Locus 1370

Sequence ID	2R_DroMel_CAF1
Location	5,294,061 – 5,294,156
Length	95
Max. P	0.970039

overview

Window 3

Location	5,294,061 – 5,294,156
Length	95
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	79.08
Mean single sequence MFE	-20.35
Consensus MFE	-11.29
Energy contribution	-13.01
Covariance contribution	1.72
Combinations/Pair	1.10
Mean z-score	-2.39
Structure conservation index	0.55
SVM decision value	1.05
SVM RNA-class probability	0.907366
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5294061 95 + 20766785
CCCACUUGGGAGACCAUGACAGCUUGGCUGUUUUUAAAUCCAAUUUCGCUUUAUAAUUUUAUAACGCGCCAGCCAAACCCCU------G---UAUCCCU---CCCCA
.......(((((......((((.(((((((................(((.(((((....))))).))).)))))))....))------)---)....))---))).. ( -23.03)
>DroSec_CAF1 11040 90 + 1
CCCACUUGGGAGACCAGGACAGCUUGGCUGUUUUUAAA-----UUUCGCUUUAUAAUUUUAUAACGCGCCAGCCAAACCCCC------G---UAUCCCU---CCCCA
....(((((....))))).....(((((((........-----...(((.(((((....))))).))).)))))))......------.---.......---..... ( -22.10)
>DroSim_CAF1 11021 90 + 1
CCCACUUGGGAGACCAGGACAGCUUGGCUGUUUUUAAAUCCAAUUUCGCUUUAUAAUUUUAUAACGCGCCAGCCAAACCCCU------G---UAUCC--------CA
......(((((...((((...(.(((((((................(((.(((((....))))).))).))))))).).)))------)---..)))--------)) ( -24.43)
>DroEre_CAF1 12420 101 + 1
CCCACUUGGGGAACCAGGACAGCUUGCCUGUUUUUAAAUCCAAUUUCGCUUUAUAAUUUUAUAACGCGCCAGCCAACCCCCC------GCCGUCUUCCCCCGUCACC
.......((((((...((((((.....))))...............(((.(((((....))))).)))..............------.))...))))))....... ( -18.40)
>DroYak_CAF1 6552 91 + 1
CCCACUUCUGGGACCAGGACAGCUUGGCUGUUUUUAAAUCCAAUUUCGCUUUAUAAUUUUAUAACGCGCUAGCCAAACCCCC------G---UAUCCCC-------C
.........((((...((...(.(((((((................(((.(((((....))))).))).))))))).)..))------.---..)))).-------. ( -18.13)
>DroAna_CAF1 5725 91 + 1
CC----------GCCAGGAUAGCUUGGCUGUUUUUAAAUCCAAUUUCGCUUCAUAAUUUUAUAACGUGCCAAGCAAACUCUUCACUUCG---CCGCCAU---CCUCA
..----------...(((((.(((((((((((..((((...................)))).)))).)))))))..............(---....)))---))).. ( -16.01)
>consensus
CCCACUUGGGAGACCAGGACAGCUUGGCUGUUUUUAAAUCCAAUUUCGCUUUAUAAUUUUAUAACGCGCCAGCCAAACCCCC______G___UAUCCCU___CC_CA
....(((((....))))).....(((((((................(((.(((((....))))).))).)))))))............................... (-11.29 = -13.01 +   1.72)

alignment

secondary structure

dotplot

Window 4

Location	5,294,061 – 5,294,156
Length	95
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	79.08
Mean single sequence MFE	-30.61
Consensus MFE	-14.96
Energy contribution	-15.38
Covariance contribution	0.42
Combinations/Pair	1.17
Mean z-score	-3.10
Structure conservation index	0.49
SVM decision value	1.65
SVM RNA-class probability	0.970039
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5294061 95 - 20766785
UGGGG---AGGGAUA---C------AGGGGUUUGGCUGGCGCGUUAUAAAAUUAUAAAGCGAAAUUGGAUUUAAAAACAGCCAAGCUGUCAUGGUCUCCCAAGUGGG
..(((---(((..((---.------.(.((((((((((.(((.(((((....))))).)))................)))))))))).)..)).))))))....... ( -30.53)
>DroSec_CAF1 11040 90 - 1
UGGGG---AGGGAUA---C------GGGGGUUUGGCUGGCGCGUUAUAAAAUUAUAAAGCGAAA-----UUUAAAAACAGCCAAGCUGUCCUGGUCUCCCAAGUGGG
..(((---(((....---(------(((((((((((((.(((.(((((....))))).)))...-----........))))))))))..)))).))))))....... ( -34.50)
>DroSim_CAF1 11021 90 - 1
UG--------GGAUA---C------AGGGGUUUGGCUGGCGCGUUAUAAAAUUAUAAAGCGAAAUUGGAUUUAAAAACAGCCAAGCUGUCCUGGUCUCCCAAGUGGG
((--------(((..---(------(((((((((((((.(((.(((((....))))).)))................))))))))))..))))...)))))...... ( -32.93)
>DroEre_CAF1 12420 101 - 1
GGUGACGGGGGAAGACGGC------GGGGGGUUGGCUGGCGCGUUAUAAAAUUAUAAAGCGAAAUUGGAUUUAAAAACAGGCAAGCUGUCCUGGUUCCCCAAGUGGG
(....)((((((...(((.------((.((.(((.(((.(((.(((((....))))).)))................))).))).)).))))).))))))....... ( -32.43)
>DroYak_CAF1 6552 91 - 1
G-------GGGGAUA---C------GGGGGUUUGGCUAGCGCGUUAUAAAAUUAUAAAGCGAAAUUGGAUUUAAAAACAGCCAAGCUGUCCUGGUCCCAGAAGUGGG
.-------.(((((.---(------((((((((((((..(((.(((((....))))).))).....(..........))))))))))..)))))))))......... ( -29.10)
>DroAna_CAF1 5725 91 - 1
UGAGG---AUGGCGG---CGAAGUGAAGAGUUUGCUUGGCACGUUAUAAAAUUAUGAAGCGAAAUUGGAUUUAAAAACAGCCAAGCUAUCCUGGC----------GG
..(((---(((((.(---((((.(....).)))))(((((.((((.((......)).))))....((..........)))))))))))))))...----------.. ( -24.20)
>consensus
UG_GG___AGGGAUA___C______AGGGGUUUGGCUGGCGCGUUAUAAAAUUAUAAAGCGAAAUUGGAUUUAAAAACAGCCAAGCUGUCCUGGUCUCCCAAGUGGG
............................((((((((((.(((.(((((....))))).)))................)))))))))).................... (-14.96 = -15.38 +   0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:19 2006