Locus 2663

Sequence ID	2L_DroMel_CAF1
Location	7,467,462 – 7,467,602
Length	140
Max. P	0.948945

overview

Window 2

Location	7,467,462 – 7,467,562
Length	100
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	91.37
Mean single sequence MFE	-30.38
Consensus MFE	-23.88
Energy contribution	-25.72
Covariance contribution	1.84
Combinations/Pair	1.04
Mean z-score	-2.20
Structure conservation index	0.79
SVM decision value	1.39
SVM RNA-class probability	0.948945
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7467462 100 - 22407834
ACCAAAAGAGGACAGCUGCUAGUCCUCCUCCGCAAUUGCGGAUGAUGGGAAAAUUCACGGCAUUGAAAUUGUUAAACCGUUGACCUGUCAAAGCCGACUU
.(((...((((((........)))))).(((((....)))))...))).........((((.((((....(((((....)))))...)))).)))).... ( -33.20)
>DroSec_CAF1 62954 100 - 1
ACCAAAAGAGGACAGCUGUUAGUCCUCCUCCGCAAUUGCGGAUGAUGGGAAAAUUCACGGCAUUGAAAUUGUUAAACCGUUGACCUGUCCAAGCCGACUU
.(((...((((((........)))))).(((((....)))))...))).........((((.(((.....(((((....))))).....))))))).... ( -30.00)
>DroSim_CAF1 65422 100 - 1
ACCAAAAGAGGACAGCUGUUAGUCCUCCUCCGCAAUUGCGGAUGAUGGGAAAAUUUACGGCAUUGAAAUUGUUAAACCGUUGACCUGUCAAAGCCGACUU
.(((...((((((........)))))).(((((....)))))...))).........((((.((((....(((((....)))))...)))).)))).... ( -33.20)
>DroEre_CAF1 66624 95 - 1
GCCAAAAGAGGACAGCUGUGAGUCCUCCUCCGCAAUUGCG----AUGGGAAAAUUCACGGCAUUGAAAUGGUUAAGCCGUUGACCUGCCA-AGCCGACUU
.((......)).(.(((((((((..((((.(((....)))----..))))..))))))((((....(((((.....)))))....)))).-))).).... ( -30.10)
>DroYak_CAF1 66080 96 - 1
ACCAAAAGCGGACAGCUGUGACUACUCCUCCGCAAUUGCG----AUGGGAAAAUGCACGGCAUUGAAAUUGUUAAAUCGUUGACCUGUCAAAGUCGACUU
.....(((..(((.((((((.....((((.(((....)))----..)))).....)))))).((((....(((((....)))))...)))).)))..))) ( -25.40)
>consensus
ACCAAAAGAGGACAGCUGUUAGUCCUCCUCCGCAAUUGCGGAUGAUGGGAAAAUUCACGGCAUUGAAAUUGUUAAACCGUUGACCUGUCAAAGCCGACUU
.(((...((((((........)))))).(((((....)))))...))).........((((.((((....(((((....)))))...)))).)))).... (-23.88 = -25.72 +   1.84)

alignment

secondary structure

dotplot

Window 3

Location	7,467,483 – 7,467,602
Length	119
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	93.09
Mean single sequence MFE	-31.04
Consensus MFE	-23.05
Energy contribution	-23.73
Covariance contribution	0.68
Combinations/Pair	1.06
Mean z-score	-1.93
Structure conservation index	0.74
SVM decision value	0.13
SVM RNA-class probability	0.599282
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7467483 119 + 22407834
CGGUUUAACAAUUUCAAUGCCGUGAAUUUUCCCAUCAUCCGCAAUUGCGGAGGAGGACUAGCAGCUGUCCUCUUUUGGUCUGCAAUCUCCGAAAAUUCCACAGUAGAAAUCACCAGUCA
.(((......(((((..(((.((((((((((......(((((....)))))(((((....((((....((......)).))))..)))))))))))).))).)))))))).)))..... ( -33.70)
>DroSec_CAF1 62975 119 + 1
CGGUUUAACAAUUUCAAUGCCGUGAAUUUUCCCAUCAUCCGCAAUUGCGGAGGAGGACUAACAGCUGUCCUCUUUUGGUCUGCAAUCUCCGAAAAUUCCACAGUAGAAAUCUCCAGUCA
.((.......(((((..(((.((((((((((......(((((....)))))(((((((........))))))).................))))))).))).))))))))..))..... ( -31.10)
>DroSim_CAF1 65443 119 + 1
CGGUUUAACAAUUUCAAUGCCGUAAAUUUUCCCAUCAUCCGCAAUUGCGGAGGAGGACUAACAGCUGUCCUCUUUUGGUCUGCAAUCUCCGAAAAUUCCACAGUAGAAAUCUCCAGUCA
.((.......(((((..(((.((.(((((((......(((((....)))))(((((((........))))))).................)))))))..)).))))))))..))..... ( -27.20)
>DroEre_CAF1 66644 115 + 1
CGGCUUAACCAUUUCAAUGCCGUGAAUUUUCCCAU----CGCAAUUGCGGAGGAGGACUCACAGCUGUCCUCUUUUGGCCUGCAAUCUGCGAAAAUUCCACAGUAGAAAUCUCCAGUCA
.((((.....(((((..(((.((((((((.....(----(((((((((((((((((((........)))))))).....))))))).)))))))))).))).))))))))....)))). ( -36.00)
>DroYak_CAF1 66101 115 + 1
CGAUUUAACAAUUUCAAUGCCGUGCAUUUUCCCAU----CGCAAUUGCGGAGGAGUAGUCACAGCUGUCCGCUUUUGGUCUGCAAUCUCCGAAAAUUCCACAGUAGAAAUCUGCAGUCA
.((((................(((.((((((....----.((....))(((((.(((((((.(((.....)))..))).))))..)))))))))))..))).((((....)))))))). ( -27.20)
>consensus
CGGUUUAACAAUUUCAAUGCCGUGAAUUUUCCCAUCAUCCGCAAUUGCGGAGGAGGACUAACAGCUGUCCUCUUUUGGUCUGCAAUCUCCGAAAAUUCCACAGUAGAAAUCUCCAGUCA
.((((.....(((((..(((.((((((((((.........(((....(((((((((((........)))))))))))...))).......))))))).))).))))))))....)))). (-23.05 = -23.73 +   0.68)

alignment

secondary structure

dotplot

Window 4

Location	7,467,483 – 7,467,602
Length	119
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	93.09
Mean single sequence MFE	-34.38
Consensus MFE	-28.28
Energy contribution	-29.56
Covariance contribution	1.28
Combinations/Pair	1.05
Mean z-score	-1.33
Structure conservation index	0.82
SVM decision value	0.03
SVM RNA-class probability	0.548870
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7467483 119 - 22407834
UGACUGGUGAUUUCUACUGUGGAAUUUUCGGAGAUUGCAGACCAAAAGAGGACAGCUGCUAGUCCUCCUCCGCAAUUGCGGAUGAUGGGAAAAUUCACGGCAUUGAAAUUGUUAAACCG
....(((..(((((..(((((((.((((((((((((((((.((......))....)))).))).))))(((((....))))).....))))).)))))))....)))))..)))..... ( -38.90)
>DroSec_CAF1 62975 119 - 1
UGACUGGAGAUUUCUACUGUGGAAUUUUCGGAGAUUGCAGACCAAAAGAGGACAGCUGUUAGUCCUCCUCCGCAAUUGCGGAUGAUGGGAAAAUUCACGGCAUUGAAAUUGUUAAACCG
((((....((((((..(((((((.((((((((((((((((.((......))....))).)))).))))(((((....))))).....))))).)))))))....))))))))))..... ( -34.50)
>DroSim_CAF1 65443 119 - 1
UGACUGGAGAUUUCUACUGUGGAAUUUUCGGAGAUUGCAGACCAAAAGAGGACAGCUGUUAGUCCUCCUCCGCAAUUGCGGAUGAUGGGAAAAUUUACGGCAUUGAAAUUGUUAAACCG
...(((((((((((......)))))))))))(((((.....(((...((((((........)))))).(((((....)))))...)))...))))).(((..((((.....)))).))) ( -33.70)
>DroEre_CAF1 66644 115 - 1
UGACUGGAGAUUUCUACUGUGGAAUUUUCGCAGAUUGCAGGCCAAAAGAGGACAGCUGUGAGUCCUCCUCCGCAAUUGCG----AUGGGAAAAUUCACGGCAUUGAAAUGGUUAAGCCG
.....(((((((((......)))))))))((.....)).(((............(((((((((..((((.(((....)))----..))))..))))))))).((((.....))))))). ( -35.00)
>DroYak_CAF1 66101 115 - 1
UGACUGCAGAUUUCUACUGUGGAAUUUUCGGAGAUUGCAGACCAAAAGCGGACAGCUGUGACUACUCCUCCGCAAUUGCG----AUGGGAAAAUGCACGGCAUUGAAAUUGUUAAAUCG
...(((.(((((((......))))))).))).((((((((.((......))...((((((.....((((.(((....)))----..)))).....)))))).......))))..)))). ( -29.80)
>consensus
UGACUGGAGAUUUCUACUGUGGAAUUUUCGGAGAUUGCAGACCAAAAGAGGACAGCUGUUAGUCCUCCUCCGCAAUUGCGGAUGAUGGGAAAAUUCACGGCAUUGAAAUUGUUAAACCG
((((....((((((..(((((((.((((((((((((((((.((......))....)))).))).))))(((((....))))).....))))).)))))))....))))))))))..... (-28.28 = -29.56 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:12 2006