Locus 1644

Sequence ID X_DroMel_CAF1
Location 4,663,120 – 4,663,336
Length 216
Max. P 0.960653
window2696 window2697 window2698 window2699

overview

Window 6

Location 4,663,120 – 4,663,220
Length 100
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 88.61
Mean single sequence MFE -26.30
Consensus MFE -19.61
Energy contribution -19.67
Covariance contribution 0.06
Combinations/Pair 1.19
Mean z-score -2.06
Structure conservation index 0.75
SVM decision value 0.69
SVM RNA-class probability 0.823079
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4663120 100 + 22224390
AGUUCAUCAGCUUACUGUUCGCCA--GACCCCCGAAGGCCUUUCCAAGCCACCUUUUGGAAUGGGCCCAGUUCAUUGCCGAAUAAUGAACAUAACAAAUCAA
.(((((((.((..((((((((...--......))))((((((((((((......))))))).))))))))).....)).))....)))))............ ( -25.40)
>DroSec_CAF1 24448 99 + 1
AGUUCUUCAGCUUACUGUUCGCCA--GAACCCCGAAGGCCUUUCCAAGCCAACC-CUGGAAUGGGGCCACUUCAUUGCCGAAUAAUGAACAUAACAAAUCAA
.(((((((.((.....((((....--))))...(((((((...(((..(((...-.)))..)))))))..)))...)).)))....))))............ ( -22.90)
>DroEre_CAF1 25235 100 + 1
AGUUCAUCAGCUUUCUGUUCGCCA--GACCCCCGAAGGCCUUUCCAUGCCACCCCGUGGAAUGGGGCCAGUUCAUUGCCGAAUAAUGAACAUAACAAAUCAA
.............((((.....))--)).....((.((((((((((((......)))))))..))))).((((((((.....))))))))........)).. ( -26.60)
>DroYak_CAF1 21590 101 + 1
AGUUCAUCAGCUUACUGUUCGGCGAAAGCCCCCAAAGGUCUUGCCAUGCCACCCCA-GGAAUGGGGCCUGUUCAUUGCCGAAUAAUGAACAUAACAAAUCAA
.((((((........((((((((((.((.(((((..((.....))...((......-))..))))).)).....))))))))))))))))............ ( -30.30)
>consensus
AGUUCAUCAGCUUACUGUUCGCCA__GACCCCCGAAGGCCUUUCCAAGCCACCCCAUGGAAUGGGGCCAGUUCAUUGCCGAAUAAUGAACAUAACAAAUCAA
.((((((........((((((.((..((((((((..(((........))).((....))..)))))...)))...)).))))))))))))............ (-19.61 = -19.67 +   0.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,663,142 – 4,663,260
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.78
Mean single sequence MFE -41.70
Consensus MFE -30.77
Energy contribution -33.52
Covariance contribution 2.75
Combinations/Pair 1.15
Mean z-score -2.97
Structure conservation index 0.74
SVM decision value 1.52
SVM RNA-class probability 0.960653
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4663142 118 + 22224390
CA--GACCCCCGAAGGCCUUUCCAAGCCACCUUUUGGAAUGGGCCCAGUUCAUUGCCGAAUAAUGAACAUAACAAAUCAACGGCUCGUCAUUAGGCGAGCCCCAGCAAAAUGGGGCUAGG
.(--(.((((.((.((((((((((((......))))))).)))))..((((((((.....))))))))........))...((((((((....))))))))..........))))))... ( -45.20)
>DroSec_CAF1 24470 117 + 1
CA--GAACCCCGAAGGCCUUUCCAAGCCAACC-CUGGAAUGGGGCCACUUCAUUGCCGAAUAAUGAACAUAACAAAUCAACGGCUCGUCAUUAGGCGAGCCCCAGUAAAAUGGGGCUAGG
..--...((((((.((((...(((..(((...-.)))..)))))))..(((((((.....))))))).........))...((((((((....))))))))..........))))..... ( -39.60)
>DroEre_CAF1 25257 114 + 1
CA--GACCCCCGAAGGCCUUUCCAUGCCACCCCGUGGAAUGGGGCCAGUUCAUUGCCGAAUAAUGAACAUAACAAAUCAACGGCUCGUCAUUAGGCC----CCGGUAAAAUGGGGCUAGG
..--(((..(((..((((((((((((......)))))))..))))).((((((((.....))))))))............)))...)))....((((----(((......)))))))... ( -43.70)
>DroYak_CAF1 21612 117 + 1
CGAAAGCCCCCAAAGGUCUUGCCAUGCCACCCCA-GGAAUGGGGCCUGUUCAUUGCCGAAUAAUGAACAUAACAAAUCAACGGCUCGUCAUUAGGCC--CCCCAGUGAAAUGGGGCUAGG
....((((((....((.....))..(((.(((((-....)))))..(((((((((.....)))))))))............)))...(((((.((..--..)))))))...))))))... ( -38.30)
>consensus
CA__GACCCCCGAAGGCCUUUCCAAGCCACCCCAUGGAAUGGGGCCAGUUCAUUGCCGAAUAAUGAACAUAACAAAUCAACGGCUCGUCAUUAGGCC__CCCCAGUAAAAUGGGGCUAGG
.......(((((..((((((((((((......)))))))..))))).((((((((.....)))))))).............((((((((....)))))))).........)))))..... (-30.77 = -33.52 +   2.75)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,663,180 – 4,663,296
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.13
Mean single sequence MFE -29.55
Consensus MFE -20.34
Energy contribution -22.65
Covariance contribution 2.31
Combinations/Pair 1.03
Mean z-score -2.56
Structure conservation index 0.69
SVM decision value 1.12
SVM RNA-class probability 0.917899
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4663180 116 - 22224390
CCCAUUCCCAUUCCCAUUCCCAUUCCCG----UUCGCAUUCCUAGCCCCAUUUUGCUGGGGCUCGCCUAAUGACGAGCCGUUGAUUUGUUAUGUUCAUUAUUCGGCAAUGAACUGGGCCC
........................((((----((((.......(((((((......))))))).(((.(((((.((((...(((....))).)))).))))).)))..))))).)))... ( -31.40)
>DroSec_CAF1 24507 108 - 1
CCCAUUCCCAUUCGCAUUUC------------UUCGCAUUCCUAGCCCCAUUUUACUGGGGCUCGCCUAAUGACGAGCCGUUGAUUUGUUAUGUUCAUUAUUCGGCAAUGAAGUGGCCCC
..............((((((------------.(((((((.(.(((((((......))))))).)...)))).)))((((.(((..........))).....))))...))))))..... ( -29.20)
>DroEre_CAF1 25295 116 - 1
CCCAUUCCCAUUCCCAUUCCAGUUCCCAUUUCUUCGCAUUCCUAGCCCCAUUUUACCGG----GGCCUAAUGACGAGCCGUUGAUUUGUUAUGUUCAUUAUUCGGCAAUGAACUGGCCCC
..................(((((((........(((((((....(((((........))----)))..)))).)))((((.(((..........))).....))))...))))))).... ( -31.00)
>DroYak_CAF1 21651 118 - 1
CCCAUUCCCAUUUCUAUUCCCGUUUCCAUUUCUUUGCAUUCCUAGCCCCAUUUCACUGGGG--GGCCUAAUGACGAGCCGUUGAUUUGUUAUGUUCAUUAUUCGGCAAUGAACAGGCCCC
..............................................((((......))))(--(((((.((((((((.......))))))))(((((((.......))))))))))))). ( -26.60)
>consensus
CCCAUUCCCAUUCCCAUUCCCGUUCCCA____UUCGCAUUCCUAGCCCCAUUUUACUGGGG__CGCCUAAUGACGAGCCGUUGAUUUGUUAUGUUCAUUAUUCGGCAAUGAACUGGCCCC
.((((((..........................(((((((.(((((((((......)))))))))...)))).)))((((.(((..........))).....))))...))).))).... (-20.34 = -22.65 +   2.31)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,663,220 – 4,663,336
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.97
Mean single sequence MFE -31.96
Consensus MFE -21.25
Energy contribution -22.88
Covariance contribution 1.62
Combinations/Pair 1.06
Mean z-score -1.67
Structure conservation index 0.66
SVM decision value 0.05
SVM RNA-class probability 0.560764
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4663220 116 + 22224390
CGGCUCGUCAUUAGGCGAGCCCCAGCAAAAUGGGGCUAGGAAUGCGAA----CGGGAAUGGGAAUGGGAAUGGGAAUGGGACCUAUGCAUAAUUUUUCAGCUCACUGAAGCAAAAACAAA
.((((((((....))))))))(((((........))).))..(((...----(((((.((..((...(.(((((.......))))).).....))..))..)).)))..)))........ ( -33.00)
>DroSec_CAF1 24547 108 + 1
CGGCUCGUCAUUAGGCGAGCCCCAGUAAAAUGGGGCUAGGAAUGCGAA------------GAAAUGCGAAUGGGAAUGGGUCCUAUGCAUAAUUUUUCAGCUCACUGAAGCAAAAACAAA
.((((((((....))))))))(((......))).(((.((...(((((------------(((((((..((((((.....))))))))))..)))))).))...))..)))......... ( -35.00)
>DroEre_CAF1 25335 116 + 1
CGGCUCGUCAUUAGGCC----CCGGUAAAAUGGGGCUAGGAAUGCGAAGAAAUGGGAACUGGAAUGGGAAUGGGAAUGGGUCCUAUGCAUAAUUUUUCAGCUCACUGAAGCAAAAACAAA
..(((((.((((.((((----(((......)))))))...)))))))......((((.((((((.....((((((.....))))))........)))))).)).))...))......... ( -32.02)
>DroYak_CAF1 21691 118 + 1
CGGCUCGUCAUUAGGCC--CCCCAGUGAAAUGGGGCUAGGAAUGCAAAGAAAUGGAAACGGGAAUAGAAAUGGGAAUGGGUCCUAUGCAUAAUUUUUCAGCUCACUGAAGCAAAAACAAA
.((((........))))--(((((......)))))......((((.......((....)).........((((((.....))))))))))....((((((....)))))).......... ( -27.80)
>consensus
CGGCUCGUCAUUAGGCC__CCCCAGUAAAAUGGGGCUAGGAAUGCGAA____UGGGAACGGGAAUGGGAAUGGGAAUGGGUCCUAUGCAUAAUUUUUCAGCUCACUGAAGCAAAAACAAA
..(((((.((((.....(((((((......)))))))...)))))))..............((((....((((((.....)))))).....))))(((((....)))))))......... (-21.25 = -22.88 +   1.62)

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 10:15:34 2006