Locus 7482

Sequence ID	2L_DroMel_CAF1
Location	20,787,575 – 20,787,688
Length	113
Max. P	0.626015

overview

Window 8

Location	20,787,575 – 20,787,668
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	87.85
Mean single sequence MFE	-35.54
Consensus MFE	-26.90
Energy contribution	-27.98
Covariance contribution	1.08
Combinations/Pair	1.21
Mean z-score	-1.50
Structure conservation index	0.76
SVM decision value	-0.02
SVM RNA-class probability	0.524815
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20787575 93 - 22407834
UUCAAGUUACCCUGGGCGGGGUUUCACUGUGAGCAGUGAGUCCUUCUUCAACCAGUUGGUAGGGACAGGAGGUCGCUCCUGCUGCAGGCUGCU
....(((...((((((((((((.((((((....))))))(.((((((((.(((....)))...)).)))))).))).)))))).))))..))) ( -36.70)
>DroSec_CAF1 10921 93 - 1
UCCGAGUCACCCUAGACGGGGAUUCACUGUGAACAGUGAGUCCUUCUCCAACCAGUUGGUAGGGACAGGAGGUCCCUCCUGCUGCAGGCUGCU
....((((.((((.((..(((((((((((....)))))))))))..))..(((....))))))).((((((....)))))).....))))... ( -43.70)
>DroSim_CAF1 11700 93 - 1
UCAGAGUCACCCUGGACGGGGUUUCACUGUGAGCAGUGAGUCCUUCUCCAACCAGUUGGUAGGGACAGGAGGUCGCUCCUGCUGCAGGCUGCU
....((((.(((((((..(((.(((((((....))))))).)))..))).(((....))))))).((((((....)))))).....))))... ( -40.10)
>DroEre_CAF1 13867 93 - 1
UUCAAUUUCCCCUGGGCCGAGUUUCACUGUGAGCGCUGAGUCCUUCUUCAACGAGUUGGUAGGGACAGGAGGUCGCUGCUGCUGCAGGCGGCU
..........((((.((((((.....)).)).)).)...((((((..((((....)))).))))))))).(((((((((....))).)))))) ( -27.80)
>DroYak_CAF1 11981 93 - 1
UCCAAGUUCCCCUGUCCGAGGUUUCACUGUGCGCAUUGAGUCCUUCUUUAACCAGUUGGUAGGGACAGGAGGUCGCUCUUGCUGCAGGCUGCU
..((((..(((((((((((((.((((.((....)).)))).)))).....(((....)))..))))))).)).....))))..((.....)). ( -29.40)
>consensus
UCCAAGUUACCCUGGACGGGGUUUCACUGUGAGCAGUGAGUCCUUCUUCAACCAGUUGGUAGGGACAGGAGGUCGCUCCUGCUGCAGGCUGCU
............((((.((((.(((((((....))))))).)))).))))..((((..((((...((((((....))))))))))..)))).. (-26.90 = -27.98 +   1.08)

alignment

secondary structure

dotplot

Window 9

Location	20,787,588 – 20,787,688
Length	100
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	75.27
Mean single sequence MFE	-30.99
Consensus MFE	-22.88
Energy contribution	-23.36
Covariance contribution	0.48
Combinations/Pair	1.16
Mean z-score	-1.11
Structure conservation index	0.74
SVM decision value	0.19
SVM RNA-class probability	0.626015
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20787588 100 - 22407834
UAUUAAGUAUU-----GAUAAGUA---------------UUUCAAGUUACCCUGGGCGGGGUUUCACUGUGAGCAGUGAGUCCUUCUUCAACCAGUUGGUAGGGACAGGAGGUCGCUCCU
....(((((((-----....))))---------------)))......(((((....))))).((((((....))))))((((((..((((....)))).))))))(((((....))))) ( -31.70)
>DroSec_CAF1 10934 100 - 1
UAUUAAGUAUU-----GUUAAGUA---------------UUCCGAGUCACCCUAGACGGGGAUUCACUGUGAACAGUGAGUCCUUCUCCAACCAGUUGGUAGGGACAGGAGGUCCCUCCU
.....((((((-----....))))---------------))........((((.((..(((((((((((....)))))))))))..))..(((....)))))))..(((((....))))) ( -37.50)
>DroSim_CAF1 11713 100 - 1
UAUUAAGUAUU-----GUUAAGCA---------------UUCAGAGUCACCCUGGACGGGGUUUCACUGUGAGCAGUGAGUCCUUCUCCAACCAGUUGGUAGGGACAGGAGGUCGCUCCU
...........-----........---------------......(((.((.((((..(((.(((((((....))))))).)))..))))(((....))).)))))(((((....))))) ( -33.30)
>DroEre_CAF1 13880 120 - 1
GCUCAAGUACUAAGUAGAUAAGCAAUUACGAAGAAAAUCUUUCAAUUUCCCCUGGGCCGAGUUUCACUGUGAGCGCUGAGUCCUUCUUCAACGAGUUGGUAGGGACAGGAGGUCGCUGCU
((((.........((((........))))((((((..................((((..((((((.....))).)))..))))))))))...)))).(((((.(((.....))).))))) ( -24.86)
>DroYak_CAF1 11994 95 - 1
ACUUAGGCAUUAAGU-------------------------UCCAAGUUCCCCUGUCCGAGGUUUCACUGUGCGCAUUGAGUCCUUCUUUAACCAGUUGGUAGGGACAGGAGGUCGCUCUU
((((((...))))))-------------------------....(((.(((((((((((((.((((.((....)).)))).)))).....(((....)))..))))))).))..)))... ( -27.60)
>consensus
UAUUAAGUAUU_____GAUAAGCA_______________UUCCAAGUUACCCUGGACGGGGUUUCACUGUGAGCAGUGAGUCCUUCUUCAACCAGUUGGUAGGGACAGGAGGUCGCUCCU
.................................................((((....))))..((((((....))))))((((((..((((....)))).))))))(((((....))))) (-22.88 = -23.36 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:37:56 2006