Locus 1982

Sequence ID	X_DroMel_CAF1
Location	5,440,087 – 5,440,249
Length	162
Max. P	0.833471

overview

Window 9

Location	5,440,087 – 5,440,177
Length	90
Sequences	4
Columns	99
Reading direction	forward
Mean pairwise identity	85.89
Mean single sequence MFE	-39.20
Consensus MFE	-27.14
Energy contribution	-28.82
Covariance contribution	1.69
Combinations/Pair	1.09
Mean z-score	-1.93
Structure conservation index	0.69
SVM decision value	0.51
SVM RNA-class probability	0.763164
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5440087 90 + 22224390
CAGCGGCGGCGG-CAGCGGCUGCCG----CCCACUGCCAAU--UGCCCGUCUUCAAUCCGGC-CAACUUCUAUGCCGCCGCCGG-CUAUGCCGCUGCAG
((((((((((((-((((((...)))----).....(((.((--((........))))..)))-.........))))))))))((-(...)))))))... ( -41.80)
>DroSec_CAF1 46912 97 + 1
CAG--GCGGCGGAGAGCGAGUGCUGUCCGCACAAAGACAAAUAUGCCCGUCUUCAAUCCGGCCCAAUUUCUAUGCCGCCACCGGAGUAUGCCGCUGCAG
..(--((((((((.(((....))).)))((...(((((..........)))))...(((((...................)))))))..)))))).... ( -30.01)
>DroEre_CAF1 57819 90 + 1
CAGCGGCGGCGG-CGGCGGCUGCCG----CCCACUGCCAAC--UGCCCGUCUUCAAUCCGGC-CAACUUCUAUGCCGCCGCCGG-CUAUGCCGCUGCAG
..((((((((((-(((((((.....----......)))...--.(((.(........).)))-..........)))))))))((-(...)))))))).. ( -43.70)
>DroYak_CAF1 48650 90 + 1
CAGCAGCGGCAG-CGGCGGCUGCCG----CCCACUGCCAAC--UGCCCGUCUUCAAUCCGGC-CAACUUCUAUGCCGCCGCCGG-CUAUGCCGCUGCAG
..(((((((((.-(((((((.((.(----(.....))....--.(((.(........).)))-..........)).))))))).-...))))))))).. ( -41.30)
>consensus
CAGCGGCGGCGG_CAGCGGCUGCCG____CCCACUGCCAAC__UGCCCGUCUUCAAUCCGGC_CAACUUCUAUGCCGCCGCCGG_CUAUGCCGCUGCAG
..(((((((((..(((((((.((.(......)............(((.(........).)))...........)).))))))).....))))))))).. (-27.14 = -28.82 +   1.69)

alignment

secondary structure

dotplot

Window 0

Location	5,440,087 – 5,440,177
Length	90
Sequences	4
Columns	99
Reading direction	reverse
Mean pairwise identity	85.89
Mean single sequence MFE	-45.42
Consensus MFE	-31.56
Energy contribution	-32.56
Covariance contribution	1.00
Combinations/Pair	1.15
Mean z-score	-2.11
Structure conservation index	0.69
SVM decision value	0.72
SVM RNA-class probability	0.833471
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5440087 90 - 22224390
CUGCAGCGGCAUAG-CCGGCGGCGGCAUAGAAGUUG-GCCGGAUUGAAGACGGGCA--AUUGGCAGUGGG----CGGCAGCCGCUG-CCGCCGCCGCUG
......((((...)-)))((((((((.....(((((-.(((.........))).))--)))((((((((.----(....)))))))-)))))))))).. ( -50.40)
>DroSec_CAF1 46912 97 - 1
CUGCAGCGGCAUACUCCGGUGGCGGCAUAGAAAUUGGGCCGGAUUGAAGACGGGCAUAUUUGUCUUUGUGCGGACAGCACUCGCUCUCCGCCGC--CUG
.(((....)))......(((((((((..(....)...)))(((..(((((((((....)))))))))((((.....))))......))))))))--).. ( -34.30)
>DroEre_CAF1 57819 90 - 1
CUGCAGCGGCAUAG-CCGGCGGCGGCAUAGAAGUUG-GCCGGAUUGAAGACGGGCA--GUUGGCAGUGGG----CGGCAGCCGCCG-CCGCCGCCGCUG
...(((((((...(-(.(((((((((........((-.(((.........))).))--((((.(....).----)))).)))))))-)))).))))))) ( -49.00)
>DroYak_CAF1 48650 90 - 1
CUGCAGCGGCAUAG-CCGGCGGCGGCAUAGAAGUUG-GCCGGAUUGAAGACGGGCA--GUUGGCAGUGGG----CGGCAGCCGCCG-CUGCCGCUGCUG
..(((((((((...-...((((((((........((-.(((.........))).))--((((.(....).----)))).)))))))-)))))))))).. ( -48.00)
>consensus
CUGCAGCGGCAUAG_CCGGCGGCGGCAUAGAAGUUG_GCCGGAUUGAAGACGGGCA__GUUGGCAGUGGG____CGGCAGCCGCCG_CCGCCGCCGCUG
...(((((((.......(((((((((...........(((.(........).)))......(((.((.(.....).)).))))))).)))))))))))) (-31.56 = -32.56 +   1.00)

alignment

secondary structure

dotplot

Window 1

Location	5,440,139 – 5,440,249
Length	110
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	83.45
Mean single sequence MFE	-56.15
Consensus MFE	-39.38
Energy contribution	-39.03
Covariance contribution	-0.36
Combinations/Pair	1.21
Mean z-score	-2.51
Structure conservation index	0.70
SVM decision value	0.47
SVM RNA-class probability	0.747655
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5440139 110 - 22224390
CCCGGAGAUAGGCGGCCGCCGCCAAGGUGGUCAUGUGGUGGUGAUGGGCUGCAGCCGCG------UUGCCCGGAUCCGCUGCAGCGGCAUAGCCGGCGGCGGCAUAGAAGUUGGCC
.((((...((....(((((((((..(((.(((.((..((((...(((((.((......)------).)))))...))))..))..)))...)))))))))))).))....)))).. ( -54.50)
>DroVir_CAF1 119248 110 - 1
CGCGCAAAUAGGCAGCCGCCGCCAGCGUCGUCAUAUGAUGAUGAUGGGCGGCCGCUGCA------UUGGCCGGAUCGGCGGCAGCGGCAUAGCCGGCGGCAGCAUAGAAAUUCGCC
.((((......)).((.((((((..(((((((((...)))))))))(((.((((((((.------...((((...)))).))))))))...))))))))).))..........)). ( -59.50)
>DroGri_CAF1 99544 110 - 1
CCCGCAGAUAGGCGGCCGCUGCCAGCGUCGUCAUGUGAUGAUGAUGGGCGGCGGCAGCG------UUCGCUGGAUCGGCGGCAGCCGCAUAGCCGGCGGCGGCAUAGAAAUUUGCC
...((((((...(.(((((((((..(((((((((...)))))))))(((.(((((.((.------..(((((...))))))).)))))...))))))))))))...)..)))))). ( -59.30)
>DroWil_CAF1 111938 116 - 1
CUCUUAGAUAGGCGGCUGCUGCCAACGUUGUCAUGUGAUGAUGAUGGGCGGCUGCUGCGGCUGAAUUAUUUGGAUCGGCGGCUGCUGCAUAGCCGGCGGCUGCAUAAAAAUUGGCC
...........(((((.((((((..(((..((....))..)))...)))))).)))))((((.((((.((((.....((((((((((......)))))))))).)))))))))))) ( -50.50)
>DroMoj_CAF1 125075 110 - 1
CGCGCAGAUAGGCGGCCGCUGCCAACGUCGUCAUGUGAUGGUGAUGGGCGGCAGCUGCA------UUAGCCGGAUCGGCGGCAGCGGCAUAGCCGGCGGCUGCAUAGAAAUUCGCC
.(((....((.(((((((((((((.(..((((....))))..).)))((.((.(((((.------...((((...)))).))))).))...)))))))))))).))......))). ( -52.60)
>DroAna_CAF1 65130 110 - 1
CCCGGAGAUAGGCGGCCGCCGCCAGCGUCGUCAUGUGGUGAUGGUGGGCAGCUGCCGCA------UUGCCCGGAUCGGCGGCGGCCGCAUAGCCGGCGGCAGCGUAGAAGUUGGCC
.((((...((.((((((((((((..((((..(....)..)))).((((((((....)).------.))))))....)))))))))))).)).)))).(.((((......)))).). ( -60.50)
>consensus
CCCGCAGAUAGGCGGCCGCCGCCAACGUCGUCAUGUGAUGAUGAUGGGCGGCAGCUGCA______UUGGCCGGAUCGGCGGCAGCGGCAUAGCCGGCGGCAGCAUAGAAAUUGGCC
...........((.((((((((((.(((((((....))))))).)))((.((.(((((...................))))).)).)).....))))))).))............. (-39.38 = -39.03 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:30 2006