Locus 4177

Sequence ID	X_DroMel_CAF1
Location	10,979,139 – 10,979,267
Length	128
Max. P	0.995814

overview

Window 7

Location	10,979,139 – 10,979,237
Length	98
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	74.04
Mean single sequence MFE	-26.43
Consensus MFE	-12.96
Energy contribution	-13.84
Covariance contribution	0.88
Combinations/Pair	1.24
Mean z-score	-2.45
Structure conservation index	0.49
SVM decision value	2.44
SVM RNA-class probability	0.993954
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10979139 98 - 22224390
GAUAACGUAGUCUCGUGUUGACAAAUCCAAAUGGGUGAAUCAACUGCUGA------------CAUCGUGCGUUAUCAAUACUCAGUAUUGGCAGAAAACAAUGCAACUUA
((((((((((((....(((((...((((....))))...)))))....))------------)....)))))))))........((((((........))))))...... ( -29.10)
>DroSec_CAF1 2990 89 - 1
GAUAACGCACGCUCGUGUUGACAAAUCCCAAUGGGUGAAUCAACUGCUGA------------CAUCGUGCGUUAUCAAUCCUCA---------GAAAACAAUGCGACUUA
(((((((((((.(((.(((((...((((....))))...)))))...)))------------...)))))))))))........---------................. ( -26.50)
>DroSim_CAF1 3048 89 - 1
GAUAACGCACGCUCGUGUUGACAAAUCCCAAUGGGUGAAUCAACUGCUGA------------CAUCGUGCGUUAUCAAUCCUCA---------GAAAACAAUGCGACUUA
(((((((((((.(((.(((((...((((....))))...)))))...)))------------...)))))))))))........---------................. ( -26.50)
>DroEre_CAF1 3627 105 - 1
GAUAACGCA--CUCGUGUUGACAAAUCCUAACGAGUGAAUCAGCUGCUGAUUGG---CGGGGCAUUAUGCGUUAUCAAUCCUCAUUAAUAGUAGAAAACAAUGCGAUUUA
(((((((((--(((((...((....))...)))))).......(((((....))---)))........))))))))..............(((........)))...... ( -26.10)
>DroYak_CAF1 3279 98 - 1
GAUAACGCA--CUCGUGUUGACAAAUU-UAGCCAUC---------GAUGAUUGGUGGUGGUGCAUCAUGCGUUAUCAAUACUCAGUAAUAGUAGUAAACAAUGAGAUUUA
(((((((((--...((((..((.....-..((((((---------((...)))))))).))))))..)))))))))....((((.................))))..... ( -23.93)
>consensus
GAUAACGCA__CUCGUGUUGACAAAUCCCAAUGGGUGAAUCAACUGCUGA____________CAUCGUGCGUUAUCAAUCCUCA_UA_U_G_AGAAAACAAUGCGACUUA
(((((((((.......(((((...((((....))))...)))))...(((..............)))))))))))).................................. (-12.96 = -13.84 +   0.88)

alignment

secondary structure

dotplot

Window 8

Location	10,979,171 – 10,979,267
Length	96
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	76.16
Mean single sequence MFE	-30.90
Consensus MFE	-15.48
Energy contribution	-16.96
Covariance contribution	1.48
Combinations/Pair	1.19
Mean z-score	-2.65
Structure conservation index	0.50
SVM decision value	2.62
SVM RNA-class probability	0.995814
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10979171 96 - 22224390
CCCGGCAUUAAUGCACAAAAUCUCGC-CGAUGAUAACGUAGUCUCGUGUUGACAAAUCCAAAUGGGUGAAUCAACUGCUGA------------CAUCGUGCGUUAUCAA
..((((..................))-)).(((((((((((((....(((((...((((....))))...)))))....))------------)....)))))))))). ( -28.67)
>DroSec_CAF1 3013 96 - 1
ACCGGCAUUAAUGCCCAAAACUGCGC-CGAUGAUAACGCACGCUCGUGUUGACAAAUCCCAAUGGGUGAAUCAACUGCUGA------------CAUCGUGCGUUAUCAA
..((((..................))-)).((((((((((((.(((.(((((...((((....))))...)))))...)))------------...)))))))))))). ( -32.37)
>DroSim_CAF1 3071 96 - 1
ACCGGCAUUAGUGCCCAAAACUGCGC-CGAUGAUAACGCACGCUCGUGUUGACAAAUCCCAAUGGGUGAAUCAACUGCUGA------------CAUCGUGCGUUAUCAA
..((((..((((.......)))).))-)).((((((((((((.(((.(((((...((((....))))...)))))...)))------------...)))))))))))). ( -35.80)
>DroEre_CAF1 3659 103 - 1
-CCGGCAUUAAUACCCAAGACUAUGCACUAAGAUAACGCA--CUCGUGUUGACAAAUCCUAACGAGUGAAUCAGCUGCUGAUUGG---CGGGGCAUUAUGCGUUAUCAA
-...((((..............)))).....(((((((((--(((((...((....))...)))))).......(((((....))---)))........)))))))).. ( -27.64)
>DroYak_CAF1 3311 95 - 1
-CCGGCAUUAAUGCCGAAGACUUCGC-CGAUGAUAACGCA--CUCGUGUUGACAAAUU-UAGCCAUC---------GAUGAUUGGUGGUGGUGCAUCAUGCGUUAUCAA
-.(((((....)))))..........-...((((((((((--...((((..((.....-..((((((---------((...)))))))).))))))..)))))))))). ( -30.00)
>consensus
_CCGGCAUUAAUGCCCAAAACUGCGC_CGAUGAUAACGCA__CUCGUGUUGACAAAUCCCAAUGGGUGAAUCAACUGCUGA____________CAUCGUGCGUUAUCAA
...((((....))))...............((((((((((.......(((((...((((....))))...)))))...(((..............))))))))))))). (-15.48 = -16.96 +   1.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:17 2006