Locus 6048

Sequence ID	2L_DroMel_CAF1
Location	17,030,152 – 17,030,319
Length	167
Max. P	0.989780

overview

Window 1

Location	17,030,152 – 17,030,243
Length	91
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	91.06
Mean single sequence MFE	-37.04
Consensus MFE	-30.67
Energy contribution	-30.55
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-2.28
Structure conservation index	0.83
SVM decision value	2.18
SVM RNA-class probability	0.989780
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17030152 91 - 22407834
UGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCUUAACGAGGUUAGUUGCGUGUGAGCGAAC------GC------------GAGCGCGCUUCAGACAAAUUA
.(((((((((((.(((((....))))).)))).))))))).......(((.(..((((((..((....------))------------..))))))..).)))...... ( -35.30)
>DroSec_CAF1 137468 97 - 1
UGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCUUAACGAGGUUAGUUGCGUGUGAGCGAACGCAAACGC------------GAACGCGCUUCAAACAAAUUA
.(((((((((((.(((((....))))).)))).)))))))....(((((..(((.(((((..((....))..))))------------))))..))))).......... ( -36.40)
>DroSim_CAF1 140702 97 - 1
UGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCUUAACGAGGUUAGUUGCGUGUGAGCGAACGCAAACGC------------GAACGCGCUUCAGACAAAUUA
.(((((((((((.(((((....))))).)))).))))))).......(((.(..((((((..(((........)))------------..))))))..).)))...... ( -36.50)
>DroEre_CAF1 139021 97 - 1
UGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCUUAACGACGUUAGUUGCGUGUGAGCGAACGCAAACGC------------GAACGCGCUGCAGACAAAUUA
.(((((((((((.(((((....))))).)))).))))))).......(((.((.((((((..(((........)))------------..)))))).)).)))...... ( -38.80)
>DroYak_CAF1 144024 109 - 1
UGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCUUAACGAGGUUAGUUGCGUGUGAGCGAACGCGAACGCAAACGCGAACGGGAACGCGCUUCAGACAAAUUA
.(((((((((((.(((((....))))).)))).))))))).......(((.(..((((((...((..((((........))))..))...))))))..).)))...... ( -38.20)
>consensus
UGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCUUAACGAGGUUAGUUGCGUGUGAGCGAACGCAAACGC____________GAACGCGCUUCAGACAAAUUA
.(((((((((((.(((((....))))).)))).))))))).......(((.(..((((((..(((........)))..............))))))..).)))...... (-30.67 = -30.55 +  -0.12)

alignment

secondary structure

dotplot

Window 2

Location	17,030,173 – 17,030,283
Length	110
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	95.31
Mean single sequence MFE	-43.34
Consensus MFE	-39.88
Energy contribution	-40.76
Covariance contribution	0.88
Combinations/Pair	1.03
Mean z-score	-1.42
Structure conservation index	0.92
SVM decision value	1.16
SVM RNA-class probability	0.924593
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17030173 110 - 22407834
CAGGUGUGUGGCAUGCGGCAUUUGCAGGCAGGUGAAAGUGUGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCUUAACGAGGUUAGUUGCGUGUGAGCGAAC------GC---
...((.(((.((((((((((((((....)))))....((..(((((((((((.(((((....))))).)))).)))))))..)).......)))))))))..))).))------..--- ( -39.60)
>DroSec_CAF1 137489 116 - 1
CAGGUGUGUGGCAUGCGGCAUUUGCAGGCAGGUGAAAGUGUGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCUUAACGAGGUUAGUUGCGUGUGAGCGAACGCAAACGC---
.....((((....((((...((..((.((((.(((...((((((((((((((.(((((....))))).)))).)))))))..)))...))).)))).))..))....)))).))))--- ( -43.10)
>DroSim_CAF1 140723 116 - 1
CAGGUGUGUGGCAUGCGGCAUUUGCAGGCAGGUGAAAGUGUGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCUUAACGAGGUUAGUUGCGUGUGAGCGAACGCAAACGC---
.....((((....((((...((..((.((((.(((...((((((((((((((.(((((....))))).)))).)))))))..)))...))).)))).))..))....)))).))))--- ( -43.10)
>DroEre_CAF1 139042 116 - 1
CAGGCGUGUGGCAUGCGGCAUUUGCAGGCAGGUGAAACUGUGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCUUAACGACGUUAGUUGCGUGUGAGCGAACGCAAACGC---
...((((((.(((((((((........((((......))))(((((((((((.(((((....))))).)))).)))))))...........)))))))))..))..))))......--- ( -43.20)
>DroYak_CAF1 144054 119 - 1
CAGGUGUGUGGCGUGCGGCAUUUGCAGGCAGGUGAAAGUGUGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCUUAACGAGGUUAGUUGCGUGUGAGCGAACGCGAACGCAAA
....(((((.((((.((...((..((.((((.(((...((((((((((((((.(((((....))))).)))).)))))))..)))...))).)))).))..)))).))))..))))).. ( -47.70)
>consensus
CAGGUGUGUGGCAUGCGGCAUUUGCAGGCAGGUGAAAGUGUGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCUUAACGAGGUUAGUUGCGUGUGAGCGAACGCAAACGC___
.....((((....((((...((..((.((((.(((...((((((((((((((.(((((....))))).)))).)))))))..)))...))).)))).))..))....)))).))))... (-39.88 = -40.76 +   0.88)

alignment

secondary structure

dotplot

Window 3

Location	17,030,203 – 17,030,319
Length	116
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	97.41
Mean single sequence MFE	-44.26
Consensus MFE	-43.42
Energy contribution	-43.02
Covariance contribution	-0.40
Combinations/Pair	1.05
Mean z-score	-1.16
Structure conservation index	0.98
SVM decision value	0.34
SVM RNA-class probability	0.693963
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17030203 116 - 22407834
GCAACUUGCAAGUGGCAGCUCAGCUAAGAGUCAGGACAGGUGUGUGGCAUGCGGCAUUUGCAGGCAGGUGAAAGUGUGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCU
((..((((((((((.(.((((......))))........(((((...)))))).))))))))))...))........(((((((((((.(((((....))))).)))).))))))) ( -40.70)
>DroSec_CAF1 137525 116 - 1
GCAACUUGCAAGUGGCAGCUCAGCUAGGAGUCAGGACAGGUGUGUGGCAUGCGGCAUUUGCAGGCAGGUGAAAGUGUGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCU
((..((((((((((.(.((...((((.(..((......))..).))))..))).))))))))))...))........(((((((((((.(((((....))))).)))).))))))) ( -42.60)
>DroSim_CAF1 140759 116 - 1
GCAACUUGCAGGUGGCAGCUCAGCUAGGAGUCAGGACAGGUGUGUGGCAUGCGGCAUUUGCAGGCAGGUGAAAGUGUGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCU
((..((((((((((.(.((...((((.(..((......))..).))))..))).))))))))))...))........(((((((((((.(((((....))))).)))).))))))) ( -42.20)
>DroEre_CAF1 139078 116 - 1
GCAACUUGCAAGUGGCAGCUCUGCCAGGAGUCAGGACAGGCGUGUGGCAUGCGGCAUUUGCAGGCAGGUGAAACUGUGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCU
....((((((((((.(.((..(((((.(.(((......))).).))))).))).))))))))))(((......))).(((((((((((.(((((....))))).)))).))))))) ( -49.80)
>DroYak_CAF1 144093 116 - 1
GCAACUUGCAAGUGGCAGCUCAGCCAGGAGUCAGGACAGGUGUGUGGCGUGCGGCAUUUGCAGGCAGGUGAAAGUGUGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCU
((..((((((((((.(.((...((((.(..((......))..).))))..))).))))))))))...))........(((((((((((.(((((....))))).)))).))))))) ( -46.00)
>consensus
GCAACUUGCAAGUGGCAGCUCAGCUAGGAGUCAGGACAGGUGUGUGGCAUGCGGCAUUUGCAGGCAGGUGAAAGUGUGGCAGGUGGGCAGGUGGCAUUUCGCCAGCUCAACUUGCU
((..((((((((((.(.((...((((.(..((......))..).))))..))).))))))))))...))........(((((((((((.(((((....))))).)))).))))))) (-43.42 = -43.02 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:42 2006