Locus 4811

Sequence ID	3R_DroMel_CAF1
Location	12,574,388 – 12,574,518
Length	130
Max. P	0.863590

overview

Window 7

Location	12,574,388 – 12,574,489
Length	101
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	81.19
Mean single sequence MFE	-27.00
Consensus MFE	-19.90
Energy contribution	-20.02
Covariance contribution	0.11
Combinations/Pair	1.18
Mean z-score	-1.20
Structure conservation index	0.74
SVM decision value	0.00
SVM RNA-class probability	0.535635
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12574388 101 + 27905053
GAGUAACAGUGGCUCUAAAACUGGACCGACAAGAUGACUCUAAAACUA---------UGAAAACC---GAAUCCAUAGAUGGCGCAUGCAACUCAGUGCCGCCAUCUGACGUA
((((.....(((.((((....)))))))........))))........---------........---.......((((((((((((........))).)))))))))..... ( -24.62)
>DroGri_CAF1 64996 111 + 1
GAGUAACAAUGACUGUCAAACUAGCCAUGCAG--UGACUCUCAGACCAACAUCGAUAUGGAUGCAUAACGACCAAUAGAUGGCGCAUGCAAUAUGCUGCUGCCAUCUAUUGCA
((((.((.(((.(((......))).)))...)--).))))...........(((.((((....)))).))).((((((((((((((.((.....))))).))))))))))).. ( -33.70)
>DroSec_CAF1 63053 101 + 1
GAGUAACAGUGGCUCUAAAACUGGACGAACAAUAUGAUUCCAAAACUA---------UGAAAACC---GAAUCCAUAGAUGGCGCAUGCGACUCAGUGCCGCCAUCUGACGUA
......((((.........)))).(((........(((((........---------........---)))))..((((((((((((........))).))))))))).))). ( -23.59)
>DroSim_CAF1 63140 101 + 1
GAGUAACAGUGGCUCUAAAACUGGACGGGCAAGAUGACUCCAAAACUA---------UGAAAACC---GAAUCCCUAGAUGGCGCAUGCGACUCAGUGCCGCCAUCUGACGUA
((((.......((((...........))))......))))........---------........---.......((((((((((((........))).)))))))))..... ( -24.02)
>DroEre_CAF1 61782 101 + 1
GAGUAACAGUGGCUCUAAAACUGGACGGGUAAGCUGACUCUCAAACUA---------UGGAAACC---GAAUGCAUAGAUGGCGCAUGCGACUCAGUGCCGCCAUCUGACGUA
(((...((((.((((...........))))..))))...)))......---------.(....).---.......((((((((((((........))).)))))))))..... ( -26.60)
>DroYak_CAF1 61970 100 + 1
GAGUAACAGUGGCUCUAAAACUGGACGGGCAA-CUGACUCUCAAACUA---------UGGAAACC---GAAUUCAUAGAUGGCGCAUGCGACUCAGUGCCGCCAUCUGACGUA
......(((((((((((....))))..((((.-((((.((.....(((---------((((....---...)))))))...((....)))).)))))))))))).)))..... ( -29.50)
>consensus
GAGUAACAGUGGCUCUAAAACUGGACGGGCAAGAUGACUCUAAAACUA_________UGAAAACC___GAAUCCAUAGAUGGCGCAUGCGACUCAGUGCCGCCAUCUGACGUA
((((.....((..((((....))))....)).....))))...................................((((((((((((........)))).))))))))..... (-19.90 = -20.02 +   0.11)

alignment

secondary structure

dotplot

Window 8

Location	12,574,428 – 12,574,518
Length	90
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	76.75
Mean single sequence MFE	-22.98
Consensus MFE	-16.29
Energy contribution	-16.32
Covariance contribution	0.03
Combinations/Pair	1.08
Mean z-score	-1.40
Structure conservation index	0.71
SVM decision value	0.84
SVM RNA-class probability	0.863590
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12574428 90 + 27905053
U-AAAACUA---------UGAAAACC---GAAUCCAUAGAUGGCGCAUGCAACUCAGUGCCGCCAUCUGACGUAAGAAAUAUGCGUUUCCCACCUAUUUUCC-----G-
.-.......---------.(((((..---.......((((((((((((........))).)))))))))((((((....).)))))..........))))).-----.- ( -21.00)
>DroSec_CAF1 63093 90 + 1
C-AAAACUA---------UGAAAACC---GAAUCCAUAGAUGGCGCAUGCGACUCAGUGCCGCCAUCUGACGUAAGAAAUCUGCAGCUCCCACCUAUUUUCC-----G-
.-.......---------.(((((..---.......((((((((((((........))).)))))))))..(((.(....))))............))))).-----.- ( -18.60)
>DroSim_CAF1 63180 90 + 1
C-AAAACUA---------UGAAAACC---GAAUCCCUAGAUGGCGCAUGCGACUCAGUGCCGCCAUCUGACGUAAGAAAUCUGCAGCUCCCACCUAUUUUCC-----G-
.-.......---------.(((((..---.......((((((((((((........))).)))))))))..(((.(....))))............))))).-----.- ( -18.40)
>DroEre_CAF1 61822 90 + 1
U-CAAACUA---------UGGAAACC---GAAUGCAUAGAUGGCGCAUGCGACUCAGUGCCGCCAUCUGACGUAAGAAACCUGCAUCUCCGACCUAUUUUCC-----G-
.-.......---------.((((((.---(((((((((((((((((((........))).))))))))).(....).....))))).)).)......)))))-----.- ( -24.60)
>DroYak_CAF1 62009 90 + 1
U-CAAACUA---------UGGAAACC---GAAUUCAUAGAUGGCGCAUGCGACUCAGUGCCGCCAUCUGACGUAAGAAAUCUGUAGCUUCGACCUAUUUUCC-----G-
.-....(((---------((((....---.......((((((((((((........))).))))))))).(....)...)))))))................-----.- ( -22.80)
>DroMoj_CAF1 73805 109 + 1
UCAAAGUCAGCAUUGACGUCAGCGCAUAACGACCCAUAGAUGGCGCAUGCAAUACGCUGCGGCCAUCUAUUGCAUAACAGCUGCAACUGCUGCUUAUUGUCAACAUCGU
............((((((..((((((..........(((((((((((.((.....))))).))))))))(((((.......))))).))).)))...))))))...... ( -32.50)
>consensus
U_AAAACUA_________UGAAAACC___GAAUCCAUAGAUGGCGCAUGCGACUCAGUGCCGCCAUCUGACGUAAGAAAUCUGCAGCUCCCACCUAUUUUCC_____G_
....................................((((((((((((........)))).))))))))........................................ (-16.29 = -16.32 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:26 2006