Locus 6538

Sequence ID	2R_DroMel_CAF1
Location	20,434,732 – 20,434,825
Length	93
Max. P	0.983361

overview

Window 2

Location	20,434,732 – 20,434,825
Length	93
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	64.74
Mean single sequence MFE	-24.05
Consensus MFE	-12.67
Energy contribution	-13.27
Covariance contribution	0.60
Combinations/Pair	1.12
Mean z-score	-2.15
Structure conservation index	0.53
SVM decision value	1.94
SVM RNA-class probability	0.983361
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20434732 93 + 20766785
CGUAGUACAUGUGUGAGAUCAACUCAGAAACACACAC---------GAAAGCUAAUUCGUGUGCUAGAUGG----ACGGAUUCCUGAACCGAAGGAAUCACCACCU
..((((((..(((((...((......))..)))))((---------(((......)))))))))))..(((----...(((((((.......))))))).)))... ( -27.60)
>DroSec_CAF1 44138 87 + 1
CAUAGUAUAUGUGUGAGAUCAA----------CACAC---------GAAAGCUAAUUCGUAUGCUAGAUGGAUGGAUGGAUUCCUGAACCGAAGGAAUCACCACUU
..(((((((((((((.......----------)))))---------(((......)))))))))))......(((...(((((((.......))))))).)))... ( -24.70)
>DroSim_CAF1 44575 87 + 1
CAUAGUAUAUGUGUGAGAUCAA----------CACAC---------GAAGGCUAAUUCGUAUGCUAGAUGGAUGGAUGGAUUCCUGAACCGAAGGAAUCACCACUU
..(((((((((((((.......----------)))))---------(((......)))))))))))......(((...(((((((.......))))))).)))... ( -25.50)
>DroYak_CAF1 45002 93 + 1
CAUAGUACAUGUGUGAGAUCAACUUAGGAAUACAAAC---------AAAAACCAAUUCGUGUGCUAGAUGA----AUGGAUUCCUGAACUGGAGGAAUCACCAUUU
..(((((((((..((((.....))))((.........---------.....))....)))))))))...((----((((((((((.......))))))..)))))) ( -20.24)
>DroAna_CAF1 40387 90 + 1
GUUGGC-UAUUCG------GAGCUGAGGAAUAUUAAUUGGCCCGCUGAGAACCAAUUCUCAUCCCAAC--------AAGAGACCUAAACCAAAGGAAUCUACAGC-
(((((.-....((------(.((..(..........)..))))).((((((....))))))..)))))--------.(((..(((.......)))..))).....- ( -22.20)
>consensus
CAUAGUAUAUGUGUGAGAUCAACU_AG_AA_ACACAC_________GAAAGCUAAUUCGUAUGCUAGAUGG____AUGGAUUCCUGAACCGAAGGAAUCACCACUU
..(((((((((..............................................)))))))))............(((((((.......)))))))....... (-12.67 = -13.27 +   0.60)

alignment

secondary structure

dotplot

Window 3

Location	20,434,732 – 20,434,825
Length	93
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	64.74
Mean single sequence MFE	-23.92
Consensus MFE	-7.99
Energy contribution	-9.43
Covariance contribution	1.44
Combinations/Pair	1.24
Mean z-score	-1.99
Structure conservation index	0.33
SVM decision value	0.15
SVM RNA-class probability	0.606093
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20434732 93 - 20766785
AGGUGGUGAUUCCUUCGGUUCAGGAAUCCGU----CCAUCUAGCACACGAAUUAGCUUUC---------GUGUGUGUUUCUGAGUUGAUCUCACACAUGUACUACG
((((((.(((((((.......)))))))...----)))))).(((((((((......)))---------)))))).....((((.....))))............. ( -30.60)
>DroSec_CAF1 44138 87 - 1
AAGUGGUGAUUCCUUCGGUUCAGGAAUCCAUCCAUCCAUCUAGCAUACGAAUUAGCUUUC---------GUGUG----------UUGAUCUCACACAUAUACUAUG
..((((.(((((((.......)))))))...))))..(((.((((((((((......)))---------)))))----------)))))................. ( -24.00)
>DroSim_CAF1 44575 87 - 1
AAGUGGUGAUUCCUUCGGUUCAGGAAUCCAUCCAUCCAUCUAGCAUACGAAUUAGCCUUC---------GUGUG----------UUGAUCUCACACAUAUACUAUG
..((((.(((((((.......)))))))...))))..(((.((((((((((......)))---------)))))----------)))))................. ( -23.20)
>DroYak_CAF1 45002 93 - 1
AAAUGGUGAUUCCUCCAGUUCAGGAAUCCAU----UCAUCUAGCACACGAAUUGGUUUUU---------GUUUGUAUUCCUAAGUUGAUCUCACACAUGUACUAUG
..(((((((......((..(.((((((.((.----.((...(((.((.....)))))..)---------)..)).)))))).)..))...)))).)))........ ( -15.70)
>DroAna_CAF1 40387 90 - 1
-GCUGUAGAUUCCUUUGGUUUAGGUCUCUU--------GUUGGGAUGAGAAUUGGUUCUCAGCGGGCCAAUUAAUAUUCCUCAGCUC------CGAAUA-GCCAAC
-((((((((..(((.......)))..))).--------(((((((....(((((((((.....))))))))).....))).))))..------...)))-)).... ( -26.10)
>consensus
AAGUGGUGAUUCCUUCGGUUCAGGAAUCCAU____CCAUCUAGCAUACGAAUUAGCUUUC_________GUGUGU_UU_CU_AGUUGAUCUCACACAUAUACUAUG
..((((((((((((.......))))))).........................................(((((.................)))))....))))). ( -7.99 =  -9.43 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:20 2006