Locus 6697

Sequence ID	3L_DroMel_CAF1
Location	17,853,809 – 17,853,941
Length	132
Max. P	0.901596

overview

Window 8

Location	17,853,809 – 17,853,910
Length	101
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	77.63
Mean single sequence MFE	-21.57
Consensus MFE	-12.70
Energy contribution	-14.09
Covariance contribution	1.39
Combinations/Pair	1.14
Mean z-score	-1.50
Structure conservation index	0.59
SVM decision value	0.05
SVM RNA-class probability	0.559930
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17853809 101 + 23771897
GAAGGUCACCUCCUAC---CCGCUGGGCGUUCCCAUUCUCAAUUACACAUGUACAAUCCACAUGUCGUGACGAAAAUACCCAUCUCA-UUCGCACGACUUUCUUG
(((((((.........---....((((....))))...........((((((.......)))))).(((.((((.............-))))))))))))))... ( -21.72)
>DroSec_CAF1 19437 94 + 1
GAAGGUCAUCGCCUAC---CCGCUGGGCGUUCUCAUUCCUAAUUACA-------AUUCCACAUGUCGUGACGAAAAUUCCCAUCUCA-UUCGCACGACUUUCUUG
(((((((..((((((.---....))))))..................-------............(((.((((.............-))))))))))))))... ( -21.82)
>DroSim_CAF1 23501 94 + 1
GAAGGUCAUCGCCUAC---CCGCUGGGCGUUCCCAUUCCCAAUUACA-------AUUCCACAUGUCGUGACGAAAAUUCCCAUCUCA-UUCGCACGACUUUCUUG
(((((....((((((.---....))))))...)).))).........-------.........((((((.((((.............-))))))))))....... ( -21.82)
>DroEre_CAF1 20961 93 + 1
GAAGGUCAUCGCCAAU---CCGCCGGGCUUUUCCAUUCUCAAUCGCA-------A-UCCACAUGUCGUGACAAAAACUCCCAUCUCA-UGCGCACGACUUUCCUG
(((((((...(((...---......)))...................-------.-..(.((((..(((...........)))..))-)).)...)))))))... ( -15.70)
>DroYak_CAF1 37300 94 + 1
GAAGGUCAUCGCCUAC---UCACUGGGCGUUCCCAUUCUCAAUCACA-------A-UCCACAUUUCGUGGGGAAAGCUUCCACGACUUUUCGCACGACUUUUUUG
(((((((..((((((.---....))))))..................-------.-..........(((.(((((((......).)))))).))))))))))... ( -24.30)
>DroAna_CAF1 17852 100 + 1
GAAGGUCAUCAGCUGGGCAACACUGGGCGGUUUCAUUCUCAGUCACA--GUCACAGUCCAAAAGUCGUGACUGAAAUUACCAUCCCA-UUCGCACGACACUUU--
(((((((........(....)..((((.(((...(((.((((((((.--.................))))))))))).)))..))))-.......))).))))-- ( -24.07)
>consensus
GAAGGUCAUCGCCUAC___CCGCUGGGCGUUCCCAUUCUCAAUCACA_______A_UCCACAUGUCGUGACGAAAAUUCCCAUCUCA_UUCGCACGACUUUCUUG
(((((....((((((........))))))...)).))).........................((((((.((((..............))))))))))....... (-12.70 = -14.09 +   1.39)

alignment

secondary structure

dotplot

Window 9

Location	17,853,835 – 17,853,941
Length	106
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	73.66
Mean single sequence MFE	-17.67
Consensus MFE	-5.74
Energy contribution	-6.33
Covariance contribution	0.58
Combinations/Pair	1.22
Mean z-score	-2.47
Structure conservation index	0.32
SVM decision value	1.02
SVM RNA-class probability	0.901596
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17853835 106 + 23771897
UUCCCAUUCUCAAUUACACAUGUACAAUCCACAUGUCGUGACGAA--AAUACCCAUCUCA-U-UCGCACGACUUUCUU-G-U--------UUAUAUACAAAUUAUGUGUCGUUAUUAAAA
...........(((.(((((((............((((((.((((--.............-)-)))))))))....((-(-(--------......))))..))))))).)))....... ( -19.82)
>DroSec_CAF1 19463 99 + 1
UUCUCAUUCCUAAUUACA-------AUUCCACAUGUCGUGACGAA--AAUUCCCAUCUCA-U-UCGCACGACUUUCUU-G-U--------UAAUAUACAAAUUAUGUGGCUUUAUUAAAA
.................(-------(..((((((((((((.((((--.............-)-)))))))))....((-(-(--------......))))...))))))..))....... ( -19.52)
>DroSim_CAF1 23527 99 + 1
UUCCCAUUCCCAAUUACA-------AUUCCACAUGUCGUGACGAA--AAUUCCCAUCUCA-U-UCGCACGACUUUCUU-G-U--------UAAUAUACAAAUUAUGUGGCUUUAUUAAAA
.................(-------(..((((((((((((.((((--.............-)-)))))))))....((-(-(--------......))))...))))))..))....... ( -19.52)
>DroEre_CAF1 20987 98 + 1
UUUCCAUUCUCAAUCGCA-------A-UCCACAUGUCGUGACAAA--AACUCCCAUCUCA-U-GCGCACGACUUUCCU-G-U--------AUAUAUCCAAAUUAUGUGGCAUUAAUAAAA
.................(-------(-(((((((((((((.....--.............-.-...)))))).....(-(-.--------.......))....)))))).)))....... ( -12.05)
>DroYak_CAF1 37326 107 + 1
UUCCCAUUCUCAAUCACA-------A-UCCACAUUUCGUGGGGAA--AGCUUCCACGACUUU-UCGCACGACUUUUUU-G-UUAUUGUUUUUAUAUUAAAAUGAUGUGGCGUUAAUAAAA
..................-------.-.((((((((((((.((((--(((......).))))-)).))))).......-.-.....(((((......))))))))))))........... ( -21.00)
>DroPer_CAF1 16110 99 + 1
UUGCCUUUCUCAGUCACA-------G-UCCGCAGGUCGUGACUGAUAAUUUCCCAAAGAA-UUUCGCAUGACAGUUUUAGAC--------UUCUAUCCAAAUUAUAUAC----AACACAA
.(((.....((((((((.-------(-.((...)).)))))))))....(((.....)))-....))).........(((..--------..)))..............----....... ( -14.10)
>consensus
UUCCCAUUCUCAAUCACA_______A_UCCACAUGUCGUGACGAA__AAUUCCCAUCUCA_U_UCGCACGACUUUCUU_G_U________UUAUAUACAAAUUAUGUGGCGUUAAUAAAA
..................................((((((.(((...................)))))))))................................................ ( -5.74 =  -6.33 +   0.58)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:52 2006