGCUUUCACACAA
..(((((((...((...(((((((((.(.(((.((((((((....))))))))...))).).))))))))).))..........)))))))......... (-22.82 = -23.66 +   0.84)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,264,971 – 3,265,062
Length 91
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 81.23
Mean single sequence MFE -27.60
Consensus MFE -19.01
Energy contribution -19.86
Covariance contribution 0.85
Combinations/Pair 1.08
Mean z-score -2.66
Structure conservation index 0.69
SVM decision value 1.99
SVM RNA-class probability 0.984985
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3264971 91 + 20766785
AACCAAAGCCGCAGCA--------AGCAAGCAGAAAUUUCAUCUUCGCUUUUGCGGCUGGUGGAACUUCUAUGUGCAACUGCAAUGGCCAUUGCCACAG
..(((.((((((((.(--------((((((..((....))..))).))))))))))))..)))........(((((((..((....))..))).)))). ( -29.90)
>DroSec_CAF1 34060 81 + 1
AACCAAAGCCG------------CAGCAGGCAGAAAUUUCAUCUUCGCUUUUGCGGCUGAUGGAACUUCUAUGUGCAACUGCAAG------UGCAACUG
..(((.(((((------------(((.((((.(((........)))))))))))))))..)))........((..(........)------..)).... ( -25.70)
>DroSim_CAF1 43431 84 + 1
AACCAAAGCCGCAGCCGCAGCCGCAGCAGGUAGAAAUUUCAUCUUCGCUUUUGCGGCUGGUGGAACUUCUAUGUGCAACUGCAA---------------
..........((((..((....)).(((.((((((.(((((((.((((....))))..))))))).)))))).)))..))))..--------------- ( -31.70)
>DroEre_CAF1 33268 87 + 1
AACCAAAGCCA------------CAGCAAACAGAAAUUUCAUCUUCGCUUUUGCGGCUGGUGGAACUUCUAUGUGCAACUGCAAUGGCCAUUGCCACAG
.......((..------------..(((...((((.(((((((.((((....))))..))))))).))))...)))....))..((((....))))... ( -24.50)
>DroYak_CAF1 33340 87 + 1
AACCAAAGCCA------------CAGCAAACAGAAAUUUCAUCUUCGCUUUUGCGGAUGGUGGAACUUCUAUGUGCAACUGCAAUGGCCAUUGCCACAG
.......((..------------..(((...((((.((((((((((((....))))).))))))).))))...)))....))..((((....))))... ( -26.20)
>consensus
AACCAAAGCCG____________CAGCAAGCAGAAAUUUCAUCUUCGCUUUUGCGGCUGGUGGAACUUCUAUGUGCAACUGCAAUGGCCAUUGCCACAG
.........................(((.(.((((.(((((((.((((....))))..))))))).)))).).)))....(((((....)))))..... (-19.01 = -19.86 +   0.85)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,264,971 – 3,265,062
Length 91
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 81.23
Mean single sequence MFE -28.42
Consensus MFE -14.13
Energy contribution -15.22
Covariance contribution 1.09
Combinations/Pair 1.05
Mean z-score -2.11
Structure conservation index 0.50
SVM decision value 0.14
SVM RNA-class probability 0.604249
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3264971 91 - 20766785
CUGUGGCAAUGGCCAUUGCAGUUGCACAUAGAAGUUCCACCAGCCGCAAAAGCGAAGAUGAAAUUUCUGCUUGCU--------UGCUGCGGCUUUGGUU
((((((((((.((....)).))))).))))).....(((..(((((((.(((((((((.......)))..)))))--------)..))))))).))).. ( -34.50)
>DroSec_CAF1 34060 81 - 1
CAGUUGCA------CUUGCAGUUGCACAUAGAAGUUCCAUCAGCCGCAAAAGCGAAGAUGAAAUUUCUGCCUGCUG------------CGGCUUUGGUU
.(((((((------...((((..(((....((((((.((((...(((....)))..)))).)))))))))))))))------------)))))...... ( -24.50)
>DroSim_CAF1 43431 84 - 1
---------------UUGCAGUUGCACAUAGAAGUUCCACCAGCCGCAAAAGCGAAGAUGAAAUUUCUACCUGCUGCGGCUGCGGCUGCGGCUUUGGUU
---------------.(((((((((((......))......(((((((..((.(.(((.......))).)))..))))))))))))))))......... ( -28.40)
>DroEre_CAF1 33268 87 - 1
CUGUGGCAAUGGCCAUUGCAGUUGCACAUAGAAGUUCCACCAGCCGCAAAAGCGAAGAUGAAAUUUCUGUUUGCUG------------UGGCUUUGGUU
((((((((((.((....)).))))).))))).....(((..(((((((...(((((.(.((....))).)))))))------------))))).))).. ( -28.80)
>DroYak_CAF1 33340 87 - 1
CUGUGGCAAUGGCCAUUGCAGUUGCACAUAGAAGUUCCACCAUCCGCAAAAGCGAAGAUGAAAUUUCUGUUUGCUG------------UGGCUUUGGUU
..........(((((..((....(((.(((((((((....(((((((....)))..)))).))))))))).)))..------------..))..))))) ( -25.90)
>consensus
CUGUGGCAAUGGCCAUUGCAGUUGCACAUAGAAGUUCCACCAGCCGCAAAAGCGAAGAUGAAAUUUCUGCUUGCUG____________CGGCUUUGGUU
.....(((((....)))))....(((..((((((((.((.(...(((....)))..).)).))))))))..)))......................... (-14.13 = -15.22 +   1.09)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:50 2006