Locus 384

Sequence ID 3L_DroMel_CAF1
Location 1,106,898 – 1,107,034
Length 136
Max. P 0.894974
window564 window565 window566

overview

Window 4

Location 1,106,898 – 1,106,997
Length 99
Sequences 3
Columns 105
Reading direction forward
Mean pairwise identity 88.00
Mean single sequence MFE -30.37
Consensus MFE -28.70
Energy contribution -28.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.74
Structure conservation index 0.95
SVM decision value 0.98
SVM RNA-class probability 0.894974
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1106898 99 + 23771897
ACUCUACACACUCUACACACUCCAAUUCGGAGGCCGUCCGUCAAUGUCCAUGUCCUGCUGCUGGACAUUGGCGAAAAAUGCGUUAGCCAACGUUGCCGG------
...................((((.....)))).(((..((((((((((((.((......))))))))))))))......(((((....)))))...)))------ ( -29.60)
>DroSec_CAF1 390 90 + 1
ACUC---------UACACACUCCAAUUCGGAGGCCGUCCGUCAAUGUCCAUGUCCUGCUGCUGGACAUUGGCGAAAAAUGCGUUAGCCAACGUUGCCGC------
....---------......((((.....))))......((((((((((((.((......))))))))))))))......(((.((((....)))).)))------ ( -29.00)
>DroYak_CAF1 229 96 + 1
UCUC---------CACACACUCCAAUUCGGAGGCCGUCCGUCAAUGUCCAUGUCCUGCUGCUGGACAUUGGCGAAAAAUGCGUUAGCCAACGUUGCCGGUUGCCG
....---------..............(((..((((..((((((((((((.((......))))))))))))))......(((((....)))))...))))..))) ( -32.50)
>consensus
ACUC_________UACACACUCCAAUUCGGAGGCCGUCCGUCAAUGUCCAUGUCCUGCUGCUGGACAUUGGCGAAAAAUGCGUUAGCCAACGUUGCCGG______
....................(((.....)))(((....((((((((((((.((......))))))))))))))......(((((....))))).)))........ (-28.70 = -28.70 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,106,937 – 1,107,034
Length 97
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.33
Mean single sequence MFE -39.42
Consensus MFE -22.19
Energy contribution -21.82
Covariance contribution -0.37
Combinations/Pair 1.11
Mean z-score -2.39
Structure conservation index 0.56
SVM decision value 0.82
SVM RNA-class probability 0.858944
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1106937 97 + 23771897
GUCAAUGUCC-------------AUGUCCUGCUGCUGGACAUUGGCGAAAAAUGCGUUAGCCA-ACGUUGCCGG-------UU--GCCGGCUUCCUCGCCGAGGAAAAGUAGAAGGCAAA
((((((((((-------------(.((......))))))))))))).............(((.-.....(((((-------..--.)))))((((((...))))))........)))... ( -36.90)
>DroPse_CAF1 490 118 + 1
GUCAAUGUCCAUGUCCAGUGUCCAUGUCCUGGUGCUGGACAUUGGCGAAAAAUGCGUUAGCCAAACGACGCCGC-CGCCA-UCGAGGAGUCGUCCGGGACUCUGGAAAGUAGAAGGCAAA
(((((((((((.((((((.(.......))))).))))))))))))).............(((...((((.((..-((...-.)).)).))))(((((....)))))........)))... ( -42.40)
>DroSec_CAF1 420 97 + 1
GUCAAUGUCC-------------AUGUCCUGCUGCUGGACAUUGGCGAAAAAUGCGUUAGCCA-ACGUUGCCGC-------UU--GCCGACUUCCUCGCCGAGGAAAAGUAGAAGGCAAA
((((((((((-------------(.((......))))))))))))).......(((.((((..-..)))).)))-------((--(((.((((((((...)))))..)))....))))). ( -35.90)
>DroYak_CAF1 259 104 + 1
GUCAAUGUCC-------------AUGUCCUGCUGCUGGACAUUGGCGAAAAAUGCGUUAGCCA-ACGUUGCCGGUUGCCGGUU--GCCGGCUUCCUCGCCGAGCAAAAGUAGAAGGCAAA
((((((((((-------------(.((......))))))))))))).......(((((....)-))))((((..((((...((--((((((......)))).))))..))))..)))).. ( -42.50)
>consensus
GUCAAUGUCC_____________AUGUCCUGCUGCUGGACAUUGGCGAAAAAUGCGUUAGCCA_ACGUUGCCGC_______UU__GCCGGCUUCCUCGCCGAGGAAAAGUAGAAGGCAAA
((((((((((..........................)))))))))).............(((...((....))..............((((......)))).............)))... (-22.19 = -21.82 +  -0.37)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,106,937 – 1,107,034
Length 97
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.33
Mean single sequence MFE -35.85
Consensus MFE -23.61
Energy contribution -21.80
Covariance contribution -1.81
Combinations/Pair 1.29
Mean z-score -1.74
Structure conservation index 0.66
SVM decision value 0.25
SVM RNA-class probability 0.652894
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1106937 97 - 23771897
UUUGCCUUCUACUUUUCCUCGGCGAGGAAGCCGGC--AA-------CCGGCAACGU-UGGCUAACGCAUUUUUCGCCAAUGUCCAGCAGCAGGACAU-------------GGACAUUGAC
...............(((..((((((((((((((.--..-------))))).....-..((....)).))))))))).((((((.......))))))-------------)))....... ( -34.00)
>DroPse_CAF1 490 118 - 1
UUUGCCUUCUACUUUCCAGAGUCCCGGACGACUCCUCGA-UGGCG-GCGGCGUCGUUUGGCUAACGCAUUUUUCGCCAAUGUCCAGCACCAGGACAUGGACACUGGACAUGGACAUUGAC
.......((((...(((((.((((((((((((.(((((.-...))-).)).))))))))((....))...........((((((.......)))))))))).)))))..))))....... ( -40.50)
>DroSec_CAF1 420 97 - 1
UUUGCCUUCUACUUUUCCUCGGCGAGGAAGUCGGC--AA-------GCGGCAACGU-UGGCUAACGCAUUUUUCGCCAAUGUCCAGCAGCAGGACAU-------------GGACAUUGAC
...............(((..(((((((((((..((--.(-------(((....)))-).))..))...))))))))).((((((.......))))))-------------)))....... ( -33.20)
>DroYak_CAF1 259 104 - 1
UUUGCCUUCUACUUUUGCUCGGCGAGGAAGCCGGC--AACCGGCAACCGGCAACGU-UGGCUAACGCAUUUUUCGCCAAUGUCCAGCAGCAGGACAU-------------GGACAUUGAC
....................((((((((((((((.--..)))))...((....)).-..((....)).)))))))))((((((((.(.....)...)-------------)))))))... ( -35.70)
>consensus
UUUGCCUUCUACUUUUCCUCGGCGAGGAAGCCGGC__AA_______CCGGCAACGU_UGGCUAACGCAUUUUUCGCCAAUGUCCAGCAGCAGGACAU_____________GGACAUUGAC
..((((........((..(((((......)))))...)).........)))).......((....)).........((((((((..........................)))))))).. (-23.61 = -21.80 +  -1.81)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:37 2006