Locus 6898

Sequence ID	3L_DroMel_CAF1
Location	18,609,528 – 18,609,643
Length	115
Max. P	0.666461

overview

Window 1

Location	18,609,528 – 18,609,643
Length	115
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	87.77
Mean single sequence MFE	-26.76
Consensus MFE	-22.40
Energy contribution	-22.32
Covariance contribution	-0.08
Combinations/Pair	1.16
Mean z-score	-1.47
Structure conservation index	0.84
SVM decision value	0.21
SVM RNA-class probability	0.636888
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18609528 115 + 23771897
UCCGCAAUUGGGGUCGUAAUUUGUUGGUUCGCCGUGUUUUCGGAA-AACUCAACAGUGGAAUCAAAAAGUUUGAACUUUAUGCACAAAAUAUGAAGUUCAAUAAAGUUAUUGAUGA
((((((((((......)))))((((((((..(((......)))..-))).))))))))))(((((.((.(((((((((((((.......)))))))))))...)).)).))))).. ( -30.30)
>DroSec_CAF1 21149 114 + 1
UCCGCAAUUGCGGUCGUAAUUUGCUGGUUCGCCGUGUUUUCGGAA-AACUCAACAGUGGAAUCAAAAAGUGUGAACUUUAUGCACGAAAUAUGAAGUUUGA-AAAAUUAUUGAUGA
(((((((((((....))))))((.(((((..(((......)))..-))).)).)))))))(((((.((...(((((((((((.......))))))))))).-....)).))))).. ( -27.00)
>DroSim_CAF1 20533 113 + 1
UCCGCAAUUGCGGUCGUAAUUUGCUGGUUCGCCGUGUUUUCGGAA-AACUCAACAGUGGAAUCAAAAAGUGUGAACUUUAUGCACAAAAUAUGAAGUUUGA-AAA-GUAUUGUUGA
((((.((..((((.((.((((....))))))))))..)).)))).-...(((((((((....((.....)).((((((((((.......))))))))))..-...-.))))))))) ( -25.20)
>DroEre_CAF1 21908 111 + 1
UCCGCAAUUGCGGUCGUAAUUUGCUGGUUCGCCCUGCUUUCGGAA-AACUCAACAGUGGAAUCAAAAAGCUUCAACUUUCUGUUCAAAACAAAAAGUUUAA-AAAGUU---UACAA
(((((((((((....))))))((.(((((..((........))..-))).)).)))))))......((((((.((((((.(((.....))).))))))...-.)))))---).... ( -21.50)
>DroYak_CAF1 22193 111 + 1
UCCGCAAUUGCGGUCGUAAUUUGCUGGUUUGCCGUGUUUUCGGAAAAACUCAACAGUGGAAUCAA-AAGCUUAAACUUUAUGCUCAAAACAUGAAGUUUAA-AAAGUU---UAUGA
(((((((((((....))))))((.((((((.(((......)))..)))).)).))))))).(((.-((((((((((((((((.......))))))))))).-..))))---).))) ( -29.80)
>consensus
UCCGCAAUUGCGGUCGUAAUUUGCUGGUUCGCCGUGUUUUCGGAA_AACUCAACAGUGGAAUCAAAAAGUUUGAACUUUAUGCACAAAAUAUGAAGUUUAA_AAAGUUAUUGAUGA
(((((((((((....))))))((.(((((..(((......)))...))).)).)))))))...........(((((((((((.......)))))))))))................ (-22.40 = -22.32 +  -0.08)

alignment

secondary structure

dotplot

Window 2

Location	18,609,528 – 18,609,643
Length	115
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	87.77
Mean single sequence MFE	-24.50
Consensus MFE	-17.52
Energy contribution	-17.80
Covariance contribution	0.28
Combinations/Pair	1.15
Mean z-score	-1.89
Structure conservation index	0.71
SVM decision value	0.28
SVM RNA-class probability	0.666461
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18609528 115 - 23771897
UCAUCAAUAACUUUAUUGAACUUCAUAUUUUGUGCAUAAAGUUCAAACUUUUUGAUUCCACUGUUGAGUU-UUCCGAAAACACGGCGAACCAACAAAUUACGACCCCAAUUGCGGA
..(((((........(((((((((((.....)))....)))))))).....)))))(((..(((((.(((-(.(((......))).))))))))).....(((......))).))) ( -20.22)
>DroSec_CAF1 21149 114 - 1
UCAUCAAUAAUUUU-UCAAACUUCAUAUUUCGUGCAUAAAGUUCACACUUUUUGAUUCCACUGUUGAGUU-UUCCGAAAACACGGCGAACCAGCAAAUUACGACCGCAAUUGCGGA
..............-..............(((((((.(((((....))))).)).......(((((.(((-(.(((......))).)))))))))...)))))((((....)))). ( -25.10)
>DroSim_CAF1 20533 113 - 1
UCAACAAUAC-UUU-UCAAACUUCAUAUUUUGUGCAUAAAGUUCACACUUUUUGAUUCCACUGUUGAGUU-UUCCGAAAACACGGCGAACCAGCAAAUUACGACCGCAAUUGCGGA
..........-...-..............(((((((.(((((....))))).)).......(((((.(((-(.(((......))).)))))))))...)))))((((....)))). ( -23.00)
>DroEre_CAF1 21908 111 - 1
UUGUA---AACUUU-UUAAACUUUUUGUUUUGAACAGAAAGUUGAAGCUUUUUGAUUCCACUGUUGAGUU-UUCCGAAAGCAGGGCGAACCAGCAAAUUACGACCGCAAUUGCGGA
(((((---(.((((-...((((((((((.....))))))))))))))..............(((((.(((-(.((........)).)))))))))..))))))((((....)))). ( -28.70)
>DroYak_CAF1 22193 111 - 1
UCAUA---AACUUU-UUAAACUUCAUGUUUUGAGCAUAAAGUUUAAGCUU-UUGAUUCCACUGUUGAGUUUUUCCGAAAACACGGCAAACCAGCAAAUUACGACCGCAAUUGCGGA
.....---.....(-((((((((.((((.....)))).)))))))))...-..........(((((.((((..(((......))).)))))))))........((((....)))). ( -25.50)
>consensus
UCAUCAAUAACUUU_UUAAACUUCAUAUUUUGUGCAUAAAGUUCAAACUUUUUGAUUCCACUGUUGAGUU_UUCCGAAAACACGGCGAACCAGCAAAUUACGACCGCAAUUGCGGA
.............................(((((((.(((((....))))).)).......(((((.(((...(((......)))..))))))))...)))))((((....)))). (-17.52 = -17.80 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:28 2006