Locus 573

Sequence ID 2L_DroMel_CAF1
Location 1,765,508 – 1,765,609
Length 101
Max. P 0.775201
window944 window945

overview

Window 4

Location 1,765,508 – 1,765,609
Length 101
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 76.52
Mean single sequence MFE -24.00
Consensus MFE -17.36
Energy contribution -17.68
Covariance contribution 0.31
Combinations/Pair 1.11
Mean z-score -1.60
Structure conservation index 0.72
SVM decision value 0.48
SVM RNA-class probability 0.751595
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1765508 101 + 22407834
UAU---CGUUUUGGGCAUUCCAGUACUCACUGCAAAAAUGCAAAUAUUAAAACU---AUGAAU------GUGAGUGCUCUUUUCCCACCCUUUAAA-CUUUCAGCUAGUGAGUC
...---.....((((......(((((((((((((....))))....(((.....---.)))..------))))))))).....))))........(-(((.(.....).)))). ( -19.10)
>DroSec_CAF1 22564 105 + 1
UAU---GGUUUUGGGCAUUCCAGCACUCACUGCAAAAAUGCAAAUAUUAAAACUGUUAUGAGU------GUGAGUGCUCCUUUCCCACCCUUUAAUUCUCUCUGCUGGCGAGUC
...---((...((((......(((((((((((((....)))).........(((......)))------))))))))).....)))).)).......(((((....)).))).. ( -25.40)
>DroEre_CAF1 22330 86 + 1
U-----GGGUUUGGACAUUCCAGCACUCACUGCAAAAAUGCAAAUAUUAAAACUGUUAUGAAU------GUGAGUGCUACUUUCC-----------------CGCUGGUGAGUC
.-----(((...((.....))(((((((((((((....))))((((.......))))......------))))))))).....))-----------------)........... ( -22.50)
>DroYak_CAF1 31454 114 + 1
UCCCGUAUAUUUGGACAUUCCAGCACUCACUGCACAAAUGCAAAUAUUAAAACUGUUAUGAAUGCGAGUGUGAGUGCUACUUUUCCACACUUUAAUCCUCACCGCUGGUGAGUC
...........((((......(((((((((((((....)))).........(((((.......)).)))))))))))).....))))..........((((((...)))))).. ( -29.00)
>consensus
UAU___GGUUUUGGACAUUCCAGCACUCACUGCAAAAAUGCAAAUAUUAAAACUGUUAUGAAU______GUGAGUGCUACUUUCCCACCCUUUAAU_CUCUCCGCUGGUGAGUC
...........((((......(((((((((((((....))))..........(......).........))))))))).....))))........................... (-17.36 = -17.68 +   0.31)

alignment

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secondary structure

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dotplot

Postscript

Window 5

Location 1,765,508 – 1,765,609
Length 101
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 76.52
Mean single sequence MFE -26.38
Consensus MFE -17.89
Energy contribution -18.70
Covariance contribution 0.81
Combinations/Pair 1.10
Mean z-score -1.70
Structure conservation index 0.68
SVM decision value 0.54
SVM RNA-class probability 0.775201
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1765508 101 - 22407834
GACUCACUAGCUGAAAG-UUUAAAGGGUGGGAAAAGAGCACUCAC------AUUCAU---AGUUUUAAUAUUUGCAUUUUUGCAGUGAGUACUGGAAUGCCCAAAACG---AUA
.(((((((.((.(((((-(.(((((((((.........)))))((------......---.)).......)))).)))))))))))))))..(((.....))).....---... ( -19.40)
>DroSec_CAF1 22564 105 - 1
GACUCGCCAGCAGAGAGAAUUAAAGGGUGGGAAAGGAGCACUCAC------ACUCAUAACAGUUUUAAUAUUUGCAUUUUUGCAGUGAGUGCUGGAAUGCCCAAAACC---AUA
..(((.......))).........((.((((.....(((((((((------(((......))).........((((....)))))))))))))......))))...))---... ( -30.80)
>DroEre_CAF1 22330 86 - 1
GACUCACCAGCG-----------------GGAAAGUAGCACUCAC------AUUCAUAACAGUUUUAAUAUUUGCAUUUUUGCAGUGAGUGCUGGAAUGUCCAAACCC-----A
...........(-----------------((.....(((((((((------.....(((.....))).....((((....)))))))))))))((.....))...)))-----. ( -24.40)
>DroYak_CAF1 31454 114 - 1
GACUCACCAGCGGUGAGGAUUAAAGUGUGGAAAAGUAGCACUCACACUCGCAUUCAUAACAGUUUUAAUAUUUGCAUUUGUGCAGUGAGUGCUGGAAUGUCCAAAUAUACGGGA
..((((((...))))))..........((((....(((((((((((((............))).........((((....)))))))))))))).....))))........... ( -30.90)
>consensus
GACUCACCAGCGGAGAG_AUUAAAGGGUGGGAAAGGAGCACUCAC______AUUCAUAACAGUUUUAAUAUUUGCAUUUUUGCAGUGAGUGCUGGAAUGCCCAAAACC___AUA
...........................((((....((((((((((...............(((......)))((((....)))))))))))))).....))))........... (-17.89 = -18.70 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:01 2006