Locus 4677

Sequence ID	2R_DroMel_CAF1
Location	15,310,059 – 15,310,157
Length	98
Max. P	0.581231

overview

Window 1

Location	15,310,059 – 15,310,157
Length	98
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	86.97
Mean single sequence MFE	-22.27
Consensus MFE	-17.32
Energy contribution	-17.88
Covariance contribution	0.56
Combinations/Pair	1.17
Mean z-score	-1.50
Structure conservation index	0.78
SVM decision value	0.03
SVM RNA-class probability	0.547337
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15310059 98 + 20766785
UUUGUCGCACAGCAUGGGCUCCUGCCGAUGGAAAUGCUCCUACUCCACC------CCCACAAUCCUGAGGAGGACACCUCAUCCUGCCACGCAUCCAACUCCGC
...((.(((...(((.(((....))).)))((..((.((((.(((....------...........))).))))))..))....))).)).............. ( -19.86)
>DroSec_CAF1 115871 98 + 1
UUUGUCGCACAGCAUGGGCUCCUGCCCAUGGAAAUGCUCCUACUCCACCC-----CCCACAAUCCUGAGGAGGACUCCUCAUCCUGCCACGCAUCCAACUCCU-
...((.(((...(((((((....)))))))....................-----..........((((((....))))))...))).)).............- ( -25.10)
>DroSim_CAF1 93011 90 + 1
UUUGUCGCACAGCAUGGGCUCCUGCCCAUGGAAAUGCUCCUACUCCACC------CCCACAAUCCUGAGGAGGACUCCUCAUCCUGCCACGCAUCC--------
...((.(((...(((((((....)))))))...................------..........((((((....))))))...))).))......-------- ( -25.10)
>DroEre_CAF1 102175 101 + 1
UUUGUCGCACAGCAUGGGCUCCUGCCCAUGGAAAUGCCCCUACUCCAGCCACCCACCCAGAAUCCUGAG---GACUCCCCAUCCUGCCACGCAUCCAACUCCGC
...((.(((...(((((((....))))))).........................(((((....))).)---)...........))).)).............. ( -21.50)
>DroYak_CAF1 105861 96 + 1
UUUGUCGCACAGCAUGGGCUCCUGCCUAUGGAAAUGCACCCACUCCACCC-----CCCACAAUCCUGAG---UACUCCUCAUCCUGUCGAGCAUCCAACUCCGC
..(((((.(((((((((((....)))))))....................-----..........((((---.....))))..))))))).))........... ( -19.80)
>consensus
UUUGUCGCACAGCAUGGGCUCCUGCCCAUGGAAAUGCUCCUACUCCACCC_____CCCACAAUCCUGAGGAGGACUCCUCAUCCUGCCACGCAUCCAACUCCGC
..(((.(((...(((((((....)))))))...................................(((((......)))))...))).)))............. (-17.32 = -17.88 +   0.56)

alignment

secondary structure

dotplot

Window 2

Location	15,310,059 – 15,310,157
Length	98
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	86.97
Mean single sequence MFE	-35.26
Consensus MFE	-24.18
Energy contribution	-24.70
Covariance contribution	0.52
Combinations/Pair	1.14
Mean z-score	-1.86
Structure conservation index	0.69
SVM decision value	0.10
SVM RNA-class probability	0.581231
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15310059 98 - 20766785
GCGGAGUUGGAUGCGUGGCAGGAUGAGGUGUCCUCCUCAGGAUUGUGGG------GGUGGAGUAGGAGCAUUUCCAUCGGCAGGAGCCCAUGCUGUGCGACAAA
.....((((.(((((((((((..(((((......)))))...))))...------(((((((.........)))))))(((....)))))))).)).))))... ( -33.40)
>DroSec_CAF1 115871 98 - 1
-AGGAGUUGGAUGCGUGGCAGGAUGAGGAGUCCUCCUCAGGAUUGUGGG-----GGGUGGAGUAGGAGCAUUUCCAUGGGCAGGAGCCCAUGCUGUGCGACAAA
-.....(((..((((..((....((((((....))))))........((-----..(((.........)))..))((((((....))))))))..)))).))). ( -36.20)
>DroSim_CAF1 93011 90 - 1
--------GGAUGCGUGGCAGGAUGAGGAGUCCUCCUCAGGAUUGUGGG------GGUGGAGUAGGAGCAUUUCCAUGGGCAGGAGCCCAUGCUGUGCGACAAA
--------...((((..(((...((((((....)))))).....((((.------.(((.........)))..))))((((....)))).)))..))))..... ( -36.30)
>DroEre_CAF1 102175 101 - 1
GCGGAGUUGGAUGCGUGGCAGGAUGGGGAGUC---CUCAGGAUUCUGGGUGGGUGGCUGGAGUAGGGGCAUUUCCAUGGGCAGGAGCCCAUGCUGUGCGACAAA
......(((..((((..(((..((((..((((---((....((((..(.(....).)..)))).))))).)..))))((((....)))).)))..)))).))). ( -39.50)
>DroYak_CAF1 105861 96 - 1
GCGGAGUUGGAUGCUCGACAGGAUGAGGAGUA---CUCAGGAUUGUGGG-----GGGUGGAGUGGGUGCAUUUCCAUAGGCAGGAGCCCAUGCUGUGCGACAAA
(((.((((((..((((.((((..((((.....---))))...)))).((-----..(((.(.....).)))..))........))))))).))).)))...... ( -30.90)
>consensus
GCGGAGUUGGAUGCGUGGCAGGAUGAGGAGUCCUCCUCAGGAUUGUGGG_____GGGUGGAGUAGGAGCAUUUCCAUGGGCAGGAGCCCAUGCUGUGCGACAAA
...............(.((((..(((((......)))))...)))).)................(..((((...(((((((....)))))))..))))..)... (-24.18 = -24.70 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:28 2006