Locus 1701

Sequence ID 3R_DroMel_CAF1
Location 4,880,062 – 4,880,159
Length 97
Max. P 0.999630
window2801 window2802

overview

Window 1

Location 4,880,062 – 4,880,159
Length 97
Sequences 3
Columns 97
Reading direction forward
Mean pairwise identity 76.34
Mean single sequence MFE -19.03
Consensus MFE -14.13
Energy contribution -14.47
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.49
Structure conservation index 0.74
SVM decision value 0.76
SVM RNA-class probability 0.844562
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4880062 97 + 27905053
UCUUGUUUUAUUUUUCUUUUCCGCUGCCUCUUUAAUUUUCAUUUGCGCCCGUUGAGCAUUGGAGCUCAACUGAGGCCGCAUGACCGAAAGCAAUGAG
(((((((((.....((......((.(((((..(((.......))).....(((((((......))))))).))))).))..))...))))))).)). ( -22.90)
>DroPse_CAF1 361 85 + 1
-----------UCUCCCUCUCC-CUCCUCCACCAUCUCGCUCUCGCUCCCGUUGAGCAUUGGAGCUCAACUGAUGCCUCAUGACCAAAAGCAAUGAG
-----------...........-.........((((..((....))....(((((((......))))))).)))).(((((...........))))) ( -17.10)
>DroPer_CAF1 355 85 + 1
-----------UCUCCCUCUCC-CUCCUCCUCCAUCUCGCUCUCGCUCCCGUUGAGCAUUGGAGCUCAACUGAUGCCUCAUGACCAAAAGCAAUGAG
-----------...........-.........((((..((....))....(((((((......))))))).)))).(((((...........))))) ( -17.10)
>consensus
___________UCUCCCUCUCC_CUCCUCCUCCAUCUCGCUCUCGCUCCCGUUGAGCAUUGGAGCUCAACUGAUGCCUCAUGACCAAAAGCAAUGAG
............................................((..(.(((((((......))))))).)..))(((((...(....)..))))) (-14.13 = -14.47 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 4,880,062 – 4,880,159
Length 97
Sequences 3
Columns 97
Reading direction reverse
Mean pairwise identity 76.34
Mean single sequence MFE -28.87
Consensus MFE -19.81
Energy contribution -19.70
Covariance contribution -0.11
Combinations/Pair 1.11
Mean z-score -2.85
Structure conservation index 0.69
SVM decision value 3.81
SVM RNA-class probability 0.999630
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4880062 97 - 27905053
CUCAUUGCUUUCGGUCAUGCGGCCUCAGUUGAGCUCCAAUGCUCAACGGGCGCAAAUGAAAAUUAAAGAGGCAGCGGAAAAGAAAAAUAAAACAAGA
........((((..((.(((.(((((.(((((((......))))))).......(((....)))...))))).)))))...))))............ ( -28.80)
>DroPse_CAF1 361 85 - 1
CUCAUUGCUUUUGGUCAUGAGGCAUCAGUUGAGCUCCAAUGCUCAACGGGAGCGAGAGCGAGAUGGUGGAGGAG-GGAGAGGGAGA-----------
(((....(((((..((....(.((((.(((((((......)))))))....((....))..)))).)....)).-.))))).))).----------- ( -28.30)
>DroPer_CAF1 355 85 - 1
CUCAUUGCUUUUGGUCAUGAGGCAUCAGUUGAGCUCCAAUGCUCAACGGGAGCGAGAGCGAGAUGGAGGAGGAG-GGAGAGGGAGA-----------
(((.(((((((((.((.(((....)))(((((((......)))))))..)).)))))))))....)))......-...........----------- ( -29.50)
>consensus
CUCAUUGCUUUUGGUCAUGAGGCAUCAGUUGAGCUCCAAUGCUCAACGGGAGCGAGAGCGAGAUGGAGGAGGAG_GGAGAGGGAGA___________
....((((((((.(((....)))....(((((((......))))))))))))))).......................................... (-19.81 = -19.70 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:13 2006