Locus 964

Sequence ID 2L_DroMel_CAF1
Location 2,782,898 – 2,783,023
Length 125
Max. P 0.996601
window1545 window1546 window1547 window1548

overview

Window 5

Location 2,782,898 – 2,783,009
Length 111
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 73.28
Mean single sequence MFE -43.62
Consensus MFE -34.76
Energy contribution -34.58
Covariance contribution -0.19
Combinations/Pair 1.25
Mean z-score -6.25
Structure conservation index 0.80
SVM decision value 2.68
SVM RNA-class probability 0.996320
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2782898 111 + 22407834
GGUUUCCAGAUUCCAGUGGUUAGAAACCAUCCUUAAAGGUGUCUGAAAGUAUGCAGUGAAAGGGCAAUCCACUUACAAGUUAUUGUUGCAUACUUUCAGACACCUAGGAUA
((((((..((((.....)))).))))))(((((...((((((((((((((((((((..(..((.....))(((....)))..)..))))))))))))))))))))))))). ( -47.10)
>DroSec_CAF1 6141 100 + 1
GGUUUCGAGACCCCAGUGGGUAAAAAUGACCCUUUAAGGUGUCUGGAAGUAUGCAGUGAGAGGG-----------CAAUUUAUUGUUGCAUACUUUUAGACACCUAGGUUA
((((.....((((....))))......)))).....((((((((((((((((((((..(.(((.-----------...))).)..))))))))))))))))))))...... ( -41.60)
>DroSim_CAF1 6250 111 + 1
GGUUUCGAGACCCCAGUGGUUAGAAAUCACCCUUUAAGGUGUCUGCAAGUAUGCAGUGAAAGGCUAAUCCACUUACAAAUUAUUGUUGCAUACUUUUAGACACCUAGGUUG
((((((..((((.....)))).))))))..(((...(((((((((.((((((((((..((((.........)))........)..)))))))))).))))))))))))... ( -38.40)
>DroEre_CAF1 6104 86 + 1
GGUUUCGAGACCCCAGUGGUUAGAAAUCGCCAUUGCAGGUGCCUGAAAGUAUGCAACACAA-------------------------UGCAUACUUUCAGGCACCCUGGUCA
........((((.(((((((.(....).)))))))..((((((((((((((((((......-------------------------))))))))))))))))))..)))). ( -47.40)
>consensus
GGUUUCGAGACCCCAGUGGUUAGAAAUCACCCUUUAAGGUGUCUGAAAGUAUGCAGUGAAAGGG___________CAA_UUAUUGUUGCAUACUUUCAGACACCUAGGUUA
((((....))))((.(((((.....)))))......((((((((((((((((((((..(.......................)..)))))))))))))))))))).))... (-34.76 = -34.58 +  -0.19)

alignment

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secondary structure

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Window 6

Location 2,782,898 – 2,783,009
Length 111
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 73.28
Mean single sequence MFE -40.69
Consensus MFE -31.02
Energy contribution -31.46
Covariance contribution 0.44
Combinations/Pair 1.21
Mean z-score -6.27
Structure conservation index 0.76
SVM decision value 2.72
SVM RNA-class probability 0.996601
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2782898 111 - 22407834
UAUCCUAGGUGUCUGAAAGUAUGCAACAAUAACUUGUAAGUGGAUUGCCCUUUCACUGCAUACUUUCAGACACCUUUAAGGAUGGUUUCUAACCACUGGAAUCUGGAAACC
.(((((((((((((((((((((((.((((....)))).((((((.......))))))))))))))))))))))))...)))))((((((((............)))))))) ( -49.00)
>DroSec_CAF1 6141 100 - 1
UAACCUAGGUGUCUAAAAGUAUGCAACAAUAAAUUG-----------CCCUCUCACUGCAUACUUCCAGACACCUUAAAGGGUCAUUUUUACCCACUGGGGUCUCGAAACC
...(((((((((((..(((((((((...........-----------.........)))))))))..))))))).....((((.......))))..))))........... ( -30.65)
>DroSim_CAF1 6250 111 - 1
CAACCUAGGUGUCUAAAAGUAUGCAACAAUAAUUUGUAAGUGGAUUAGCCUUUCACUGCAUACUUGCAGACACCUUAAAGGGUGAUUUCUAACCACUGGGGUCUCGAAACC
...(((((((((((..((((((((.((((....)))).((((((.......))))))))))))))..))))))))...)))(.(((..(........)..))).)...... ( -39.70)
>DroEre_CAF1 6104 86 - 1
UGACCAGGGUGCCUGAAAGUAUGCA-------------------------UUGUGUUGCAUACUUUCAGGCACCUGCAAUGGCGAUUUCUAACCACUGGGGUCUCGAAACC
.((((.(((((((((((((((((((-------------------------......))))))))))))))))))).((.(((..........))).)).))))........ ( -43.40)
>consensus
UAACCUAGGUGUCUAAAAGUAUGCAACAAUAA_UUG___________CCCUUUCACUGCAUACUUUCAGACACCUUAAAGGGUGAUUUCUAACCACUGGGGUCUCGAAACC
...((((((((((((((((((((((...............................)))))))))))))))))))...)))..((((((........))))))........ (-31.02 = -31.46 +   0.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,782,933 – 2,783,023
Length 90
Sequences 4
Columns 90
Reading direction forward
Mean pairwise identity 78.54
Mean single sequence MFE -32.24
Consensus MFE -30.77
Energy contribution -30.90
Covariance contribution 0.13
Combinations/Pair 1.10
Mean z-score -5.95
Structure conservation index 0.95
SVM decision value 2.24
SVM RNA-class probability 0.990955
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2782933 90 + 22407834
AAGGUGUCUGAAAGUAUGCAGUGAAAGGGCAAUCCACUUACAAGUUAUUGUUGCAUACUUUCAGACACCUAGGAUAUUUGUUUUCUUUUC
.((((((((((((((((((((..(..((.....))(((....)))..)..))))))))))))))))))))((((........)))).... ( -36.50)
>DroSec_CAF1 6176 79 + 1
AAGGUGUCUGGAAGUAUGCAGUGAGAGGG-----------CAAUUUAUUGUUGCAUACUUUUAGACACCUAGGUUAUUUGUAUACUUUUC
.((((((((((((((((((((..(.(((.-----------...))).)..)))))))))))))))))))).................... ( -32.70)
>DroSim_CAF1 6285 85 + 1
AAGGUGUCUGCAAGUAUGCAGUGAAAGGCUAAUCCACUUACAAAUUAUUGUUGCAUACUUUUAGACACCUAGGUUGU-----UACUUUUC
.(((((((((.((((((((((..((((.........)))........)..)))))))))).))))))))).......-----........ ( -27.80)
>DroYak_CAF1 4874 85 + 1
AAGGUGUCUGAAAGUAUGCAGUGAAAGGGCAACCCACUUAAAAUUUAUUGUUGCAUACUUUCCGACACCUAGAUAA-----UAUCAAUGC
.(((((((.((((((((((((..(..((....)).............)..)))))))))))).)))))))......-----......... ( -31.96)
>consensus
AAGGUGUCUGAAAGUAUGCAGUGAAAGGGCAAUCCACUUACAAUUUAUUGUUGCAUACUUUCAGACACCUAGGUUAU____UUACUUUUC
.((((((((((((((((((((..(.......................)..)))))))))))))))))))).................... (-30.77 = -30.90 +   0.13)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,782,933 – 2,783,023
Length 90
Sequences 4
Columns 90
Reading direction reverse
Mean pairwise identity 78.54
Mean single sequence MFE -29.66
Consensus MFE -25.67
Energy contribution -28.55
Covariance contribution 2.88
Combinations/Pair 1.04
Mean z-score -6.29
Structure conservation index 0.87
SVM decision value 2.22
SVM RNA-class probability 0.990594
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2782933 90 - 22407834
GAAAAGAAAACAAAUAUCCUAGGUGUCUGAAAGUAUGCAACAAUAACUUGUAAGUGGAUUGCCCUUUCACUGCAUACUUUCAGACACCUU
....................((((((((((((((((((.((((....)))).((((((.......)))))))))))))))))))))))). ( -37.10)
>DroSec_CAF1 6176 79 - 1
GAAAAGUAUACAAAUAACCUAGGUGUCUAAAAGUAUGCAACAAUAAAUUG-----------CCCUCUCACUGCAUACUUCCAGACACCUU
....................((((((((..(((((((((...........-----------.........)))))))))..)))))))). ( -22.35)
>DroSim_CAF1 6285 85 - 1
GAAAAGUA-----ACAACCUAGGUGUCUAAAAGUAUGCAACAAUAAUUUGUAAGUGGAUUAGCCUUUCACUGCAUACUUGCAGACACCUU
........-----.......((((((((..((((((((.((((....)))).((((((.......))))))))))))))..)))))))). ( -30.80)
>DroYak_CAF1 4874 85 - 1
GCAUUGAUA-----UUAUCUAGGUGUCGGAAAGUAUGCAACAAUAAAUUUUAAGUGGGUUGCCCUUUCACUGCAUACUUUCAGACACCUU
.........-----......(((((((.((((((((((...((......)).((((((.......)))))))))))))))).))))))). ( -28.40)
>consensus
GAAAAGAAA____AUAACCUAGGUGUCUAAAAGUAUGCAACAAUAAAUUGUAAGUGGAUUGCCCUUUCACUGCAUACUUUCAGACACCUU
....................(((((((((((((((((((((((....))))..(((((.......)))))))))))))))))))))))). (-25.67 = -28.55 +   2.88)

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 09:49:48 2006