Locus 1950

Sequence ID 3L_DroMel_CAF1
Location 5,402,299 – 5,402,459
Length 160
Max. P 0.988107
window3050 window3051

overview

Window 0

Location 5,402,299 – 5,402,419
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.28
Mean single sequence MFE -33.80
Consensus MFE -31.73
Energy contribution -32.40
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.21
Structure conservation index 0.94
SVM decision value 2.11
SVM RNA-class probability 0.988107
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5402299 120 + 23771897
AAUGAACUUGGCAAACCGAAAGCCGAGAGCCGAAAACAACCAACGGCCAAACAAGCAACCAGUCAUAACCCCCUUCAUUGCUGGGGGAUUUCCCAUUUCCCGGUAAUGAAAUGAAGCAAC
.((((.((((((.........)))))).((((...........))))...............)))).......((((((((((((..((.....))..)))))))))))).......... ( -35.30)
>DroSec_CAF1 51031 117 + 1
AAUGAACUUGGCAAACCGAAAGCCGAGAGCCGAAAACAACCAACGGCCAAACAAGUAACCAGUCAUAACCCCCUUCAUUGCUUGGGGAUUUCCCAUUUCCCGGUAAUGAAA---AGCAAC
.((((.((((((.........)))))).((((...........))))...............)))).......(((((((((.(((((........)))))))))))))).---...... ( -30.70)
>DroYak_CAF1 51286 117 + 1
AAUGAACUUGGCAAACCGAAAGCCGAUCGCCGAAUACAACCAACGGCCAAACAGCCAACCAGUCAUAACCCCGUUCAUUGCUGGGGGAUUUCCCAUUUCCCGGUAAUGAAA---AGCAAG
.((((..(((((....(....)......((((...........))))......)))))....)))).......((((((((((((..((.....))..)))))))))))).---...... ( -35.40)
>consensus
AAUGAACUUGGCAAACCGAAAGCCGAGAGCCGAAAACAACCAACGGCCAAACAAGCAACCAGUCAUAACCCCCUUCAUUGCUGGGGGAUUUCCCAUUUCCCGGUAAUGAAA___AGCAAC
.((((.((((((.........)))))).((((...........))))...............)))).......((((((((((((..((.....))..)))))))))))).......... (-31.73 = -32.40 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 5,402,339 – 5,402,459
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.40
Mean single sequence MFE -29.44
Consensus MFE -28.39
Energy contribution -28.50
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.90
Structure conservation index 0.96
SVM decision value 0.84
SVM RNA-class probability 0.863476
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5402339 120 + 23771897
CAACGGCCAAACAAGCAACCAGUCAUAACCCCCUUCAUUGCUGGGGGAUUUCCCAUUUCCCGGUAAUGAAAUGAAGCAACCUGCAUUGCGUACGCCCAUUGUUCCCCGACCACUAAAAUG
...(((...(((((((......((((.......((((((((((((..((.....))..)))))))))))))))).((((......))))....))...)))))..)))............ ( -31.11)
>DroSec_CAF1 51071 117 + 1
CAACGGCCAAACAAGUAACCAGUCAUAACCCCCUUCAUUGCUUGGGGAUUUCCCAUUUCCCGGUAAUGAAA---AGCAACCUGCAUUGCGUACGCCCAUUGUUCCCCGACCACUAAAAUG
...(((...(((((.......(((.........(((((((((.(((((........)))))))))))))).---.((((......))))).)).....)))))..)))............ ( -25.30)
>DroYak_CAF1 51326 117 + 1
CAACGGCCAAACAGCCAACCAGUCAUAACCCCGUUCAUUGCUGGGGGAUUUCCCAUUUCCCGGUAAUGAAA---AGCAAGCUGCAUUGCGUACGCCCAUUGUUCCCCGACCACUAAAACG
....(((......))).....(((.........((((((((((((..((.....))..)))))))))))).---.((((......))))..................))).......... ( -31.90)
>consensus
CAACGGCCAAACAAGCAACCAGUCAUAACCCCCUUCAUUGCUGGGGGAUUUCCCAUUUCCCGGUAAUGAAA___AGCAACCUGCAUUGCGUACGCCCAUUGUUCCCCGACCACUAAAAUG
...(((...(((((...................((((((((((((..((.....))..)))))))))))).....((((......)))).........)))))..)))............ (-28.39 = -28.50 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:52 2006