Locus 3479

Sequence ID	2L_DroMel_CAF1
Location	10,133,764 – 10,133,877
Length	113
Max. P	0.988782

overview

Window 1

Location	10,133,764 – 10,133,877
Length	113
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	70.35
Mean single sequence MFE	-28.55
Consensus MFE	-10.08
Energy contribution	-12.68
Covariance contribution	2.60
Combinations/Pair	1.26
Mean z-score	-2.15
Structure conservation index	0.35
SVM decision value	0.95
SVM RNA-class probability	0.887462
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10133764 113 + 22407834
U-UUCUGGCUGGGACAGCAACUUCUUGCUGGCUUUUGGCCAAUUGUUUAUGGCUUAUUGUUUCAGCUCUCCGGCUUUUUCGCCGGCAACUUGGAAUCGCUUUUGCAAAAGUUUC
.-...((((..(((((((((....))))))..)))..)))).((((....(((.....(((((((....(((((......)))))....))))))).)))...))))....... ( -33.80)
>DroSec_CAF1 60092 113 + 1
U-UUCUGGCUGGGACAGCAACUGCUCGCUGGCUUUUGGCCAAUUGUUUAUGGCUUAUUGUUUCAGCUCUCCGGCUUUUCCGCCGGCAACUUGGAAUCGCUUUUCCAAAACUUUC
.-....(((((..(((((((..(((....)))..)))((((........))))...))))..)))))..(((((......)))))....((((((......))))))....... ( -36.40)
>DroSim_CAF1 63531 113 + 1
U-UUCUGUCUGGGACAGCAACUGCUCGCUGGCUUUUGGCCAAUUGUUUAUGGCUUAUUGUUUCAGCUCUCCGGCUUUUUCGCCGGCAACUUGGAAUCGCUUUUCCAAAACUUUC
.-....(.(((..(((((((..(((....)))..)))((((........))))...))))..))))...(((((......)))))....((((((......))))))....... ( -31.90)
>DroEre_CAF1 58695 111 + 1
U-UUCUGGCUGGGACAGCAACUCCUUGCUGGCUUUUGGCCAAUUGUUUAUGGCUUAUUGUUUCAGCUCUCCGGCUUUUUCGCCGGCAACUUGGAAUCGCUUUU-C-AAAGUUUC
.-....(((((..(((((((....))))).......(((((........)))))....))..)))))..(((((......))))).(((((.(((......))-)-.))))).. ( -34.10)
>DroWil_CAF1 90608 95 + 1
CAGGCCAUAAAAAACACAGACUUCCAUCUGGCUGGCUCCCAAUUGUUUUUGGUUUU-UGUU------GGUU--UUUUUU--------UUUUGGUGUAUCCUGC-C-AAAGUUAC
(((((((.((((((..((((......))))((..((..((((......))))....-.)).------.)).--..))))--------)).))).....)))).-.-........ ( -18.50)
>DroAna_CAF1 64378 86 + 1
-------------AAAACUCCUACUUGCUGGCUUUUGGCCAAUUGUUUAUGCCUUAUUGUUUCUGCUCUUUGGCUUUUGCAGCG---------AA-----UUUCU-AAAGUUUC
-------------...........((((((.(....((((((..((....((......))....))...))))))...))))))---------).-----.....-........ ( -16.60)
>consensus
U_UUCUGGCUGGGACAGCAACUGCUUGCUGGCUUUUGGCCAAUUGUUUAUGGCUUAUUGUUUCAGCUCUCCGGCUUUUUCGCCGGCAACUUGGAAUCGCUUUUCC_AAAGUUUC
...((((.((((((((((........))((((.....))))................))))))))....(((((......))))).....)))).................... (-10.08 = -12.68 +   2.60)

alignment

secondary structure

dotplot

Window 2

Location	10,133,764 – 10,133,877
Length	113
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	70.35
Mean single sequence MFE	-27.83
Consensus MFE	-10.68
Energy contribution	-12.85
Covariance contribution	2.17
Combinations/Pair	1.22
Mean z-score	-2.54
Structure conservation index	0.38
SVM decision value	2.13
SVM RNA-class probability	0.988782
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10133764 113 - 22407834
GAAACUUUUGCAAAAGCGAUUCCAAGUUGCCGGCGAAAAAGCCGGAGAGCUGAAACAAUAAGCCAUAAACAAUUGGCCAAAAGCCAGCAAGAAGUUGCUGUCCCAGCCAGAA-A
..(((((((((....))))....))))).(((((......))))).(.((((.........((((........)))).......((((((....))))))...)))))....-. ( -31.70)
>DroSec_CAF1 60092 113 - 1
GAAAGUUUUGGAAAAGCGAUUCCAAGUUGCCGGCGGAAAAGCCGGAGAGCUGAAACAAUAAGCCAUAAACAAUUGGCCAAAAGCCAGCGAGCAGUUGCUGUCCCAGCCAGAA-A
......(((((((......)))))))...(((((......))))).(.((((.........((((........)))).......((((((....))))))...)))))....-. ( -32.80)
>DroSim_CAF1 63531 113 - 1
GAAAGUUUUGGAAAAGCGAUUCCAAGUUGCCGGCGAAAAAGCCGGAGAGCUGAAACAAUAAGCCAUAAACAAUUGGCCAAAAGCCAGCGAGCAGUUGCUGUCCCAGACAGAA-A
....((((.(((..(((((((.(......(((((......)))))...((((.........((((........)))).......))))..).))))))).))).))))....-. ( -34.09)
>DroEre_CAF1 58695 111 - 1
GAAACUUU-G-AAAAGCGAUUCCAAGUUGCCGGCGAAAAAGCCGGAGAGCUGAAACAAUAAGCCAUAAACAAUUGGCCAAAAGCCAGCAAGGAGUUGCUGUCCCAGCCAGAA-A
......((-(-...(((((((((......(((((......)))))...((((.........((((........)))).......))))..)))))))))....)))......-. ( -34.09)
>DroWil_CAF1 90608 95 - 1
GUAACUUU-G-GCAGGAUACACCAAAA--------AAAAAA--AACC------AACA-AAAACCAAAAACAAUUGGGAGCCAGCCAGAUGGAAGUCUGUGUUUUUUAUGGCCUG
.......(-(-((.((.....))....--------......--....------....-....((((......))))..))))((((...(((((......)))))..))))... ( -16.50)
>DroAna_CAF1 64378 86 - 1
GAAACUUU-AGAAA-----UU---------CGCUGCAAAAGCCAAAGAGCAGAAACAAUAAGGCAUAAACAAUUGGCCAAAAGCCAGCAAGUAGGAGUUUU-------------
........-.((((-----((---------(.((((....(((..................)))........(((((.....)))))...)))))))))))------------- ( -17.77)
>consensus
GAAACUUU_GGAAAAGCGAUUCCAAGUUGCCGGCGAAAAAGCCGGAGAGCUGAAACAAUAAGCCAUAAACAAUUGGCCAAAAGCCAGCAAGAAGUUGCUGUCCCAGCCAGAA_A
..............(((((((.(......(((((......)))))...........................(((((.....)))))...).)))))))............... (-10.68 = -12.85 +   2.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:30 2006