Locus 6172

Sequence ID X_DroMel_CAF1
Location 15,743,786 – 15,743,910
Length 124
Max. P 0.999597
window10051 window10052 window10053

overview

Window 1

Location 15,743,786 – 15,743,899
Length 113
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 78.27
Mean single sequence MFE -24.73
Consensus MFE -15.19
Energy contribution -17.25
Covariance contribution 2.06
Combinations/Pair 1.24
Mean z-score -3.51
Structure conservation index 0.61
SVM decision value 3.77
SVM RNA-class probability 0.999597
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15743786 113 - 22224390
UUUUUAUUAUAAGGGUAAGACCCUUUUAUAGUCCAUCAAACCCAUUGAUGGAUUAUAAGUUUUUAAUGUUCUAAUA-ACAACCCUAAGUGAAACAUAUUUCACAAGCAACAAGU
...........(((((.........((((((((((((((.....))))))))))))))(((.(((......))).)-)).)))))..((((((....))))))........... ( -29.10)
>DroSec_CAF1 2783 113 - 1
UUUUUACUAAAAGGGUAAGACAGUUUUAUGGUCCAUCAAGCCCAUUGAUGGAUUAUAAGUUUUUAAUAUUCUAAAA-ACAACCCUAAGUGAAACAUAUGUUACAAGCAACAAGU
.(((((((...(((((.........((((((((((((((.....))))))))))))))(((((((......)))))-)).))))).)))))))....((((......))))... ( -32.60)
>DroSim_CAF1 2789 113 - 1
UUUUUAUUAAACGGGUAAGACCGUUUUAUGGUCCAUCAAAUCCAUUGAUGGAUUAUAAGUUUUUAAUAUUCUAAAA-ACAACCCUAAUUAAAACAUAUGUUACAAGCAACAAGU
............((((.........((((((((((((((.....))))))))))))))(((((((......)))))-)).)))).............((((......))))... ( -26.70)
>DroYak_CAF1 2821 108 - 1
UUUUUACAAAAAGUGUUU-CCUCUUUUAUUGUGCAUCAAACCCAUUUU-----UAAGAGUUUUUAUUAUUCUAAAGAAUAACACUCUAUGCUAGACAUUUCACAAAAAAACAGC
..........((((((((-.(((((.....(((.........)))...-----.)))))......((((((....))))))...........)))))))).............. ( -10.50)
>consensus
UUUUUACUAAAAGGGUAAGACCCUUUUAUGGUCCAUCAAACCCAUUGAUGGAUUAUAAGUUUUUAAUAUUCUAAAA_ACAACCCUAAGUGAAACAUAUGUCACAAGCAACAAGU
.(((((((...(((((.........((((((((((((((.....))))))))))))))(((((((......))))).)).))))).)))))))..................... (-15.19 = -17.25 +   2.06)

alignment

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secondary structure

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Window 2

Location 15,743,820 – 15,743,910
Length 90
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 68.88
Mean single sequence MFE -18.52
Consensus MFE -2.14
Energy contribution -4.38
Covariance contribution 2.24
Combinations/Pair 1.17
Mean z-score -2.55
Structure conservation index 0.12
SVM decision value 1.34
SVM RNA-class probability 0.943682
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15743820 90 + 22224390
UGU-UAUUAGAACAUUAAAAACUUAUAAUCCAUCAAUGGGUUUGAUGGACUAUAAAAGGGUCUUACCCUUAUAAUAAAAACAAAGUUCU-----UC
...-....(((((.........(((((.((((((((.....)))))))).)))))(((((.....)))))..............)))))-----.. ( -24.20)
>DroSec_CAF1 2817 90 + 1
UGU-UUUUAGAAUAUUAAAAACUUAUAAUCCAUCAAUGGGCUUGAUGGACCAUAAAACUGUCUUACCCUUUUAGUAAAAACGAAGUUCU-----UC
.((-((((..............((((..((((((((.....))))))))..)))).((((...........))))))))))........-----.. ( -13.80)
>DroSim_CAF1 2823 90 + 1
UGU-UUUUAGAAUAUUAAAAACUUAUAAUCCAUCAAUGGAUUUGAUGGACCAUAAAACGGUCUUACCCGUUUAAUAAAAACGAAGUUCU-----UC
.((-(((((..............(((..((((((((.....))))))))..)))((((((......))))))..)))))))........-----.. ( -20.80)
>DroEre_CAF1 2849 78 + 1
UAUAUUUUAGAAUAAUAAAAACUCUCU-----UAAAUGGGUUUGAUGGGGUGUGAAAGGGG-UG-----------GAAACUCA-CUUCUUAGCUCC
..................((((((...-----.....))))))...(((((..(((..(((-(.-----------...)))).-.)))...))))) ( -18.20)
>DroYak_CAF1 2855 89 + 1
UAUUCUUUAGAAUAAUAAAAACUCUUA-----AAAAUGGGUUUGAUGCACAAUAAAAGAGG-AAACACUUUUUGUAAAAACCA-AUUCUAAGCUUC
.....((((((((.....((((((...-----.....))))))..((((....(((((.(.-...).))))))))).......-)))))))).... ( -15.60)
>consensus
UGU_UUUUAGAAUAUUAAAAACUUAUAAUCCAUCAAUGGGUUUGAUGGACCAUAAAAGGGUCUUACCCUUUUAAUAAAAACCAAGUUCU_____UC
......................((((..((((((((.....))))))))..))))......................................... ( -2.14 =  -4.38 +   2.24)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,743,820 – 15,743,910
Length 90
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 68.88
Mean single sequence MFE -19.44
Consensus MFE -6.64
Energy contribution -9.24
Covariance contribution 2.60
Combinations/Pair 1.27
Mean z-score -2.68
Structure conservation index 0.34
SVM decision value 2.74
SVM RNA-class probability 0.996734
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15743820 90 - 22224390
GA-----AGAACUUUGUUUUUAUUAUAAGGGUAAGACCCUUUUAUAGUCCAUCAAACCCAUUGAUGGAUUAUAAGUUUUUAAUGUUCUAAUA-ACA
..-----(((((..............(((((.....)))))((((((((((((((.....)))))))))))))).........)))))....-... ( -26.50)
>DroSec_CAF1 2817 90 - 1
GA-----AGAACUUCGUUUUUACUAAAAGGGUAAGACAGUUUUAUGGUCCAUCAAGCCCAUUGAUGGAUUAUAAGUUUUUAAUAUUCUAAAA-ACA
((-----(....)))(((((.(((.....))))))))....((((((((((((((.....))))))))))))))(((((((......)))))-)). ( -25.00)
>DroSim_CAF1 2823 90 - 1
GA-----AGAACUUCGUUUUUAUUAAACGGGUAAGACCGUUUUAUGGUCCAUCAAAUCCAUUGAUGGAUUAUAAGUUUUUAAUAUUCUAAAA-ACA
((-----(....)))(((((((...(((((......)))))((((((((((((((.....)))))))))))))).............)))))-)). ( -26.70)
>DroEre_CAF1 2849 78 - 1
GGAGCUAAGAAG-UGAGUUUC-----------CA-CCCCUUUCACACCCCAUCAAACCCAUUUA-----AGAGAGUUUUUAUUAUUCUAAAAUAUA
((((((......-..))))))-----------..-.............................-----..(((((.......)))))........ (  -5.80)
>DroYak_CAF1 2855 89 - 1
GAAGCUUAGAAU-UGGUUUUUACAAAAAGUGUUU-CCUCUUUUAUUGUGCAUCAAACCCAUUUU-----UAAGAGUUUUUAUUAUUCUAAAGAAUA
((((((((((((-.(((((.(((((((((.....-...))))..)))))....))))).)))))-----...)))))))...(((((....))))) ( -13.20)
>consensus
GA_____AGAACUUCGUUUUUACUAAAAGGGUAAGACCCUUUUAUAGUCCAUCAAACCCAUUGAUGGAUUAUAAGUUUUUAAUAUUCUAAAA_ACA
........................................(((((((((((((((.....)))))))))))))))..................... ( -6.64 =  -9.24 +   2.60)

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 12:06:19 2006