Locus 4361

Sequence ID 2R_DroMel_CAF1
Location 14,333,564 – 14,333,701
Length 137
Max. P 0.902294
window6980 window6981 window6982

overview

Window 0

Location 14,333,564 – 14,333,672
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.23
Mean single sequence MFE -24.35
Consensus MFE -19.10
Energy contribution -19.52
Covariance contribution 0.42
Combinations/Pair 1.10
Mean z-score -2.33
Structure conservation index 0.78
SVM decision value 0.77
SVM RNA-class probability 0.846742
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14333564 108 + 20766785
GGGGCACAGAUAAUUUCUC------------CGGCCGAUUUAAAUUCCUUUCCGCUCCAGCACACUGGAGCUAUUCGCUUGAAAUUGUAAUUGUCACAAAUUUACAAAAAAAAAAAAAAA
..((((...((((((((..------------.(((.((.......))......(((((((....))))))).....))).))))))))...))))......................... ( -24.50)
>DroSec_CAF1 9772 98 + 1
GGGGCAUAAAUAAUUUCUC------------CGGCCGAUUUAAAUUCCUUUCCGCUCCAGCACACUGGAGCUAUUCGCUUGAAAUUGUAAUUGUCACAAUUUUACAAAA----------A
..((((...((((((((..------------.(((.((.......))......(((((((....))))))).....))).))))))))...))))..............----------. ( -24.10)
>DroSim_CAF1 10509 98 + 1
GGGGCAUAAAUAAUUUCUC------------UGGCCGAUUUAAAUUCCUUUCCGCUCCAGCACACUGGAGCUAUUCGCUUGAAAAUGUAAUUGUCACAAUUUUACAAAA----------A
..((((...(((.((((..------------.(((.((.......))......(((((((....))))))).....))).)))).)))...))))..............----------. ( -21.10)
>DroEre_CAF1 9783 98 + 1
GGGGCACAAAUAAUUUCUC------------CGGGCGAUUUGGAUUCCUUUCCGCUCCAGCACACUGGAGCUAUUCGCUUGAAAUUGUAAUUGUCACAAUUUAACAAAA----------A
..((((...((((((((..------------.((((((...(((......)))(((((((....)))))))...))))))))))))))...))))..............----------. ( -31.30)
>DroYak_CAF1 10268 98 + 1
GGGGCAUAAAUAAUUUCUC------------CGGACGAUUUAAAUUCCUUUCCGCUCCAGCACACUGGAGCUAUUCGCUUGAAAUUGUAAUUGUCACAAUUUUACAAAA----------A
..((((...((((((((..------------.(((.((.......))...)))(((((((....))))))).........))))))))...))))..............----------. ( -24.60)
>DroAna_CAF1 10845 109 + 1
GGGGCAUAAAUUCUAGCACAAAGACCGCUCAUCACCGAUUUAAAUUCCUUUACGCUCCAGCAACCUGGAGUUAUGCACUGGAAUUAGUAAUUGUCGCAAUUUUACAGAC-----------
(.((((..((((((((..((..((....)).......................(((((((....)))))))..))..))))))))......)))).)............----------- ( -20.50)
>consensus
GGGGCAUAAAUAAUUUCUC____________CGGCCGAUUUAAAUUCCUUUCCGCUCCAGCACACUGGAGCUAUUCGCUUGAAAUUGUAAUUGUCACAAUUUUACAAAA__________A
..((((...((((((((...................((.......))......(((((((....))))))).........))))))))...))))......................... (-19.10 = -19.52 +   0.42)

alignment

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secondary structure

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Window 1

Location 14,333,592 – 14,333,701
Length 109
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 83.88
Mean single sequence MFE -26.40
Consensus MFE -18.25
Energy contribution -20.08
Covariance contribution 1.84
Combinations/Pair 1.12
Mean z-score -3.74
Structure conservation index 0.69
SVM decision value 1.02
SVM RNA-class probability 0.902294
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14333592 109 + 20766785
UAAAUUCCUUUCCGCUCCAGCACACUGGAGCUAUUCGCUUGAAAUUGUAAUUGUCACAAAUUUACAAAAAAAAAAAAAAAAAACACAACAUGUGAGUUUAA--GUGCUGCA
.............(((((((....)))))))....((((((((.((((((...........))))))................(((.....)))..)))))--)))..... ( -23.50)
>DroSec_CAF1 9800 99 + 1
UAAAUUCCUUUCCGCUCCAGCACACUGGAGCUAUUCGCUUGAAAUUGUAAUUGUCACAAUUUUACAAAA----------AACUCACAACAUGUGAGUUUAA--GUGCUGCA
.............(((((((....)))))))....(((((((((((((.......)))))))).....(----------(((((((.....))))))))))--)))..... ( -29.30)
>DroSim_CAF1 10537 99 + 1
UAAAUUCCUUUCCGCUCCAGCACACUGGAGCUAUUCGCUUGAAAAUGUAAUUGUCACAAUUUUACAAAA----------AACUCACAACAUGUGAGUUUAA--GUGCUGCA
.............(((((((....)))))))....(((((((...(((((...........)))))...----------.((((((.....))))))))))--)))..... ( -26.70)
>DroEre_CAF1 9811 99 + 1
UGGAUUCCUUUCCGCUCCAGCACACUGGAGCUAUUCGCUUGAAAUUGUAAUUGUCACAAUUUAACAAAA----------AACUCACAACAGGUGAGUUUAA--GUGCUGCA
.(((......)))(((((((....)))))))....(((((.(((((((.......)))))))......(----------(((((((.....))))))))))--)))..... ( -30.90)
>DroYak_CAF1 10296 99 + 1
UAAAUUCCUUUCCGCUCCAGCACACUGGAGCUAUUCGCUUGAAAUUGUAAUUGUCACAAUUUUACAAAA----------AACUCACAACAGGUGAGUUUAA--GUGCUGCA
.............(((((((....)))))))....(((((((((((((.......)))))))).....(----------(((((((.....))))))))))--)))..... ( -28.90)
>DroAna_CAF1 10885 87 + 1
UAAAUUCCUUUACGCUCCAGCAACCUGGAGUUAUGCACUGGAAUUAGUAAUUGUCGCAAUUUUACAGAC------------------------GAAUUCAAAUGUGCUGAC
.............(((((((....)))))))...((((..((((......(((((...........)))------------------------))))))....)))).... ( -19.10)
>consensus
UAAAUUCCUUUCCGCUCCAGCACACUGGAGCUAUUCGCUUGAAAUUGUAAUUGUCACAAUUUUACAAAA__________AACUCACAACAUGUGAGUUUAA__GUGCUGCA
.............(((((((....)))))))....(((.(((((((((.......)))))))))...............(((((((.....))))))).....)))..... (-18.25 = -20.08 +   1.84)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,333,592 – 14,333,701
Length 109
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 83.88
Mean single sequence MFE -28.15
Consensus MFE -19.09
Energy contribution -21.20
Covariance contribution 2.11
Combinations/Pair 1.04
Mean z-score -2.80
Structure conservation index 0.68
SVM decision value 0.41
SVM RNA-class probability 0.724589
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14333592 109 - 20766785
UGCAGCAC--UUAAACUCACAUGUUGUGUUUUUUUUUUUUUUUUUUGUAAAUUUGUGACAAUUACAAUUUCAAGCGAAUAGCUCCAGUGUGCUGGAGCGGAAAGGAAUUUA
.((((((.--...........))))))((((((((((......(((((....((((((...))))))......)))))..(((((((....)))))))))))))))))... ( -24.40)
>DroSec_CAF1 9800 99 - 1
UGCAGCAC--UUAAACUCACAUGUUGUGAGUU----------UUUUGUAAAAUUGUGACAAUUACAAUUUCAAGCGAAUAGCUCCAGUGUGCUGGAGCGGAAAGGAAUUUA
.((.(((.--..((((((((.....)))))))----------)..))).(((((((((...)))))))))...)).....(((((((....)))))))............. ( -31.50)
>DroSim_CAF1 10537 99 - 1
UGCAGCAC--UUAAACUCACAUGUUGUGAGUU----------UUUUGUAAAAUUGUGACAAUUACAUUUUCAAGCGAAUAGCUCCAGUGUGCUGGAGCGGAAAGGAAUUUA
.((.(((.--..((((((((.....)))))))----------)..))).(((.(((((...))))).)))...)).....(((((((....)))))))............. ( -28.30)
>DroEre_CAF1 9811 99 - 1
UGCAGCAC--UUAAACUCACCUGUUGUGAGUU----------UUUUGUUAAAUUGUGACAAUUACAAUUUCAAGCGAAUAGCUCCAGUGUGCUGGAGCGGAAAGGAAUCCA
.((((((.--..((((((((.....)))))))----------)..))))(((((((((...)))))))))...)).....(((((((....)))))))(((......))). ( -33.60)
>DroYak_CAF1 10296 99 - 1
UGCAGCAC--UUAAACUCACCUGUUGUGAGUU----------UUUUGUAAAAUUGUGACAAUUACAAUUUCAAGCGAAUAGCUCCAGUGUGCUGGAGCGGAAAGGAAUUUA
.((.(((.--..((((((((.....)))))))----------)..))).(((((((((...)))))))))...)).....(((((((....)))))))............. ( -30.50)
>DroAna_CAF1 10885 87 - 1
GUCAGCACAUUUGAAUUC------------------------GUCUGUAAAAUUGCGACAAUUACUAAUUCCAGUGCAUAACUCCAGGUUGCUGGAGCGUAAAGGAAUUUA
(((.(((.((((......------------------------.......)))))))))).......((((((..(((....((((((....)))))).)))..)))))).. ( -20.62)
>consensus
UGCAGCAC__UUAAACUCACAUGUUGUGAGUU__________UUUUGUAAAAUUGUGACAAUUACAAUUUCAAGCGAAUAGCUCCAGUGUGCUGGAGCGGAAAGGAAUUUA
....((.......(((((((.....))))))).................(((((((((...)))))))))...)).....(((((((....)))))))............. (-19.09 = -21.20 +   2.11)

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 11:17:50 2006