Locus 768

Sequence ID	3L_DroMel_CAF1
Location	2,305,484 – 2,305,628
Length	144
Max. P	0.894972

overview

Window 3

Location	2,305,484 – 2,305,588
Length	104
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	82.74
Mean single sequence MFE	-23.78
Consensus MFE	-16.42
Energy contribution	-17.06
Covariance contribution	0.64
Combinations/Pair	1.15
Mean z-score	-2.18
Structure conservation index	0.69
SVM decision value	0.96
SVM RNA-class probability	0.890161
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2305484 104 - 23771897
AAUUGGUAUUAUCCUGUAUCAAGUAUCCUGAAUCCUUGAAUUCGUGCUGCUCAAAUUAAGAGCGGUACAAAUGGCAUUCUUUCUGGUUAAACUUAACCCCCGAA
..(((((((......))))))).......((((((....(((.(((((((((.......))))))))).))))).)))).....(((((....)))))...... ( -24.80)
>DroSec_CAF1 54703 104 - 1
UAUUGGUAUUAUCCUGUAUCAAGUAUCCUAAAUCCUUGAAUUAGUGCUGCUCAAAUUAAGAGCGGCACAAAUGGCAUUCUUUCUGGUUAAACUAAACCCCCGAA
..((((........(((.(((((.((.....)).)))))....(((((((((.......))))))))).....)))........((((......)))).)))). ( -25.30)
>DroSim_CAF1 54644 104 - 1
UAUUGGUAUUAUCCUCUAUCAAGUAGCCUAAAUCCUUGAAUUAGUGCUGCUCAAAUUAAGAGCGGCACAAAUGGCAUUCUUUCUGGUUAAACUAAGCCCCCGAA
..((((((........)))))).(((((..((....((.(((.(((((((((.......))))))))).)))..))....))..)))))............... ( -25.10)
>DroEre_CAF1 57903 92 - 1
------------CAUAUCUGAAGUGUCCCAAAUCCUUGAAUUAGUGUGGCGCAAAUUAAGAGCGUCACAAAUGGCAUUUUCUCUGGUUAAACUAAACCCCAGAA
------------....(((((((((((.(((....)))......((((((((.........))))))))...))))))).....((((......)))).)))). ( -22.60)
>DroYak_CAF1 57407 95 - 1
-AUU--------UAUGUUUCAAGUGUACUAAAUCCUUGAAUUAGUGUUGCUCAAAUUAAGAGCGUCACAAAUGGCAUUCUCUCUGGUUGAACUAAACCUCAGAA
-...--------.((((((((((.(........)))))))...(((.(((((.......))))).))).....))))..(((..((((......))))..))). ( -21.10)
>consensus
_AUUGGUAUUAUCCUGUAUCAAGUAUCCUAAAUCCUUGAAUUAGUGCUGCUCAAAUUAAGAGCGGCACAAAUGGCAUUCUUUCUGGUUAAACUAAACCCCCGAA
..................(((((.((.....)).)))))....(((((((((.......)))))))))................((((......))))...... (-16.42 = -17.06 +   0.64)

alignment

secondary structure

dotplot

Window 4

Location	2,305,508 – 2,305,628
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	76.34
Mean single sequence MFE	-26.59
Consensus MFE	-16.70
Energy contribution	-17.50
Covariance contribution	0.80
Combinations/Pair	1.11
Mean z-score	-1.89
Structure conservation index	0.63
SVM decision value	0.98
SVM RNA-class probability	0.894972
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2305508 120 - 23771897
AAGGCUGAAUAACCAUUUCCAACUCAUUGUGUUCAGUACGAAUUGGUAUUAUCCUGUAUCAAGUAUCCUGAAUCCUUGAAUUCGUGCUGCUCAAAUUAAGAGCGGUACAAAUGGCAUUCU
......((((..((((((.....(((..(..(((((......(((((((......))))))).....)))))..).)))....(((((((((.......))))))))))))))).)))). ( -33.00)
>DroSec_CAF1 54727 110 - 1
AAGGCUGAA----------CAACUUAUUGUGUGCAGUACAUAUUGGUAUUAUCCUGUAUCAAGUAUCCUAAAUCCUUGAAUUAGUGCUGCUCAAAUUAAGAGCGGCACAAAUGGCAUUCU
...((((.(----------(((....))))...)))).(((.(((((((......))))))).....................(((((((((.......)))))))))..)))....... ( -27.90)
>DroSim_CAF1 54668 110 - 1
AAGGCUGAA----------CAACUUAUUGUGUGCAGUACAUAUUGGUAUUAUCCUCUAUCAAGUAGCCUAAAUCCUUGAAUUAGUGCUGCUCAAAUUAAGAGCGGCACAAAUGGCAUUCU
.((((((..----------.....(((((....)))))....((((((........)))))).)))))).......((.(((.(((((((((.......))))))))).)))..)).... ( -29.80)
>DroEre_CAF1 57927 106 - 1
AAGGCUGAACAACCAUUUGAAACUUAUUGUGUGUAUAA--------------CAUAUCUGAAGUGUCCCAAAUCCUUGAAUUAGUGUGGCGCAAAUUAAGAGCGUCACAAAUGGCAUUUU
...(((...(((..(((((..((((..(((((.....)--------------))))....))))....)))))..)))......((((((((.........))))))))...)))..... ( -24.40)
>DroYak_CAF1 57431 109 - 1
AAGGCUGAACAAUCAUAUCAAACUUAUUAGGUAUAUAU---AUU--------UAUGUUUCAAGUGUACUAAAUCCUUGAAUUAGUGUUGCUCAAAUUAAGAGCGUCACAAAUGGCAUUCU
...(((...........((((....(((.(((((((..---...--------..........))))))).)))..))))....(((.(((((.......))))).)))....)))..... ( -17.86)
>consensus
AAGGCUGAA_AA_CAU_U_CAACUUAUUGUGUGCAGUAC__AUUGGUAUUAUCCUGUAUCAAGUAUCCUAAAUCCUUGAAUUAGUGCUGCUCAAAUUAAGAGCGGCACAAAUGGCAUUCU
...(((....................................................(((((.((.....)).)))))....(((((((((.......)))))))))....)))..... (-16.70 = -17.50 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:45 2006