Locus 4303

Sequence ID	3R_DroMel_CAF1
Location	11,422,593 – 11,422,751
Length	158
Max. P	0.816253

overview

Window 1

Location	11,422,593 – 11,422,713
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.67
Mean single sequence MFE	-23.50
Consensus MFE	-21.98
Energy contribution	-22.38
Covariance contribution	0.40
Combinations/Pair	1.08
Mean z-score	-1.17
Structure conservation index	0.94
SVM decision value	0.43
SVM RNA-class probability	0.732891
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11422593 120 - 27905053
AAACCGUGGAAAACUAUUACUCCAAGGAUGCUCAAAUCCAAACACACACAAAACGCAGACCGAGACUCCAAUUCGUAUAGCGCACACACACAGACACAAGCUCGCUUACGUGCUCGACGG
...(((((((..........)))..((((......)))).....................((((.........((((.((((..(..............)..))))))))..)))))))) ( -19.14)
>DroSec_CAF1 170118 120 - 1
AAACCGUGGAAAACUAUUACUCCAAGGAUGCUCAAAUCCAAACACAUACAAAACGCACACCUAGACUCCAAUUCGUAUGGCGCACACACACAGAUACAAGCGCGCUUACGUGCUCGACGG
...((((.((...............((((......))))...............((((.....((.......))(((.(((((.(..............).)))))))))))))).)))) ( -26.14)
>DroSim_CAF1 163979 120 - 1
AAACCGUGGAAAACUAUUACUCCAAGGAUGCUCAAAUCCAAACACAUACAAAACGCACACCGAGACUCCAAUUCGUAUAGCGCACACACACAGAUACAAGCGCGCUUACGUGCUCGACGG
...((((.((...............((((......))))...............((((...(((.......)))(((.(((((.(..............).)))))))))))))).)))) ( -26.74)
>DroEre_CAF1 158175 120 - 1
AAACCGUGGAAAACUAUUACUCCAAGGAUGCUCAAAUCCAAACACAUACAAAACGCACACCGAGACCACCAUUCGUAUACCGCACAUACACAGAUAGAAGCGCGCUUACGUGCUCGGCGG
...((((.((...(((((.......((((......))))...............((....((((.......))))......)).........)))))..(((((....))))))).)))) ( -23.70)
>DroYak_CAF1 162384 120 - 1
AAACCGUGGAAAACUAUUACUCCAAGGAUGCUCAAAUCCAAACACAUACAAAACGCACACCGAGACCCCCAUUCGUACACCGCACACACACAGAUACAAGCGCGCUUACGUGCUCGGCGG
...((((.((...............((((......))))...............((((...(((.......)))(((..((((................))).)..))))))))).)))) ( -21.79)
>consensus
AAACCGUGGAAAACUAUUACUCCAAGGAUGCUCAAAUCCAAACACAUACAAAACGCACACCGAGACUCCAAUUCGUAUAGCGCACACACACAGAUACAAGCGCGCUUACGUGCUCGACGG
...((((.((...............((((......))))...............((((.....((.......))(((.(((((.(..............).)))))))))))))).)))) (-21.98 = -22.38 +   0.40)

alignment

secondary structure

dotplot

Window 2

Location	11,422,633 – 11,422,751
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.47
Mean single sequence MFE	-30.95
Consensus MFE	-26.68
Energy contribution	-27.44
Covariance contribution	0.76
Combinations/Pair	1.04
Mean z-score	-1.43
Structure conservation index	0.86
SVM decision value	0.67
SVM RNA-class probability	0.816253
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11422633 118 - 27905053
UGGAGUUGGGCG--CCGAAUUGGGGGAAGCUCGGAAUUAUAAACCGUGGAAAACUAUUACUCCAAGGAUGCUCAAAUCCAAACACACACAAAACGCAGACCGAGACUCCAAUUCGUAUAG
.((.(.....).--))(((((((((....(((((............((((..........)))).((((......))))....................))))).)))))))))...... ( -31.10)
>DroSec_CAF1 170158 120 - 1
UGGAGUUGGGCCCUCCGAAUUGGGGGAAGCUCGGAAUUAUAAACCGUGGAAAACUAUUACUCCAAGGAUGCUCAAAUCCAAACACAUACAAAACGCACACCUAGACUCCAAUUCGUAUGG
((((((((((((((((.....)))))..))))((............((((..........)))).((((......))))....................))..))))))).......... ( -30.00)
>DroSim_CAF1 164019 119 - 1
UGGAGUUGGGCCC-CCGAAUUGGGGGAAGCUCGGAAUUAUAAACCGUGGAAAACUAUUACUCCAAGGAUGCUCAAAUCCAAACACAUACAAAACGCACACCGAGACUCCAAUUCGUAUAG
..(((((((.(((-((.....))))).(((((((............((((..........)))).((((......))))....................))))).)))))))))...... ( -35.00)
>DroEre_CAF1 158215 118 - 1
UGGAGUUGGGGCC--CGAAUUGGGGGAAGCUCGGAAUUAUAAACCGUGGAAAACUAUUACUCCAAGGAUGCUCAAAUCCAAACACAUACAAAACGCACACCGAGACCACCAUUCGUAUAC
..((((.((((((--(......)))....(((((............((((..........)))).((((......))))....................))))).)).))))))...... ( -26.60)
>DroYak_CAF1 162424 119 - 1
GGGAGUUGGGGCU-GCGAAUUGGGGGAAGCCCGGAAUUAUAAACCGUGGAAAACUAUUACUCCAAGGAUGCUCAAAUCCAAACACAUACAAAACGCACACCGAGACCCCCAUUCGUACAC
(((.(((.((..(-(((..((((((....(((((.........))).))..........))))))((((......))))..............))))..))..))).))).......... ( -32.04)
>consensus
UGGAGUUGGGCCC_CCGAAUUGGGGGAAGCUCGGAAUUAUAAACCGUGGAAAACUAUUACUCCAAGGAUGCUCAAAUCCAAACACAUACAAAACGCACACCGAGACUCCAAUUCGUAUAG
...............((((((((((....(((((............((((..........)))).((((......))))....................))))).))))))))))..... (-26.68 = -27.44 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:21 2006