Locus 388

Sequence ID 2R_DroMel_CAF1
Location 2,364,564 – 2,364,804
Length 240
Max. P 0.998781
window759 window760 window761 window762

overview

Window 9

Location 2,364,564 – 2,364,684
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.15
Mean single sequence MFE -32.48
Consensus MFE -28.04
Energy contribution -27.72
Covariance contribution -0.32
Combinations/Pair 1.14
Mean z-score -1.61
Structure conservation index 0.86
SVM decision value 1.11
SVM RNA-class probability 0.916008
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2364564 120 + 20766785
GAACCAGUGGACCCAGAACCCACUUGUUGGCCACGGUUCACCCGGCAGCGAACUCUUAAUUGAUUUCGCGCUAAUUGGUCCGACCCAACAACGACGCUGGUUGAUGUUUAACAAUUUGCA
.((((((((......(....)..(((((((...(((..((...(((.(((((.((......)).))))))))...))..)))..)))))))...)))))))).................. ( -34.80)
>DroSec_CAF1 14107 112 + 1
UC--------ACCCGAAACCCACUUGUUGGACACGGUUCACCCAGCAGCGAACUCUUAAUUGAUUUCGCGCUAAUUGGUCCGACCCACCAACGACGCUGGUUGAUGUUUAACAAUUUGCA
..--------.............((((((((((....(((.(((((.(((((.((......)).))))).....(((((.......)))))....))))).)))))))))))))...... ( -31.80)
>DroSim_CAF1 14202 112 + 1
UC--------ACCCGAAACCCACUUGUUGGACACGGUUCACCCAGCAGCGAACUCUUAAUUGAUUUCGCGCUAAUUGGUCCGACCCGACAACGACGCUGGUUGAUGUUUAACAAUUUGCA
..--------.............((((((((((....(((.(((((.(((((.((......)).))))).....((((......)))).......))))).)))))))))))))...... ( -30.70)
>DroEre_CAF1 13771 112 + 1
UC--------ACCCGGAACCCACUUGUUGGACACGGUUCACCCGGCAGCGAGCUCUUAAUUGAUUUCGCGCUAAUUGGUGCGACCCACCAGCGACGCUGGUUGAUGUUUAACAAUUUGCA
..--------.............((((((((((.((((((((.(((.(((((.((......)).))))))))....)))).)))).((((((...))))))...))))))))))...... ( -35.80)
>DroYak_CAF1 13510 112 + 1
UU--------ACCCAGAACCCACUUGUUGGUCACGGUUCAUCCGGCAGCGAACUCUUAAUUGAUUUCGUGCUAAUUGGUCCGACCCAACAACUACGCUGGUUGAUGUUUAACAAUUUGCA
((--------(.((((.......(((((((...(((..((...((((.((((.((......)).))))))))...))..)))..))))))).....)))).)))................ ( -29.30)
>consensus
UC________ACCCGGAACCCACUUGUUGGACACGGUUCACCCGGCAGCGAACUCUUAAUUGAUUUCGCGCUAAUUGGUCCGACCCAACAACGACGCUGGUUGAUGUUUAACAAUUUGCA
.......................((((((((((....(((.(((((.(((((.((......)).)))))......(((......)))........))))).)))))))))))))...... (-28.04 = -27.72 +  -0.32)

alignment

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secondary structure

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Window 0

Location 2,364,604 – 2,364,724
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.00
Mean single sequence MFE -29.76
Consensus MFE -27.06
Energy contribution -26.54
Covariance contribution -0.52
Combinations/Pair 1.12
Mean z-score -1.45
Structure conservation index 0.91
SVM decision value 1.06
SVM RNA-class probability 0.909054
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2364604 120 + 20766785
CCCGGCAGCGAACUCUUAAUUGAUUUCGCGCUAAUUGGUCCGACCCAACAACGACGCUGGUUGAUGUUUAACAAUUUGCAAAUAUAAAUAUUACCAACGGUGUCCAAUUAUGGAUUUCCC
.(((((.(((((.((......)).))))).....((((......)))).......))))).(((((((((..............))))))))).....((.(((((....)))))..)). ( -27.84)
>DroSec_CAF1 14139 120 + 1
CCCAGCAGCGAACUCUUAAUUGAUUUCGCGCUAAUUGGUCCGACCCACCAACGACGCUGGUUGAUGUUUAACAAUUUGCAAAUAUAAAUAUUACCAACGGUGUCCAAUUAUGGAUUUCGC
.(((((.(((((.((......)).))))).....(((((.......)))))....))))).(((((((((..............)))))))))....(((.(((((....))))).))). ( -30.04)
>DroSim_CAF1 14234 120 + 1
CCCAGCAGCGAACUCUUAAUUGAUUUCGCGCUAAUUGGUCCGACCCGACAACGACGCUGGUUGAUGUUUAACAAUUUGCAAAUAUAAAUAUUACCAACGGUGUCCAAUUAUGGAUUUCGC
.(((((.(((((.((......)).)))))))(((((((((......)))...(((((((..(((((((((..............)))))))))....))))))))))))))))....... ( -30.74)
>DroEre_CAF1 13803 120 + 1
CCCGGCAGCGAGCUCUUAAUUGAUUUCGCGCUAAUUGGUGCGACCCACCAGCGACGCUGGUUGAUGUUUAACAAUUUGCAAAUAUAAAUAUUACCAACGGUGUCCAAUUAUGGAUUUCGC
.......(((((.(((((((((...(((((((....))))))).........(((((((..(((((((((..............)))))))))....))))))))))))).))).))))) ( -33.84)
>DroYak_CAF1 13542 120 + 1
UCCGGCAGCGAACUCUUAAUUGAUUUCGUGCUAAUUGGUCCGACCCAACAACUACGCUGGUUGAUGUUUAACAAUUUGCAAAUAUAAAUAUUACCCACGGUGUCCAAUUAUGGAUUUCGC
(((((((.((((.((......)).)))))))(((((((.(((..(((.(......).))).(((((((((..............)))))))))....)))...)))))))))))...... ( -26.34)
>consensus
CCCGGCAGCGAACUCUUAAUUGAUUUCGCGCUAAUUGGUCCGACCCAACAACGACGCUGGUUGAUGUUUAACAAUUUGCAAAUAUAAAUAUUACCAACGGUGUCCAAUUAUGGAUUUCGC
.(((((.(((((.((......)).)))))......(((......)))........))))).(((((((((..............)))))))))....(((.(((((....))))).))). (-27.06 = -26.54 +  -0.52)

alignment

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secondary structure

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Window 1

Location 2,364,644 – 2,364,764
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.50
Mean single sequence MFE -28.58
Consensus MFE -26.48
Energy contribution -26.72
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -2.31
Structure conservation index 0.93
SVM decision value 3.22
SVM RNA-class probability 0.998781
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2364644 120 + 20766785
CGACCCAACAACGACGCUGGUUGAUGUUUAACAAUUUGCAAAUAUAAAUAUUACCAACGGUGUCCAAUUAUGGAUUUCCCAAUGCACUCAUGUGCAUUCAUAUUCAAUUAUCUUCCUGGG
...((((.....(((((((..(((((((((..............)))))))))....)))))))......(((((.....(((((((....)))))))...)))))..........)))) ( -28.64)
>DroSec_CAF1 14179 120 + 1
CGACCCACCAACGACGCUGGUUGAUGUUUAACAAUUUGCAAAUAUAAAUAUUACCAACGGUGUCCAAUUAUGGAUUUCGCAAUGCACUCAUGUGCAUUCAUAUUCAAUUAUCUUCCUGGG
...((((.....(((((((..(((((((((..............)))))))))....)))))))......(((((...(.(((((((....))))))))..)))))..........)))) ( -28.64)
>DroSim_CAF1 14274 120 + 1
CGACCCGACAACGACGCUGGUUGAUGUUUAACAAUUUGCAAAUAUAAAUAUUACCAACGGUGUCCAAUUAUGGAUUUCGCAAUGCACUCAUGUGCAUUCAUAUUCAAUUAUCUUCCUGGG
...(((((((....((.((((.((((((((..............)))))))))))).)).))))......(((((...(.(((((((....))))))))..)))))...........))) ( -28.74)
>DroEre_CAF1 13843 120 + 1
CGACCCACCAGCGACGCUGGUUGAUGUUUAACAAUUUGCAAAUAUAAAUAUUACCAACGGUGUCCAAUUAUGGAUUUCGCAAUGCACUCAUGUGCAUUCAUAUUCAAUUAUCUUCCUGGG
...((((...((((((.((((.((((((((..............)))))))))))).))..(((((....))))).))))(((((((....)))))))..................)))) ( -31.44)
>DroYak_CAF1 13582 120 + 1
CGACCCAACAACUACGCUGGUUGAUGUUUAACAAUUUGCAAAUAUAAAUAUUACCCACGGUGUCCAAUUAUGGAUUUCGCAAUGCACUCAUGUGCAUUCAUAUUCAAUUAUCUUCCUGGA
....(((........(((((.(((((((((..............))))))))).))).((.(((((....))))).))))(((((((....)))))))..................))). ( -25.44)
>consensus
CGACCCAACAACGACGCUGGUUGAUGUUUAACAAUUUGCAAAUAUAAAUAUUACCAACGGUGUCCAAUUAUGGAUUUCGCAAUGCACUCAUGUGCAUUCAUAUUCAAUUAUCUUCCUGGG
...((((.....(((((((..(((((((((..............)))))))))....)))))))......(((((.....(((((((....)))))))...)))))..........)))) (-26.48 = -26.72 +   0.24)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,364,684 – 2,364,804
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.50
Mean single sequence MFE -28.94
Consensus MFE -27.34
Energy contribution -27.54
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 0.94
SVM decision value 1.09
SVM RNA-class probability 0.913206
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2364684 120 + 20766785
AAUAUAAAUAUUACCAACGGUGUCCAAUUAUGGAUUUCCCAAUGCACUCAUGUGCAUUCAUAUUCAAUUAUCUUCCUGGGCGGGCUUGUUAAUUGCUCUUAAAUCUGUGCGAGCCGGAAA
.............(((..((.(((((....)))))...))(((((((....)))))))..................))).(.(((((((..(((.......)))....))))))).)... ( -28.10)
>DroSec_CAF1 14219 120 + 1
AAUAUAAAUAUUACCAACGGUGUCCAAUUAUGGAUUUCGCAAUGCACUCAUGUGCAUUCAUAUUCAAUUAUCUUCCUGGGCGGGCAUGUUAAUUGCUCUUAAAUCUGUGCGAGCCGGAAA
.................(((((((((....))))).(((((((((((....))))))........................(((((.......))))).........))))))))).... ( -29.30)
>DroSim_CAF1 14314 120 + 1
AAUAUAAAUAUUACCAACGGUGUCCAAUUAUGGAUUUCGCAAUGCACUCAUGUGCAUUCAUAUUCAAUUAUCUUCCUGGGCGGGCAUGUUAAUUGCUCUUAAAUCUGUGCGAGCCGGAAA
.................(((((((((....))))).(((((((((((....))))))........................(((((.......))))).........))))))))).... ( -29.30)
>DroEre_CAF1 13883 120 + 1
AAUAUAAAUAUUACCAACGGUGUCCAAUUAUGGAUUUCGCAAUGCACUCAUGUGCAUUCAUAUUCAAUUAUCUUCCUGGGCGGGCAUGUUAAUUGCUCUUAAAUCUGUGCGAGCCGGAAA
.................(((((((((....))))).(((((((((((....))))))........................(((((.......))))).........))))))))).... ( -29.30)
>DroYak_CAF1 13622 120 + 1
AAUAUAAAUAUUACCCACGGUGUCCAAUUAUGGAUUUCGCAAUGCACUCAUGUGCAUUCAUAUUCAAUUAUCUUCCUGGACGGGCUUGUUAAUUGCUCUUAAAUCUGUGCGAGCCGGAAA
.................(((((((((....))))).(((((((((((....)))))).......((((((.(..(((....)))...).))))))............))))))))).... ( -28.70)
>consensus
AAUAUAAAUAUUACCAACGGUGUCCAAUUAUGGAUUUCGCAAUGCACUCAUGUGCAUUCAUAUUCAAUUAUCUUCCUGGGCGGGCAUGUUAAUUGCUCUUAAAUCUGUGCGAGCCGGAAA
.................(((((((((....))))).(((((((((((....)))))).......((((((.(..(((....)))...).))))))............))))))))).... (-27.34 = -27.54 +   0.20)

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 09:37:14 2006