Locus 1135

Sequence ID	X_DroMel_CAF1
Location	3,364,707 – 3,364,824
Length	117
Max. P	0.822318

overview

Window 3

Location	3,364,707 – 3,364,797
Length	90
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	84.12
Mean single sequence MFE	-23.84
Consensus MFE	-17.75
Energy contribution	-17.95
Covariance contribution	0.20
Combinations/Pair	1.32
Mean z-score	-2.22
Structure conservation index	0.74
SVM decision value	0.34
SVM RNA-class probability	0.696612
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3364707 90 + 22224390
GGCAGUCAUCACAAACUGAUGAAAAGAUA-CGGCUGCAAGCCAAAAAUUUGGUU---CAAGCUGGGCUAUUGGCUUUAGCCAAAACACGUAGAA---
(((..((((((.....)))))).......-(((((...((((((....))))))---..))))).))).(((((....)))))...........--- ( -26.70)
>DroSec_CAF1 11045 90 + 1
GGCAGUCAUCUCAAACUGAUUAAAAGAUA-CGGCUGCAAGCCAAAAAUUUGGUU---CAAGCUGGGCUAUUGGCUUUAGCCAAAACACGUAGAA---
.((((((((((.............)))).-.))))))..........(((((((---.((((..(....)..)))).)))))))..........--- ( -23.42)
>DroSim_CAF1 11292 90 + 1
GGCAGUCAUCACAAACUGAUGAAAAGAUA-CGGCUGCAAGCCAAAAAUUUGGUU---CAAGCUGGGCUAUUGGCUUUAGCCAAAACACGUAGAA---
(((..((((((.....)))))).......-(((((...((((((....))))))---..))))).))).(((((....)))))...........--- ( -26.70)
>DroEre_CAF1 15182 90 + 1
GGCAGUCAUCACAAACUGAUGAAAAGAUA-CGACUGCAAGCCAAAAAUUUGGUU---CAAGCUGGGCUAUUGGCUUUGGCCAAAACACGUAGAA---
.((((((((((.....))))(........-)))))))..........((((((.---.((((..(....)..))))..))))))..........--- ( -23.70)
>DroYak_CAF1 13986 90 + 1
GGCAGUCAUCACAAACUGAUGAAAAGAUA-CGGCUGCAAGCCAAAAAUUUGGUU---CAAGCUGGACUAUUGGCUUUGGCCAAAACACGUAGAA---
.((..((((((.....)))))).......-.(((((.(((((((.....(((((---(.....)))))))))))))))))).......))....--- ( -25.70)
>DroAna_CAF1 29979 91 + 1
GCCAGUCAUC---AACUGAUGGAAAGAUAACGGCUCCGAGCCAAG--UUCCCUUACACAAAUCCAGUUAUUUGCUCUCC-UUGCACUGACAGAAAUU
..((((((((---....))))((.((((((((((.....)))..(--(......)).........)))))))..))...-....))))......... ( -16.80)
>consensus
GGCAGUCAUCACAAACUGAUGAAAAGAUA_CGGCUGCAAGCCAAAAAUUUGGUU___CAAGCUGGGCUAUUGGCUUUAGCCAAAACACGUAGAA___
.....(((((.......))))).........(((((.(((((((...((..(((.....)))..))...))))))))))))................ (-17.75 = -17.95 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	3,364,731 – 3,364,824
Length	93
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	74.05
Mean single sequence MFE	-23.67
Consensus MFE	-14.55
Energy contribution	-14.72
Covariance contribution	0.17
Combinations/Pair	1.35
Mean z-score	-1.51
Structure conservation index	0.61
SVM decision value	0.69
SVM RNA-class probability	0.822318
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3364731 93 + 22224390
AGAUA-CGGCUGCAAGCCAAAAAUUUGGUU---CAAGCUGGGCUAUUGGCUUUAGCCAAAACACGUAGAA-----AAGGGGGG-----------GGGGUGUGUCUAAAAACGU
(((((-((.((.(...((.....(((((((---.((((..(....)..)))).)))))))...(......-----..)))..)-----------.)).)))))))........ ( -26.80)
>DroSec_CAF1 11069 86 + 1
AGAUA-CGGCUGCAAGCCAAAAAUUUGGUU---CAAGCUGGGCUAUUGGCUUUAGCCAAAACACGUAGAA-----AAAGGGGG------------------GUCUAAACUCGU
.....-.(((((.(((((((.....(((((---(.....)))))))))))))))))).............-----......((------------------((....)))).. ( -22.90)
>DroSim_CAF1 11316 86 + 1
AGAUA-CGGCUGCAAGCCAAAAAUUUGGUU---CAAGCUGGGCUAUUGGCUUUAGCCAAAACACGUAGAA-----AAAGGGGG------------------GUCUAAAAACGU
(((..-((((.....))).....(((((((---.((((..(....)..)))).)))))))..........-----......).------------------.)))........ ( -21.50)
>DroEre_CAF1 15206 86 + 1
AGAUA-CGACUGCAAGCCAAAAAUUUGGUU---CAAGCUGGGCUAUUGGCUUUGGCCAAAACACGUAGAA-----AAAGGGUG------------------GUCUAGAAACGU
....(-((.((...((((((....))))))---..))((((((..(((((....)))))..(((.(....-----...).)))------------------))))))...))) ( -21.10)
>DroYak_CAF1 14010 86 + 1
AGAUA-CGGCUGCAAGCCAAAAAUUUGGUU---CAAGCUGGACUAUUGGCUUUGGCCAAAACACGUAGAA-----AAAGGGGG------------------GUCAAAAAACGU
.....-(((((...((((((....))))))---..)))))((((.(((((....)))))....(.(....-----..).)..)------------------)))......... ( -21.10)
>DroAna_CAF1 30000 110 + 1
AGAUAACGGCUCCGAGCCAAG--UUCCCUUACACAAAUCCAGUUAUUUGCUCUCC-UUGCACUGACAGAAAUUCCAAGGGGGUGUCUUGGCAAAGGGGUGUAUUCAUAACCAA
.((..(((.((((..((((((--.((((((.......((..((((..(((.....-..))).)))).)).......))))))...))))))...)))))))..))........ ( -28.64)
>consensus
AGAUA_CGGCUGCAAGCCAAAAAUUUGGUU___CAAGCUGGGCUAUUGGCUUUAGCCAAAACACGUAGAA_____AAAGGGGG__________________GUCUAAAAACGU
.......(((((.(((((((...((..(((.....)))..))...))))))))))))........................................................ (-14.55 = -14.72 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:11 2006