Locus 3608

Sequence ID	2L_DroMel_CAF1
Location	10,520,630 – 10,520,760
Length	130
Max. P	0.930730

overview

Window 7

Location	10,520,630 – 10,520,742
Length	112
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	74.78
Mean single sequence MFE	-19.67
Consensus MFE	-10.43
Energy contribution	-10.15
Covariance contribution	-0.28
Combinations/Pair	1.14
Mean z-score	-2.05
Structure conservation index	0.53
SVM decision value	1.21
SVM RNA-class probability	0.930730
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10520630 112 + 22407834
GCCCCCCCAAAAAAAACCCUACUUCCACAUAAAGUCCACGUUGGUGGGGAGGGGGA--GUGGGACAGUAAAAACUCCAUUAACUGUCAUCAAAAAUGCAUUUCGCAUGCAUCAA
.(((((((............((((.......))))((((....)))))).))))).--.(((((((((.............)))))).)))...((((((.....))))))... ( -30.02)
>DroSec_CAF1 8936 97 + 1
GCC---CCAAAAAUACCCCCACUGCCACAUAAAG------------AGGAAGGGGG--UGGAGGCAGUAAAAACUCCAUUAACUGUCAUCAAAAAUGCAUUUCGCAUGCAUCAA
...---.......(((((((....((.(.....)------------.))..)))))--))((((((((.............)))))).))....((((((.....))))))... ( -24.62)
>DroSim_CAF1 8947 99 + 1
GCC---CCAAAAAUACCCACACUGCCACAUAACA------------AGGAUGCGGGAUGGGGGGCAGUAAAAACUCCAUUAACUGUCAUCAAAAAUGCAUUUCGCAUGCAUCAA
.((---(((......(((.((...((........------------.)).)).))).)))))((((((.............)))))).......((((((.....))))))... ( -23.32)
>DroEre_CAF1 9354 95 + 1
CCC---CCAAAAAAAUCUCCACUGCCACAUAAACUCCACGU----------------UGGGAGACAGUAAAAACUCCAUUAACUGUCAUCAAAAAUGCAUUUCGCAUGCAUCAA
..(---((((..............................)----------------)))).((((((.............)))))).......((((((.....))))))... ( -14.43)
>DroYak_CAF1 9260 95 + 1
CCC---CCAAAAAUACUCCCACUGCCACAUAAAGUCCACGU----------------UGGGAGACAGUAAAAACUCCAUUAACUGUCAUCAAAAAUGCAUUUCGCAUGCAUCAA
...---..........(((((.((..((.....))...)).----------------)))))((((((.............)))))).......((((((.....))))))... ( -17.12)
>DroPer_CAF1 9529 90 + 1
CCC---CCCAG-----------CCUCCCAUAAAGUCCACGCUC--------AGAGA--CAGAGACAGUAAAAACUCCAUUAACCGUCAUCAAAAAUGCAUUUCGCAUGCAUCAA
...---.....-----------...........((((......--------.).))--).(((((.((.............)).))).))....((((((.....))))))... (  -8.52)
>consensus
CCC___CCAAAAAUACCCCCACUGCCACAUAAAGUCCACGU__________GGGG___GGGAGACAGUAAAAACUCCAUUAACUGUCAUCAAAAAUGCAUUUCGCAUGCAUCAA
............................................................((((((((.............)))))).))....((((((.....))))))... (-10.43 = -10.15 +  -0.28)

alignment

secondary structure

dotplot

Window 8

Location	10,520,664 – 10,520,760
Length	96
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	80.46
Mean single sequence MFE	-19.03
Consensus MFE	-12.13
Energy contribution	-11.69
Covariance contribution	-0.44
Combinations/Pair	1.18
Mean z-score	-1.47
Structure conservation index	0.64
SVM decision value	0.05
SVM RNA-class probability	0.559681
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10520664 96 + 22407834
UCCACGUUGGUGGGGAGGGGGA--GUGGGACAGUAAAAACUCCAUUAACUGUCAUCAAAAAUGCAUUUCGCAUGCAUCAAACCGAAAAUGGUAAUGGC
.(((..(((((..(((.((..(--((((...(((....))))))))..)).)).......((((((.....)))))))..)))))...)))....... ( -23.10)
>DroSec_CAF1 8967 84 + 1
------------AGGAAGGGGG--UGGAGGCAGUAAAAACUCCAUUAACUGUCAUCAAAAAUGCAUUUCGCAUGCAUCAAACCGAAAAUGGUAAUGGC
------------....((..((--(((((..........)))))))..))(((((.....((((((.....))))))...(((......))).))))) ( -19.60)
>DroSim_CAF1 8978 86 + 1
------------AGGAUGCGGGAUGGGGGGCAGUAAAAACUCCAUUAACUGUCAUCAAAAAUGCAUUUCGCAUGCAUCAAACCGAAAAUGGUAAUGGC
------------.(.(((((..(((.(.((((((.............))))))........).)))..))))).).....(((......)))...... ( -21.52)
>DroEre_CAF1 9385 82 + 1
UCCACGU----------------UGGGAGACAGUAAAAACUCCAUUAACUGUCAUCAAAAAUGCAUUUCGCAUGCAUCAAACCGAAAACGGUAAUGGC
.(((..(----------------(((..((((((.............)))))).))))..((((((.....))))))...((((....))))..))). ( -17.22)
>DroYak_CAF1 9291 82 + 1
UCCACGU----------------UGGGAGACAGUAAAAACUCCAUUAACUGUCAUCAAAAAUGCAUUUCGCAUGCAUCAAACCGAAAAUGGUAAUGGC
.(((..(----------------(((((((((((.............)))))).))....((((((.....))))))....))))...)))....... ( -18.02)
>DroAna_CAF1 9534 73 + 1
-------------------------UGAGGCAGUAAAAACUCCAUUAACUGUCAUCAAAAAUGCAUUUCGCAUGCAUCAAAUCCGAAAUGGCCAUGGC
-------------------------(((((((((.............)))))).)))......(((((((.((.......)).)))))))((....)) ( -14.72)
>consensus
________________________GGGAGACAGUAAAAACUCCAUUAACUGUCAUCAAAAAUGCAUUUCGCAUGCAUCAAACCGAAAAUGGUAAUGGC
..........................((((((((.............)))))).))....((((((.....))))))...(((......)))...... (-12.13 = -11.69 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:47 2006