Locus 5447

Sequence ID	2R_DroMel_CAF1
Location	17,519,383 – 17,519,492
Length	109
Max. P	0.886948

overview

Window 3

Location	17,519,383 – 17,519,492
Length	109
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	77.13
Mean single sequence MFE	-31.14
Consensus MFE	-20.29
Energy contribution	-22.21
Covariance contribution	1.92
Combinations/Pair	1.19
Mean z-score	-1.70
Structure conservation index	0.65
SVM decision value	0.94
SVM RNA-class probability	0.886948
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17519383 109 + 20766785
CCCUAAGUCGAAAUGGCUGCUGCGUGCCCGAAAUUUCUAAAUAGCCAACAUAAAUUGAGAUUUAUAUGGGCGCUUAGGUGGCCAUGAUGGCCUGG------UUCUUGGUCCUGCU
..(((.((((..(((((..((..((((((((((((((...................)))))))...)))))))...))..)))))..)))).)))------.............. ( -34.21)
>DroVir_CAF1 42825 92 + 1
GCCUA-ACCCAAAUGGCAGCAGCGUGCCCAAAAUGCCUAAAUAGGCAACAUAAAUUGAGAUUUAUAUGGGCGCUUAGUUGGGCAGGUC-UU------------C---------CA
(((((-((.......((....))(((((((...(((((....)))))..((((((....)))))).)))))))...))))))).((..-..------------)---------). ( -33.70)
>DroPse_CAF1 35689 115 + 1
ACCUAAGCCGAAAUGGUUGCUGCGUGCCCAAAAUUUCUAAAUAGCCAACAUAAAUUGAGAUUUAUAUGGCCGCUUAGGUGGCCAUCAUGACUUGCCCAAUGAUUUUGGUCCUUUG
......((((((((.((((..(((......(((((((...................)))))))..((((((((....)))))))).......))).)))).))))))))...... ( -30.01)
>DroSec_CAF1 25847 103 + 1
CCCUAAGUCGAAAUGGCUGCUGCGUGCCCGAAAUUUCUAAAUAGCCAACAUAAAUUGAGAUUUAUAUGAGCGCUUAGGUGGCCAUGAUGGCCUGG------UUCUUGGU------
..(((.((((..(((((..((((((.....(((((((...................)))))))......))))...))..)))))..)))).)))------........------ ( -27.31)
>DroEre_CAF1 33278 109 + 1
CCCUAAGUCGAAAUGGCUGCUGCGUGCCCGAAAUUUCUAAAUAGCCAACAUAAAUUGAGAUUUAUAUGGGCGCUUAGGUGGUCAUGAUGGCCUGG------UUGUAGGUCCUUCU
............(((((..((..((((((((((((((...................)))))))...)))))))...))..)))))((.((((((.------...))))))..)). ( -32.01)
>DroAna_CAF1 31719 91 + 1
CCCUGAGUCGGAAUGGCUGCUGCGUGCCCAAAAUUUCUAAAUAGCCGACAUAAAUUGAGAUUUAUAAGGCCGCUUAGGUGGCCAUCCCGGG------------------------
.......((((.(((((..(((((.(((..(((((((...................)))))))....))))))...))..))))).)))).------------------------ ( -29.61)
>consensus
CCCUAAGUCGAAAUGGCUGCUGCGUGCCCAAAAUUUCUAAAUAGCCAACAUAAAUUGAGAUUUAUAUGGGCGCUUAGGUGGCCAUGAUGGCCUGG______UUCUUGGU____C_
......((((..(((((((((..((((((((((((((...................)))))))...)))))))...)))))))))..))))........................ (-20.29 = -22.21 +   1.92)

alignment

secondary structure

dotplot

Window 4

Location	17,519,383 – 17,519,492
Length	109
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	77.13
Mean single sequence MFE	-30.63
Consensus MFE	-12.55
Energy contribution	-13.47
Covariance contribution	0.92
Combinations/Pair	1.10
Mean z-score	-2.23
Structure conservation index	0.41
SVM decision value	0.22
SVM RNA-class probability	0.641201
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17519383 109 - 20766785
AGCAGGACCAAGAA------CCAGGCCAUCAUGGCCACCUAAGCGCCCAUAUAAAUCUCAAUUUAUGUUGGCUAUUUAGAAAUUUCGGGCACGCAGCAGCCAUUUCGACUUAGGG
....((........------)).((((.....)))).((((((((((.((((((((....)))))))).)))......(((((....(((........))))))))).)))))). ( -32.40)
>DroVir_CAF1 42825 92 - 1
UG---------G------------AA-GACCUGCCCAACUAAGCGCCCAUAUAAAUCUCAAUUUAUGUUGCCUAUUUAGGCAUUUUGGGCACGCUGCUGCCAUUUGGGU-UAGGC
..---------.------------..-..(((((((((....(.((((((((((((....))))))))(((((....)))))....)))).)((....))...))))).-)))). ( -29.80)
>DroPse_CAF1 35689 115 - 1
CAAAGGACCAAAAUCAUUGGGCAAGUCAUGAUGGCCACCUAAGCGGCCAUAUAAAUCUCAAUUUAUGUUGGCUAUUUAGAAAUUUUGGGCACGCAGCAACCAUUUCGGCUUAGGU
....((.(((...((((.((.....)))))))))))((((((((((((((((((((....))))))).))))).....(((((.....((.....))....))))).)))))))) ( -32.20)
>DroSec_CAF1 25847 103 - 1
------ACCAAGAA------CCAGGCCAUCAUGGCCACCUAAGCGCUCAUAUAAAUCUCAAUUUAUGUUGGCUAUUUAGAAAUUUCGGGCACGCAGCAGCCAUUUCGACUUAGGG
------........------...((((.....)))).((((((((((.((((((((....)))))))).)))......(((((....(((........))))))))).)))))). ( -29.90)
>DroEre_CAF1 33278 109 - 1
AGAAGGACCUACAA------CCAGGCCAUCAUGACCACCUAAGCGCCCAUAUAAAUCUCAAUUUAUGUUGGCUAUUUAGAAAUUUCGGGCACGCAGCAGCCAUUUCGACUUAGGG
.((.((.(((....------..))))).)).......((((((((((.((((((((....)))))))).)))......(((((....(((........))))))))).)))))). ( -30.00)
>DroAna_CAF1 31719 91 - 1
------------------------CCCGGGAUGGCCACCUAAGCGGCCUUAUAAAUCUCAAUUUAUGUCGGCUAUUUAGAAAUUUUGGGCACGCAGCAGCCAUUCCGACUCAGGG
------------------------..(((((((((...(((((..(((.(((((((....)))))))..)))..))))).........((.....)).)))))))))........ ( -29.50)
>consensus
_G____ACCAAGAA______CCAGGCCAUCAUGGCCACCUAAGCGCCCAUAUAAAUCUCAAUUUAUGUUGGCUAUUUAGAAAUUUCGGGCACGCAGCAGCCAUUUCGACUUAGGG
.....................................((((((((.((((((((((....))))))).)))................(((........)))....)).)))))). (-12.55 = -13.47 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:08 2006