Locus 2353

Sequence ID X_DroMel_CAF1
Location 6,283,707 – 6,283,867
Length 160
Max. P 0.751328
window3830 window3831

overview

Window 0

Location 6,283,707 – 6,283,827
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 84.70
Mean single sequence MFE -34.83
Consensus MFE -25.61
Energy contribution -27.17
Covariance contribution 1.56
Combinations/Pair 1.07
Mean z-score -1.77
Structure conservation index 0.74
SVM decision value 0.02
SVM RNA-class probability 0.541578
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6283707 120 + 22224390
GGAAGCUUUUCAAGUUUAGGCCAACUAACGUAUGCCGGCAACGCUUGAAAGAUGGCCGCGAUAAUGAGAGCGGCACAUAAAACAAUCAAGGUGCCUCCACACUCCAUGGAUGGAGGGGCG
.((...(((((((((...(((..((....))..)))(....))))))))))((((((((..........))))).))).......))...((.((((((..(.....)..)))))).)). ( -41.80)
>DroSec_CAF1 20679 107 + 1
GGAAGCUUUUCAAGUUUAGGCCAACUAACGUAUGCCGGCAACGCUUGAAAGAUGGCCGCGAUAAUGAGAGCGGCACAUAAAACAAUCAAGGUGGCUC-------UAUGGAAGGG------
.....(((((((......(((..((....))..)))(((.((.(((((...((((((((..........))))).))).......))))))).))).-------..))))))).------ ( -31.50)
>DroYak_CAF1 17774 110 + 1
GGAAGCUUUUCAAGUUUAGGCCAACUAACGUAUGCCGGCAACGUUUGAAAGAUGGCCGCGAUAAUGAGAGCGGCACAUAAAACAAUCAAGGUGGCCG-------UGCAAA---AGGGGGG
.....(((..(..(((.((.....)))))...(((((((.((.(((((...((((((((..........))))).))).......))))))).))))-------.)))..---.)..))) ( -31.20)
>consensus
GGAAGCUUUUCAAGUUUAGGCCAACUAACGUAUGCCGGCAACGCUUGAAAGAUGGCCGCGAUAAUGAGAGCGGCACAUAAAACAAUCAAGGUGGCUC_______UAUGGA_GGAGGGG_G
((..(((((((((((...(((..((....))..)))(....))))))))).((((((((..........))))).)))...........)))..))........................ (-25.61 = -27.17 +   1.56)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,283,747 – 6,283,867
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 72.38
Mean single sequence MFE -20.52
Consensus MFE -12.77
Energy contribution -13.10
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.47
Structure conservation index 0.62
SVM decision value 0.48
SVM RNA-class probability 0.751328
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6283747 120 - 22224390
CUCCCCCUCCCUCGUUCCUCUAACAGCCAAUACCCCGCCGCGCCCCUCCAUCCAUGGAGUGUGGAGGCACCUUGAUUGUUUUAUGUGCCGCUCUCAUUAUCGCGGCCAUCUUUCAAGCGU
....................................(((...((((((((....))))).).)).)))(((((((..(....(((.(((((..........)))))))))..))))).)) ( -30.00)
>DroSec_CAF1 20719 93 - 1
AUCCCCC---------CCUCUAACAGCCAAUCCCC-----------CCCUUCCAUA-------GAGCCACCUUGAUUGUUUUAUGUGCCGCUCUCAUUAUCGCGGCCAUCUUUCAAGCGU
.......---------.(((((.............-----------........))-------)))..(((((((..(....(((.(((((..........)))))))))..))))).)) ( -16.50)
>DroYak_CAF1 17814 99 - 1
A-CCCCC---------CUUCUAGCAGCCAAUCC-CCGCCUCCCCCCU---UUUGCA-------CGGCCACCUUGAUUGUUUUAUGUGCCGCUCUCAUUAUCGCGGCCAUCUUUCAAACGU
.-.....---------.....((((..(((...-..(((........---......-------.)))....)))..))))..(((.(((((..........))))))))........... ( -15.06)
>consensus
AUCCCCC_________CCUCUAACAGCCAAUCCCCCGCC_C_CCCCUCC_UCCAUA_______GAGCCACCUUGAUUGUUUUAUGUGCCGCUCUCAUUAUCGCGGCCAUCUUUCAAGCGU
....................................................................(((((((..(....(((.(((((..........)))))))))..))))).)) (-12.77 = -13.10 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:31 2006