Locus 6399

Sequence ID	3R_DroMel_CAF1
Location	16,777,075 – 16,777,270
Length	195
Max. P	0.909495

overview

Window 2

Location	16,777,075 – 16,777,170
Length	95
Sequences	4
Columns	95
Reading direction	forward
Mean pairwise identity	98.77
Mean single sequence MFE	-26.75
Consensus MFE	-26.20
Energy contribution	-26.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.36
Structure conservation index	0.98
SVM decision value	1.05
SVM RNA-class probability	0.907682
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16777075 95 + 27905053
AAUUAUCACCUCGCCCAUUGACUGUUUGCUGUCACAUCCAGCACACAGAUUGCAUUCGACAAGGACUUCGAUUUGUUUCGCUGCGGUGUGAUAUU
...((((((.((((.......((((.(((((.......))))).))))...(((.((((........))))..)))......)))).)))))).. ( -26.40)
>DroSec_CAF1 9475 95 + 1
AAUUAUCACCUCGCCCAUUGACUGUUUGCUGUCACAUCCAGCACACAGACUGCACUCGACAAGGACUUCGAUUUGUUUCGCUGCGGUGUGAUAUU
...((((((............((((.(((((.......))))).))))(((((((..((((((........))))))..).)))))))))))).. ( -27.20)
>DroSim_CAF1 11122 95 + 1
AAUUAUCACCUCGCCCAUUGACUGUUUGCUGUCACAUCCAGCACACAGACUGCACUCGACAAGGACUUCGAUUUGUUUCGCUGCGGUGUGAUAUU
...((((((............((((.(((((.......))))).))))(((((((..((((((........))))))..).)))))))))))).. ( -27.20)
>DroEre_CAF1 5296 95 + 1
AAUUAUCACCUCGCCCAUUGACUGUUUGCUGUCACAUCCAGCACACAGAUUGCACUCGACAAGGACUUCGAUUUGUUUCGCUGCGGUGUGAUAUU
...((((((.((((.......((((.(((((.......))))).))))...((....((((((........))))))..)).)))).)))))).. ( -26.20)
>consensus
AAUUAUCACCUCGCCCAUUGACUGUUUGCUGUCACAUCCAGCACACAGACUGCACUCGACAAGGACUUCGAUUUGUUUCGCUGCGGUGUGAUAUU
...((((((.((((.......((((.(((((.......))))).))))...((....((((((........))))))..)).)))).)))))).. (-26.20 = -26.20 +  -0.00)

alignment

secondary structure

dotplot

Window 3

Location	16,777,075 – 16,777,170
Length	95
Sequences	4
Columns	95
Reading direction	reverse
Mean pairwise identity	98.77
Mean single sequence MFE	-30.07
Consensus MFE	-28.75
Energy contribution	-28.75
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.52
Structure conservation index	0.96
SVM decision value	1.07
SVM RNA-class probability	0.909495
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16777075 95 - 27905053
AAUAUCACACCGCAGCGAAACAAAUCGAAGUCCUUGUCGAAUGCAAUCUGUGUGCUGGAUGUGACAGCAAACAGUCAAUGGGCGAGGUGAUAAUU
..((((((...((..(((......)))..)).((((((.(.((....((((.(((((.......))))).)))).)).).))))))))))))... ( -28.60)
>DroSec_CAF1 9475 95 - 1
AAUAUCACACCGCAGCGAAACAAAUCGAAGUCCUUGUCGAGUGCAGUCUGUGUGCUGGAUGUGACAGCAAACAGUCAAUGGGCGAGGUGAUAAUU
..((((((..(((.(((.......((((........)))).))).(.((((.(((((.......))))).)))).).....)))..))))))... ( -31.20)
>DroSim_CAF1 11122 95 - 1
AAUAUCACACCGCAGCGAAACAAAUCGAAGUCCUUGUCGAGUGCAGUCUGUGUGCUGGAUGUGACAGCAAACAGUCAAUGGGCGAGGUGAUAAUU
..((((((..(((.(((.......((((........)))).))).(.((((.(((((.......))))).)))).).....)))..))))))... ( -31.20)
>DroEre_CAF1 5296 95 - 1
AAUAUCACACCGCAGCGAAACAAAUCGAAGUCCUUGUCGAGUGCAAUCUGUGUGCUGGAUGUGACAGCAAACAGUCAAUGGGCGAGGUGAUAAUU
..((((((..(((.(((.......((((........)))).)))...((((.(((((.......))))).)))).......)))..))))))... ( -29.30)
>consensus
AAUAUCACACCGCAGCGAAACAAAUCGAAGUCCUUGUCGAGUGCAAUCUGUGUGCUGGAUGUGACAGCAAACAGUCAAUGGGCGAGGUGAUAAUU
..((((((..(((.(((.......((((........)))).)))...((((.(((((.......))))).)))).......)))..))))))... (-28.75 = -28.75 +   0.00)

alignment

secondary structure

dotplot

Window 4

Location	16,777,170 – 16,777,270
Length	100
Sequences	4
Columns	104
Reading direction	reverse
Mean pairwise identity	93.14
Mean single sequence MFE	-29.27
Consensus MFE	-24.58
Energy contribution	-24.20
Covariance contribution	-0.38
Combinations/Pair	1.08
Mean z-score	-1.53
Structure conservation index	0.84
SVM decision value	0.07
SVM RNA-class probability	0.568652
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16777170 100 - 27905053
ACCGAUACCUGGGAAACUGGAGGCCCAGACCCCUAAUAGCGGGUUAUGCAAUCGUUAGUAAUUAAGACCCUACCCAUUGACGCAAACUGGGC----AUGUGCCA
...(.((((..(....)..)..(((((((((((.....).))))........(((((((................)))))))....))))))----..))).). ( -25.69)
>DroSec_CAF1 9570 100 - 1
ACGGAUACCUGGGAAACUGGAGGCCCAGACCCCUAACACCGGGUUAUGCAAUCGUUAGUAAUUAAAACCCUAUCCAUUGACGCAAACUGGGC----AUGUGCCA
..((.((((..(....)..)..((((((((((........))))........(((((((...((......))...)))))))....))))))----..))))). ( -28.90)
>DroSim_CAF1 11217 100 - 1
ACGGAUACCUGGGAAACUGGAGGCCCAGACCCCUAACAGCGGGUUAUGCAAUCGUUAGUAAUUAAAACCCUAUCCAUUGACGCAAACUGGGC----AUGUGCCA
..((.((((..(....)..)..(((((((((((.....).))))........(((((((...((......))...)))))))....))))))----..))))). ( -29.20)
>DroEre_CAF1 5391 104 - 1
ACAGAUACCUGGGAAACUGGAGGCCCAGACCCCUAACAGUGGGUUAUGCAAUUGUCAGUAAUUAAAACCCUACCUAUUGACGCAAACUGGGCAGCCAUGUGCCA
.(((....)))((....(((..(((((((((((.....).))))..(((....(((((((..((......))..))))))))))..))))))..)))....)). ( -33.30)
>consensus
ACGGAUACCUGGGAAACUGGAGGCCCAGACCCCUAACAGCGGGUUAUGCAAUCGUUAGUAAUUAAAACCCUACCCAUUGACGCAAACUGGGC____AUGUGCCA
...(.((((..(....)..)..((((((((((........))))........(((((((...((......))...)))))))....))))))......))).). (-24.58 = -24.20 +  -0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:35 2006