Locus 199

Sequence ID 2R_DroMel_CAF1
Location 1,462,523 – 1,462,720
Length 197
Max. P 0.999950
window457 window458 window459 window460 window461

overview

Window 7

Location 1,462,523 – 1,462,640
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.23
Mean single sequence MFE -41.66
Consensus MFE -37.96
Energy contribution -38.68
Covariance contribution 0.72
Combinations/Pair 1.08
Mean z-score -3.02
Structure conservation index 0.91
SVM decision value 4.79
SVM RNA-class probability 0.999950
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1462523 117 + 20766785
U---CAGAAGAGUAGAAAAGUUCGUUGUGCAACAAUUACAAUAAGCUGGAUGGGACAACAGCUGGAGACAGAUGUCGCGGCGUUGUCCGGCAGAGUCCUGGACAAAGGACUCUGUUUGCU
.---......(((((...((((..(((((.......)))))..)))).....(((((((.((((..(((....))).))))))))))).((((((((((......))))))))))))))) ( -45.40)
>DroSec_CAF1 83042 117 + 1
U---CAGAAGAGUAGAAAAGUUCGUUGUGCAACAAUUACAAUAAGCUGGAUGGGACAACAGCUGGAGACAGAUGUCGCGGUGUUGUCCGGCAGAGUCCUGGACAAAGGACUCUGUUUGCU
.---......(((((...((((..(((((.......)))))..)))).....((((((((.(((..(((....))).))))))))))).((((((((((......))))))))))))))) ( -43.90)
>DroSim_CAF1 82521 117 + 1
U---CAGAAGAGUAGAAAAGUUCGUUGUGCAACAAUUACAAUAAGCUGGAUGGGACAACAGCUGGAGACAGAUGUCGCGGCGUUGUCCGGCAGAGUCCUGGACAAAGGACUCUGUUUGCU
.---......(((((...((((..(((((.......)))))..)))).....(((((((.((((..(((....))).))))))))))).((((((((((......))))))))))))))) ( -45.40)
>DroEre_CAF1 94032 119 + 1
UCUCCAAAAGAGUAGAAAAGUUCGUUGUGCAGCAAUUACAAUAAGCUGGAUGGGACAACAGCUGGAGACAAAUGUCGCGGCGUUGUCCGGU-GAGUCCUGGACAAAGGACUGUGUUUGCC
...........(((((..(((((.((((.(((...((((......(.....)(((((((.((((..(((....))).))))))))))).))-))...))).)))).)))))...))))). ( -39.50)
>DroYak_CAF1 89108 117 + 1
U---CAGAAGAGUAGGAAAGUUCGUUGUGCAACAAUUACAAUAAGCUAGAUGGGACAACAGCUGGAGCCGGACGUCGAGGCGUUGUCCGGCAGAGCACUGGACAAAGGUCUCUGUUUGCU
.---((((((((.......(((((..((((...............((((.((......)).)))).((((((((.((...)).))))))))...)))))))))......)))).)))).. ( -34.12)
>consensus
U___CAGAAGAGUAGAAAAGUUCGUUGUGCAACAAUUACAAUAAGCUGGAUGGGACAACAGCUGGAGACAGAUGUCGCGGCGUUGUCCGGCAGAGUCCUGGACAAAGGACUCUGUUUGCU
...........(((((..((((..(((((.......)))))..)))).....(((((((.((((..(((....))).)))))))))))..(((((((((......)))))))))))))). (-37.96 = -38.68 +   0.72)

alignment

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secondary structure

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Window 8

Location 1,462,523 – 1,462,640
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.23
Mean single sequence MFE -31.36
Consensus MFE -26.26
Energy contribution -27.34
Covariance contribution 1.08
Combinations/Pair 1.07
Mean z-score -2.10
Structure conservation index 0.84
SVM decision value 1.98
SVM RNA-class probability 0.984768
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1462523 117 - 20766785
AGCAAACAGAGUCCUUUGUCCAGGACUCUGCCGGACAACGCCGCGACAUCUGUCUCCAGCUGUUGUCCCAUCCAGCUUAUUGUAAUUGUUGCACAACGAACUUUUCUACUCUUCUG---A
(((...(((((((((......)))))))))..(((((((((.(.(((....))).)..)).)))))))......)))........(((((....))))).................---. ( -33.50)
>DroSec_CAF1 83042 117 - 1
AGCAAACAGAGUCCUUUGUCCAGGACUCUGCCGGACAACACCGCGACAUCUGUCUCCAGCUGUUGUCCCAUCCAGCUUAUUGUAAUUGUUGCACAACGAACUUUUCUACUCUUCUG---A
(((...(((((((((......)))))))))..((((((((.(..(((....)))....).))))))))......)))........(((((....))))).................---. ( -32.80)
>DroSim_CAF1 82521 117 - 1
AGCAAACAGAGUCCUUUGUCCAGGACUCUGCCGGACAACGCCGCGACAUCUGUCUCCAGCUGUUGUCCCAUCCAGCUUAUUGUAAUUGUUGCACAACGAACUUUUCUACUCUUCUG---A
(((...(((((((((......)))))))))..(((((((((.(.(((....))).)..)).)))))))......)))........(((((....))))).................---. ( -33.50)
>DroEre_CAF1 94032 119 - 1
GGCAAACACAGUCCUUUGUCCAGGACUC-ACCGGACAACGCCGCGACAUUUGUCUCCAGCUGUUGUCCCAUCCAGCUUAUUGUAAUUGCUGCACAACGAACUUUUCUACUCUUUUGGAGA
(((((..((((((((......)))))..-...(((((((((.(.(((....))).)..)).)))))))............)))..)))))..................(((.....))). ( -29.30)
>DroYak_CAF1 89108 117 - 1
AGCAAACAGAGACCUUUGUCCAGUGCUCUGCCGGACAACGCCUCGACGUCCGGCUCCAGCUGUUGUCCCAUCUAGCUUAUUGUAAUUGUUGCACAACGAACUUUCCUACUCUUCUG---A
......(((((((....)))..((((...(((((((..((...))..)))))))...(((((..........))))).............))))..................))))---. ( -27.70)
>consensus
AGCAAACAGAGUCCUUUGUCCAGGACUCUGCCGGACAACGCCGCGACAUCUGUCUCCAGCUGUUGUCCCAUCCAGCUUAUUGUAAUUGUUGCACAACGAACUUUUCUACUCUUCUG___A
(((...(((((((((......)))))))))..((((((((.(..(((....)))....).))))))))......)))........(((((....)))))..................... (-26.26 = -27.34 +   1.08)

alignment

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secondary structure

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Window 9

Location 1,462,560 – 1,462,680
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.42
Mean single sequence MFE -52.18
Consensus MFE -44.44
Energy contribution -46.20
Covariance contribution 1.76
Combinations/Pair 1.10
Mean z-score -4.23
Structure conservation index 0.85
SVM decision value 4.05
SVM RNA-class probability 0.999775
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1462560 120 + 20766785
AUAAGCUGGAUGGGACAACAGCUGGAGACAGAUGUCGCGGCGUUGUCCGGCAGAGUCCUGGACAAAGGACUCUGUUUGCUAUGCCGGAUCGCCGCUUGGAGUGGAAACACUUUUCUUAUU
........(((((((..(((.(((....))).))).((((((..(((((((((((((((......))))))))(....)...)))))))))))))..((((((....))))))))))))) ( -55.70)
>DroSec_CAF1 83079 120 + 1
AUAAGCUGGAUGGGACAACAGCUGGAGACAGAUGUCGCGGUGUUGUCCGGCAGAGUCCUGGACAAAGGACUCUGUUUGCUAUGCCGGAUCGCCGCGUGGAGUGGAAACACUUUUCUUAUU
........(((((((..(((.(((....))).)))(((((((..(((((((((((((((......))))))))(....)...)))))))))))))).((((((....))))))))))))) ( -55.40)
>DroSim_CAF1 82558 120 + 1
AUAAGCUGGAUGGGACAACAGCUGGAGACAGAUGUCGCGGCGUUGUCCGGCAGAGUCCUGGACAAAGGACUCUGUUUGCUAUGCCGGAUCGCCGCGUGGAGUGGAAACACUUUUCUUAUU
........(((((((..(((.(((....))).)))(((((((..(((((((((((((((......))))))))(....)...)))))))))))))).((((((....))))))))))))) ( -57.30)
>DroEre_CAF1 94072 119 + 1
AUAAGCUGGAUGGGACAACAGCUGGAGACAAAUGUCGCGGCGUUGUCCGGU-GAGUCCUGGACAAAGGACUGUGUUUGCCAUGCCGGAUCGCCGCGUGGAGUGGAAACACUUUUCUUAUU
...(((((..........)))))...(((....)))((((((..(((((((-.((((((......))))))(((.....))))))))))))))))(..(((((....)))))..)..... ( -50.40)
>DroYak_CAF1 89145 120 + 1
AUAAGCUAGAUGGGACAACAGCUGGAGCCGGACGUCGAGGCGUUGUCCGGCAGAGCACUGGACAAAGGUCUCUGUUUGCUUUGCAAAUUCGUAGCAUGGAGUGGAAACACUUUUCUUAUU
....((((((..(((((((.((((....))).)((....))))))))).((((((((..((((....)))).....))))))))....)).))))..((((((....))))))....... ( -42.10)
>consensus
AUAAGCUGGAUGGGACAACAGCUGGAGACAGAUGUCGCGGCGUUGUCCGGCAGAGUCCUGGACAAAGGACUCUGUUUGCUAUGCCGGAUCGCCGCGUGGAGUGGAAACACUUUUCUUAUU
........(((((((..(((.(((....))).))).((((((..(((((((((((((((......))))))))(....)...)))))))))))))..((((((....))))))))))))) (-44.44 = -46.20 +   1.76)

alignment

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secondary structure

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Window 0

Location 1,462,560 – 1,462,680
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.42
Mean single sequence MFE -38.10
Consensus MFE -30.10
Energy contribution -31.86
Covariance contribution 1.76
Combinations/Pair 1.11
Mean z-score -2.69
Structure conservation index 0.79
SVM decision value 2.06
SVM RNA-class probability 0.986858
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1462560 120 - 20766785
AAUAAGAAAAGUGUUUCCACUCCAAGCGGCGAUCCGGCAUAGCAAACAGAGUCCUUUGUCCAGGACUCUGCCGGACAACGCCGCGACAUCUGUCUCCAGCUGUUGUCCCAUCCAGCUUAU
.........((((....))))....((((((.((((((...(....)((((((((......))))))))))))))...))))))(((....)))...(((((..........)))))... ( -42.60)
>DroSec_CAF1 83079 120 - 1
AAUAAGAAAAGUGUUUCCACUCCACGCGGCGAUCCGGCAUAGCAAACAGAGUCCUUUGUCCAGGACUCUGCCGGACAACACCGCGACAUCUGUCUCCAGCUGUUGUCCCAUCCAGCUUAU
....(((..((((....))))...(((((.(.((((((...(....)((((((((......))))))))))))))...).)))))...)))......(((((..........)))))... ( -38.00)
>DroSim_CAF1 82558 120 - 1
AAUAAGAAAAGUGUUUCCACUCCACGCGGCGAUCCGGCAUAGCAAACAGAGUCCUUUGUCCAGGACUCUGCCGGACAACGCCGCGACAUCUGUCUCCAGCUGUUGUCCCAUCCAGCUUAU
....(((..((((....))))...(((((((.((((((...(....)((((((((......))))))))))))))...)))))))...)))......(((((..........)))))... ( -43.40)
>DroEre_CAF1 94072 119 - 1
AAUAAGAAAAGUGUUUCCACUCCACGCGGCGAUCCGGCAUGGCAAACACAGUCCUUUGUCCAGGACUC-ACCGGACAACGCCGCGACAUUUGUCUCCAGCUGUUGUCCCAUCCAGCUUAU
....(((.((((((..........(((((((.(((((..((.....)).((((((......)))))).-.)))))...))))))))))))).)))..(((((..........)))))... ( -36.10)
>DroYak_CAF1 89145 120 - 1
AAUAAGAAAAGUGUUUCCACUCCAUGCUACGAAUUUGCAAAGCAAACAGAGACCUUUGUCCAGUGCUCUGCCGGACAACGCCUCGACGUCCGGCUCCAGCUGUUGUCCCAUCUAGCUUAU
.........((((....))))....((((.((....(((((((....((((..((......))..))))(((((((..((...))..)))))))....))).))))....)))))).... ( -30.40)
>consensus
AAUAAGAAAAGUGUUUCCACUCCACGCGGCGAUCCGGCAUAGCAAACAGAGUCCUUUGUCCAGGACUCUGCCGGACAACGCCGCGACAUCUGUCUCCAGCUGUUGUCCCAUCCAGCUUAU
.(((((...((((....))))....((((((.(((((((.........(((((((......))))))))))))))...))))))((((.(((....))).))))...........))))) (-30.10 = -31.86 +   1.76)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,462,600 – 1,462,720
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.58
Mean single sequence MFE -36.78
Consensus MFE -31.78
Energy contribution -32.58
Covariance contribution 0.80
Combinations/Pair 1.12
Mean z-score -3.57
Structure conservation index 0.86
SVM decision value 4.18
SVM RNA-class probability 0.999828
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1462600 120 + 20766785
CGUUGUCCGGCAGAGUCCUGGACAAAGGACUCUGUUUGCUAUGCCGGAUCGCCGCUUGGAGUGGAAACACUUUUCUUAUUACACAAUAUACAAUCAUAAUAACAAUCAUAGUAACAACAA
.(((((..(((((((((((......)))))))))))(((((((.(((....)))...((((((....)))))).................................)))))))))))).. ( -38.70)
>DroSec_CAF1 83119 120 + 1
UGUUGUCCGGCAGAGUCCUGGACAAAGGACUCUGUUUGCUAUGCCGGAUCGCCGCGUGGAGUGGAAACACUUUUCUUAUUACACAAUAUACAAUCAUAAUAACAAUCAUGGUAACAACAA
((((((..(((((((((((......)))))))))))(((((((.(((....))).(..(((((....)))))..)...............................))))))))))))). ( -39.90)
>DroSim_CAF1 82598 120 + 1
CGUUGUCCGGCAGAGUCCUGGACAAAGGACUCUGUUUGCUAUGCCGGAUCGCCGCGUGGAGUGGAAACACUUUUCUUAUUACACAAUAUACAAUCAUAAUAACAAUCAUGGUAACAACAA
.(((((..(((((((((((......)))))))))))(((((((.(((....))).(..(((((....)))))..)...............................)))))))))))).. ( -39.50)
>DroEre_CAF1 94112 119 + 1
CGUUGUCCGGU-GAGUCCUGGACAAAGGACUGUGUUUGCCAUGCCGGAUCGCCGCGUGGAGUGGAAACACUUUUCUUAUUACACAAUAUACAAUCAUAAUAACAAUCAUAGUAACAACAA
.(((((...((-(((((((......)))))(((((...((((((.((....))))))))((((....)))).........)))))....................))))....))))).. ( -36.60)
>DroYak_CAF1 89185 120 + 1
CGUUGUCCGGCAGAGCACUGGACAAAGGUCUCUGUUUGCUUUGCAAAUUCGUAGCAUGGAGUGGAAACACUUUUCUUAUUACACAAUAUACAAUCAUAAUAACAAUCAUAGCAACAACAA
.(((((...((((((((..((((....)))).....))))))))......((((...((((((....)))))).....))))............................)))))..... ( -29.20)
>consensus
CGUUGUCCGGCAGAGUCCUGGACAAAGGACUCUGUUUGCUAUGCCGGAUCGCCGCGUGGAGUGGAAACACUUUUCUUAUUACACAAUAUACAAUCAUAAUAACAAUCAUAGUAACAACAA
.(((((..(((((((((((......)))))))))))(((((((.(((....)))...((((((....)))))).................................)))))))))))).. (-31.78 = -32.58 +   0.80)

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 09:32:17 2006