Locus 238

Sequence ID	X_DroMel_CAF1
Location	818,711 – 818,850
Length	139
Max. P	0.857475

overview

Window 9

Location	818,711 – 818,810
Length	99
Sequences	4
Columns	108
Reading direction	forward
Mean pairwise identity	90.64
Mean single sequence MFE	-28.62
Consensus MFE	-25.83
Energy contribution	-26.58
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-1.69
Structure conservation index	0.90
SVM decision value	0.81
SVM RNA-class probability	0.857475
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 818711 99 + 22224390
---------UCCCUUUCCCUUCCUGCUUUGUCCUGGACUGUACUGGCUGUCUGUCUUGUCCAGCAAAAAAGGGACACCCGGGGCUUGCUGCAAUUUGUUGAAUUAAUA
---------.(((......(((((..((((..((((((......(((.....)))..))))))))))..))))).....)))((.....))................. ( -23.00)
>DroSec_CAF1 20050 95 + 1
---------UCCCUUUCCCUUCCUGCUUUGUCCUGGGCUGUCCUGGCUG----UCUUGUCCAGCAAAAAAGGGACACCCGGGGCUUGCUGCAAUUUGUUGAAUUAAUA
---------..............(((...((((((((.((((((.((((----.......))))......)))))))))))))).....)))................ ( -31.40)
>DroSim_CAF1 16372 95 + 1
---------UCCCUUUCCCUUCCUGCUUUGUCCUGGGCUGUCCUGGCUG----UCUUGUCCAGCAAAAAAGGGACACCCGGGGCUUGCUGCAAUUUGUUGAAUUAAUA
---------..............(((...((((((((.((((((.((((----.......))))......)))))))))))))).....)))................ ( -31.40)
>DroEre_CAF1 20197 103 + 1
CAUUCCCAUUCCCAUUCCCGUCCUGCUUUGUCCUGGGCUGUCC-GGCUG----UCUUGUCCAGCAAAAAAGGGACACCCGGGGCUUACUGCAAUUUGUUGAAUUAAUA
.............((((.((...(((...((((((((.(((((-.((((----.......)))).......))))))))))))).....)))...))..))))..... ( -28.70)
>consensus
_________UCCCUUUCCCUUCCUGCUUUGUCCUGGGCUGUCCUGGCUG____UCUUGUCCAGCAAAAAAGGGACACCCGGGGCUUGCUGCAAUUUGUUGAAUUAAUA
.......................(((...((((((((.((((((.((((...........))))......)))))))))))))).....)))................ (-25.83 = -26.58 +   0.75)

alignment

secondary structure

dotplot

Window 0

Location	818,730 – 818,850
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.34
Mean single sequence MFE	-33.35
Consensus MFE	-30.88
Energy contribution	-31.50
Covariance contribution	0.63
Combinations/Pair	1.06
Mean z-score	-1.48
Structure conservation index	0.93
SVM decision value	0.13
SVM RNA-class probability	0.597224
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 818730 120 + 22224390
UGUCCUGGACUGUACUGGCUGUCUGUCUUGUCCAGCAAAAAAGGGACACCCGGGGCUUGCUGCAAUUUGUUGAAUUAAUAACAACACUCAGUCCUUUGAAAAUUGAAUUUAUAGAGUGAA
.(((((((........(((.....))).(((((..........))))).)))))))..........((((((......))))))(((((.((..((..(...)..))...)).))))).. ( -25.10)
>DroSec_CAF1 20069 116 + 1
UGUCCUGGGCUGUCCUGGCUG----UCUUGUCCAGCAAAAAAGGGACACCCGGGGCUUGCUGCAAUUUGUUGAAUUAAUAACAACACUCAGUGCUUUGAAAAUUGAAUUUAGAGAGUGAA
.((((((((.((((((.((((----.......))))......))))))))))))))..((((....((((((......))))))....)))).(((((((.......)))))))...... ( -37.10)
>DroSim_CAF1 16391 116 + 1
UGUCCUGGGCUGUCCUGGCUG----UCUUGUCCAGCAAAAAAGGGACACCCGGGGCUUGCUGCAAUUUGUUGAAUUAAUAACAACACUCAGUGCUUUGAAAAUUGAAUUUAGAGAGUGAA
.((((((((.((((((.((((----.......))))......))))))))))))))..((((....((((((......))))))....)))).(((((((.......)))))))...... ( -37.10)
>DroEre_CAF1 20225 115 + 1
UGUCCUGGGCUGUCC-GGCUG----UCUUGUCCAGCAAAAAAGGGACACCCGGGGCUUACUGCAAUUUGUUGAAUUAAUAACAACACUCAGUGCUUUGGAAAUUGAAUUUAGAGAGUGAA
.((((((((.(((((-.((((----.......)))).......))))))))))))).(((((....((((((......))))))....)))))(((((((.......)))))))...... ( -34.10)
>consensus
UGUCCUGGGCUGUCCUGGCUG____UCUUGUCCAGCAAAAAAGGGACACCCGGGGCUUGCUGCAAUUUGUUGAAUUAAUAACAACACUCAGUGCUUUGAAAAUUGAAUUUAGAGAGUGAA
.((((((((.((((((.((((...........))))......))))))))))))))..((((....((((((......))))))....)))).(((((((.......)))))))...... (-30.88 = -31.50 +   0.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:42 2006