Locus 5847

Sequence ID	X_DroMel_CAF1
Location	15,109,199 – 15,109,310
Length	111
Max. P	0.864307

overview

Window 6

Location	15,109,199 – 15,109,310
Length	111
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	79.56
Mean single sequence MFE	-29.15
Consensus MFE	-16.83
Energy contribution	-17.07
Covariance contribution	0.25
Combinations/Pair	1.15
Mean z-score	-2.26
Structure conservation index	0.58
SVM decision value	0.84
SVM RNA-class probability	0.864307
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15109199 111 + 22224390
AAA------AUGCCGAGCAUUAACUUGUCAACUUGGUUGAAU---UCAUUCUUAGCUGGCAAUCUGCUCAAAAGUAUUUACAUUCGAUUGCCAACAGUGGCAUCGUCAUAUGCAGCUAUA
...------..((.(((((.....((((((.((.((.((...---.))..)).)).))))))..)))))....((((.......((((.((((....))))))))....)))).)).... ( -25.80)
>DroSec_CAF1 21038 117 + 1
AAACCGUUAAUGCCGAGCAUUAACUUGUCAACUUGGUUGAAU---UCAUUCUUAGCUGCCAAUCUGCUCAAAAGUAUUUACAUUCGAUUGCCAACACUGGCACAGUCAUAUGCAGCUAUU
.....((((((((...))))))))...(((((...)))))..---.......(((((((.....((((....)))).........((((((((....)))))..)))....))))))).. ( -29.20)
>DroEre_CAF1 28706 105 + 1
AAA------GUGCGGAGUAUUAACUUGUAAGCUGGCUUGAAUGGCUCAUUGCUGGCUGGCAAUCUGCGCAGCAGUGUUUACACUCGAUUGCCAACUCUGGCAA---------CAGUUAUA
...------(((((((((....))((((.(((..((.(((.....)))..))..))).)))))))))))(((((((....)))).(.((((((....))))))---------).)))... ( -34.70)
>DroYak_CAF1 27204 103 + 1
AAA------AUGCCGAGUAUUAACUUGUCAACUUGGUUCAAU---UCAUUCUUAGCUGGCAAUCUGCUCGCAAGUAUUUACAUUCGAUUGCCAGCACUGGCAA--------GCAGCUAUA
...------..(((((((............))))))).....---.........((((((((((((....)).((....))....))))))))))..((((..--------...)))).. ( -26.90)
>consensus
AAA______AUGCCGAGCAUUAACUUGUCAACUUGGUUGAAU___UCAUUCUUAGCUGGCAAUCUGCUCAAAAGUAUUUACAUUCGAUUGCCAACACUGGCAA________GCAGCUAUA
..........(((.(((((.....((((((.((.((.(((.....)))..)).)).))))))..)))))...................(((((....))))).........)))...... (-16.83 = -17.07 +   0.25)

alignment

secondary structure

dotplot

Window 7

Location	15,109,199 – 15,109,310
Length	111
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	79.56
Mean single sequence MFE	-30.00
Consensus MFE	-17.91
Energy contribution	-17.97
Covariance contribution	0.06
Combinations/Pair	1.12
Mean z-score	-2.09
Structure conservation index	0.60
SVM decision value	0.65
SVM RNA-class probability	0.812227
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15109199 111 - 22224390
UAUAGCUGCAUAUGACGAUGCCACUGUUGGCAAUCGAAUGUAAAUACUUUUGAGCAGAUUGCCAGCUAAGAAUGA---AUUCAACCAAGUUGACAAGUUAAUGCUCGGCAU------UUU
....(((((((.((((.........((((((((((.....((((....))))....)))))))))).........---..(((((...)))))...))))))))..)))..------... ( -28.20)
>DroSec_CAF1 21038 117 - 1
AAUAGCUGCAUAUGACUGUGCCAGUGUUGGCAAUCGAAUGUAAAUACUUUUGAGCAGAUUGGCAGCUAAGAAUGA---AUUCAACCAAGUUGACAAGUUAAUGCUCGGCAUUAACGGUUU
..(((((((......(((((((......)))..(((((.((....)).)))))))))....))))))).......---..(((((...)))))...((((((((...))))))))..... ( -32.80)
>DroEre_CAF1 28706 105 - 1
UAUAACUG---------UUGCCAGAGUUGGCAAUCGAGUGUAAACACUGCUGCGCAGAUUGCCAGCCAGCAAUGAGCCAUUCAAGCCAGCUUACAAGUUAAUACUCCGCAC------UUU
..((((((---------((((..(.((((((((((..(((((........))))).))))))))))).)))))((((...........))))...)))))...........------... ( -29.90)
>DroYak_CAF1 27204 103 - 1
UAUAGCUGC--------UUGCCAGUGCUGGCAAUCGAAUGUAAAUACUUGCGAGCAGAUUGCCAGCUAAGAAUGA---AUUGAACCAAGUUGACAAGUUAAUACUCGGCAU------UUU
.........--------.((((((((((((((((((..(((((....)))))..).)))))))))).........---..........(((((....)))))))).)))).------... ( -29.10)
>consensus
UAUAGCUGC________UUGCCAGUGUUGGCAAUCGAAUGUAAAUACUUUUGAGCAGAUUGCCAGCUAAGAAUGA___AUUCAACCAAGUUGACAAGUUAAUACUCGGCAU______UUU
..................((((...((((((((((.....................)))))))))).............................(((....))).)))).......... (-17.91 = -17.97 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:47 2006