Locus 4578

Sequence ID 2R_DroMel_CAF1
Location 14,961,059 – 14,961,215
Length 156
Max. P 0.993343
window7340 window7341 window7342

overview

Window 0

Location 14,961,059 – 14,961,176
Length 117
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 94.18
Mean single sequence MFE -20.75
Consensus MFE -17.04
Energy contribution -16.24
Covariance contribution -0.80
Combinations/Pair 1.24
Mean z-score -1.59
Structure conservation index 0.82
SVM decision value 0.56
SVM RNA-class probability 0.783590
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14961059 117 + 20766785
AAUAUUUAUAUUUUAUCUUACUUGUCAAAUAUCAGUCAGUGACACCCACACACCGCCGCACGGUACGCACACACACACACAAUCAAUACACACUGUGCACACUGUUUUUGGCGUCCC
.......................((((((...((((..(((.....)))..((((.....))))..(((((......................)))))..))))..))))))..... ( -19.95)
>DroSec_CAF1 976 117 + 1
AAUAUUUAUAUUUUAUCUUACUUGUCAAAUAUCAGUCAGUGACACCCACACACGGCCGCACGGUACACACACACACACGCAAUCAAUACACACUGUGCACACUGUUUUUGGCGGCCC
.....................((((((((...((((..(((.....)))........(((((((...........................)))))))..))))..))))))))... ( -20.23)
>DroSim_CAF1 1173 117 + 1
AAUAUUUAUAUUUUAUCUUACUUGUCAAAUAUCAGUCAGUGACACCCACACACGGCCGCACGGUACACACACACACACGCAAUCAAUACACACUGUGCACACUGUUUUCGGCGGCCC
......................(((((............))))).........((((((.(((.(((....((((..................)))).....)))..))))))))). ( -20.37)
>DroEre_CAF1 1054 115 + 1
AUUAUUUAUAUUUUAUCUUACUUGUCAAAUAUCAGUCAGUGACACUCACACACGGCCGCACGAAACGCACACA--CACACAAUCAAUACACACUGUGCACACUGUUUUCGGUGGCCC
......................................(((.....)))....((((((.(((((.(((....--..((((............)))).....)))))))))))))). ( -21.60)
>DroYak_CAF1 1235 115 + 1
AUUAUUUAUAUUUUAUCUUACUUGUCAAAUAUCAGUCAGUGACACUCACACACGGCCGCACGAAACGCACACA--CACACAAUCAAUACACACUGUGCACACUGUUUUCGGUGGCCC
......................................(((.....)))....((((((.(((((.(((....--..((((............)))).....)))))))))))))). ( -21.60)
>consensus
AAUAUUUAUAUUUUAUCUUACUUGUCAAAUAUCAGUCAGUGACACCCACACACGGCCGCACGGUACGCACACACACACACAAUCAAUACACACUGUGCACACUGUUUUCGGCGGCCC
......................(((((............))))).........((((((.(((...(((......((((..............)))).....)))..))))))))). (-17.04 = -16.24 +  -0.80)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,961,096 – 14,961,215
Length 119
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 92.09
Mean single sequence MFE -33.22
Consensus MFE -29.14
Energy contribution -27.82
Covariance contribution -1.32
Combinations/Pair 1.25
Mean z-score -2.01
Structure conservation index 0.88
SVM decision value 2.39
SVM RNA-class probability 0.993343
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14961096 119 + 20766785
AGUGACACCCACACACCGCCGCACGGUACGCACACACACACACAAUCAAUACACACUGUGCACACUGUUUUUGGCGUCCCUGGCAGCGCAGUGUUGUCAAUCGAUAAAUUAUCGAUUUU
..(((((...((((..(((.((..((.((((.((.(.(((((((............)))).....))).).)))))).))..)).)))..)))))))))(((((((...)))))))... ( -30.20)
>DroSec_CAF1 1013 119 + 1
AGUGACACCCACACACGGCCGCACGGUACACACACACACACGCAAUCAAUACACACUGUGCACACUGUUUUUGGCGGCCCUGGCAGCGCAGUGUUGUCAAUCGAUAAGUUAUCGAUUUU
.(((.....)))....(((((((((((...((((......................))))...))))).....))))))..((((((.....))))))((((((((...)))))))).. ( -30.65)
>DroSim_CAF1 1210 119 + 1
AGUGACACCCACACACGGCCGCACGGUACACACACACACACGCAAUCAAUACACACUGUGCACACUGUUUUCGGCGGCCCUGGCAGCGCAGUGUUGUCAAUCGAUAAGUUAUCGAUUUU
.(((.....)))....((((((.(((.(((....((((..................)))).....)))..)))))))))..((((((.....))))))((((((((...)))))))).. ( -31.57)
>DroEre_CAF1 1091 117 + 1
AGUGACACUCACACACGGCCGCACGAAACGCACACA--CACACAAUCAAUACACACUGUGCACACUGUUUUCGGUGGCCCUGGCAACGCAGUGUUGCCAGUCGAUAAGUAAUCGAUUUU
.(((.....)))....((((((.(((((.(((....--..((((............)))).....))))))))))))))((((((((.....))))))))(((((.....))))).... ( -37.60)
>DroYak_CAF1 1272 117 + 1
AGUGACACUCACACACGGCCGCACGAAACGCACACA--CACACAAUCAAUACACACUGUGCACACUGUUUUCGGUGGCCCUGGCAACGCAGUGUUGCCAGCCGAUAAGUAAUCGAUUUU
.(((.....)))....((((((.(((((.(((....--..((((............)))).....))))))))))))))((((((((.....)))))))).((((.....))))..... ( -36.10)
>consensus
AGUGACACCCACACACGGCCGCACGGUACGCACACACACACACAAUCAAUACACACUGUGCACACUGUUUUCGGCGGCCCUGGCAGCGCAGUGUUGUCAAUCGAUAAGUUAUCGAUUUU
.(((.....)))....((((((.(((...(((......((((..............)))).....)))..))))))))).(((((((.....)))))))((((((.....))))))... (-29.14 = -27.82 +  -1.32)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,961,096 – 14,961,215
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 92.09
Mean single sequence MFE -43.52
Consensus MFE -33.30
Energy contribution -32.34
Covariance contribution -0.96
Combinations/Pair 1.17
Mean z-score -2.19
Structure conservation index 0.77
SVM decision value 0.97
SVM RNA-class probability 0.891835
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14961096 119 - 20766785
AAAAUCGAUAAUUUAUCGAUUGACAACACUGCGCUGCCAGGGACGCCAAAAACAGUGUGCACAGUGUGUAUUGAUUGUGUGUGUGUGUGCGUACCGUGCGGCGGUGUGUGGGUGUCACU
..((((((((...))))))))((((.(((.((((((((.((.((((((...(((...((((((((........))))))))))).)).)))).))....)))))))))))..))))... ( -45.10)
>DroSec_CAF1 1013 119 - 1
AAAAUCGAUAACUUAUCGAUUGACAACACUGCGCUGCCAGGGCCGCCAAAAACAGUGUGCACAGUGUGUAUUGAUUGCGUGUGUGUGUGUGUACCGUGCGGCCGUGUGUGGGUGUCACU
..((((((((...))))))))((((...(..(((.((...((((((.....((.(((..(((((..((((.....))))..)...))))..))).)))))))))))))..).))))... ( -42.80)
>DroSim_CAF1 1210 119 - 1
AAAAUCGAUAACUUAUCGAUUGACAACACUGCGCUGCCAGGGCCGCCGAAAACAGUGUGCACAGUGUGUAUUGAUUGCGUGUGUGUGUGUGUACCGUGCGGCCGUGUGUGGGUGUCACU
..((((((((...))))))))((((...(..(((.((...((((((((......(((..(((((..((((.....))))..)...))))..))))).)))))))))))..).))))... ( -43.00)
>DroEre_CAF1 1091 117 - 1
AAAAUCGAUUACUUAUCGACUGGCAACACUGCGUUGCCAGGGCCACCGAAAACAGUGUGCACAGUGUGUAUUGAUUGUGUG--UGUGUGCGUUUCGUGCGGCCGUGUGUGAGUGUCACU
......(((.((((((...((((((((.....))))))))((((.((((((...(..((((((((........))))))))--..).....))))).).))))....)))))))))... ( -43.50)
>DroYak_CAF1 1272 117 - 1
AAAAUCGAUUACUUAUCGGCUGGCAACACUGCGUUGCCAGGGCCACCGAAAACAGUGUGCACAGUGUGUAUUGAUUGUGUG--UGUGUGCGUUUCGUGCGGCCGUGUGUGAGUGUCACU
......(((.((((((...((((((((.....))))))))((((.((((((...(..((((((((........))))))))--..).....))))).).))))....)))))))))... ( -43.20)
>consensus
AAAAUCGAUAACUUAUCGAUUGACAACACUGCGCUGCCAGGGCCGCCGAAAACAGUGUGCACAGUGUGUAUUGAUUGUGUGUGUGUGUGCGUACCGUGCGGCCGUGUGUGGGUGUCACU
..(((((((.....)))))))((((.(((.((((.(((.....((((((...(((((..(.....)..))))).))).))).....(..((...))..)))).)))))))..))))... (-33.30 = -32.34 +  -0.96)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:36 2006