Locus 988

Sequence ID	3L_DroMel_CAF1
Location	2,946,902 – 2,947,077
Length	175
Max. P	0.875307

overview

Window 5

Location	2,946,902 – 2,947,021
Length	119
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	79.53
Mean single sequence MFE	-33.88
Consensus MFE	-22.94
Energy contribution	-23.58
Covariance contribution	0.64
Combinations/Pair	1.08
Mean z-score	-1.55
Structure conservation index	0.68
SVM decision value	0.49
SVM RNA-class probability	0.756194
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2946902 119 - 23771897
CCUGCAGGACCCCUGCUCUGCUCUGCUCCGCUACUCACCGCCAUCAGUGUGGGCAAGGACAUUUGCAUGAACCAGGACACGUCCAGCCUGAAUCCCCGGUUCGUGCGCAUCAGCAUCAU
...(((((...)))))..((((.((((((....((((((.......).)))))...))).....(((((((((.(((....))).....(......)))))))))))))..)))).... ( -38.60)
>DroSec_CAF1 182906 100 - 1
C---------CC----------CUGCUCCGCUACUCACCGCCAUCAGCGUGGGCAAGGACAUUUGCAUGAACCAGGACACGUCCAGCCGGAAUCCCCGGUUCGUGCGCAUCAGCAUCAU
.---------((----------.(((((((((.............)))).))))).))......(((((((((.(((....)))....((.....)))))))))))((....))..... ( -35.82)
>DroSim_CAF1 169049 100 - 1
C---------CC----------CUGCUCCGCUACUCACCGCCAUCAGCGUGGGCAAGGACAUUUGCAUGAACCAGGACACGUCCAGCCGGAAUCCCCGGUUCGUGCGCAUCAGCAUCAU
.---------((----------.(((((((((.............)))).))))).))......(((((((((.(((....)))....((.....)))))))))))((....))..... ( -35.82)
>DroEre_CAF1 190949 91 - 1
----------------------------UGCUACUCACCGCCAUUAGAGUGGGCAAGGACAUUUGCAUGAACCAGGACACGUCCAGCCGGAAUCCCCGGUUCGUGCGCAUCAGCAUCAU
----------------------------((((.((((((.......).)))))...........(((((((((.(((....)))....((.....))))))))))).....)))).... ( -29.10)
>DroYak_CAF1 192568 114 - 1
CCUUCAGGACCUCUGCA-----CUACUCUGCUACUCACCGCCAUCAGUGUGGGCAAGGACAUUUGCAUGAACCAGGACACGUCCAGCCGGAAUCCCCGGUUCGUGCGCAUCAGCAUCAU
((....)).(((.(((.-----((((.(((..............))).))))))))))......(((((((((.(((....)))....((.....)))))))))))((....))..... ( -35.24)
>DroMoj_CAF1 224267 94 - 1
------------------------AGGGAG-CACUCACCGACAUCAGGGUGGGCAGCGACAUUUUGGUGAACCAGGAUACGUCCAGGCUGAAGCUCAGAUUCGUGCGCAUUAUCAUCAU
------------------------...(((-(.((((((........))))))((((((((((((((....)))))))..)))...))))..))))....................... ( -28.70)
>consensus
C_________CC__________CUGCUCCGCUACUCACCGCCAUCAGCGUGGGCAAGGACAUUUGCAUGAACCAGGACACGUCCAGCCGGAAUCCCCGGUUCGUGCGCAUCAGCAUCAU
.............................(((.((((((.......).)))))..........((((((((((.(((....)))....((.....))))))))))))....)))..... (-22.94 = -23.58 +   0.64)

alignment

secondary structure

dotplot

Window 6

Location	2,946,982 – 2,947,077
Length	95
Sequences	3
Columns	95
Reading direction	reverse
Mean pairwise identity	80.00
Mean single sequence MFE	-39.13
Consensus MFE	-26.83
Energy contribution	-27.17
Covariance contribution	0.34
Combinations/Pair	1.10
Mean z-score	-2.00
Structure conservation index	0.69
SVM decision value	0.89
SVM RNA-class probability	0.875307
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2946982 95 - 23771897
AGUGGAACUGGCUGUAGGAGGGGACCCUUGGGGGUGGACCUGCAGGACCUGCAGGACCUGCAGGACCCCUGCUCUGCUCUGCUCCGCUACUCACC
((((((.(.(((.(.((.(((((((((....))))...((((((((.((....)).)))))))).))))).))).)))..).))))))....... ( -48.70)
>DroSim_CAF1 169129 76 - 1
AGUGGAACGGGCUGUAGGAGGGGACCCUUGGGGGUGGACCUGCAGGACCUGCAGGAC---------CC----------CUGCUCCGCUACUCACC
.((((....(((.(.((.(((((((((....))))...(((((((...))))))).)---------))----------)).))).)))..)))). ( -35.90)
>DroYak_CAF1 192648 90 - 1
AGUGGAACGAGCUGUAGGAUGGGAUCCUUUGGGGUGGACCUGCAGGACCUGCAGGACCUUCAGGACCUCUGCA-----CUACUCUGCUACUCACC
.((((....(((.((((...(((.((((..(((((...(((((((...)))))))))))).)))).)))....-----))))...)))..)))). ( -32.80)
>consensus
AGUGGAACGGGCUGUAGGAGGGGACCCUUGGGGGUGGACCUGCAGGACCUGCAGGACCU_CAGGACCCCUGC______CUGCUCCGCUACUCACC
.((((....(((.....((((....)))).(((((((.(((((((...)))))))....((((.....))))......))))))))))..)))). (-26.83 = -27.17 +   0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:12 2006