Locus 9393

Sequence ID	3R_DroMel_CAF1
Location	24,914,909 – 24,915,061
Length	152
Max. P	0.952306

overview

Window 9

Location	24,914,909 – 24,915,025
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.38
Mean single sequence MFE	-20.88
Consensus MFE	-17.20
Energy contribution	-17.95
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-2.21
Structure conservation index	0.82
SVM decision value	1.20
SVM RNA-class probability	0.929977
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24914909 116 - 27905053
UCAAGACGUGCGCUUUACACUUCUGCGCCCCAA-AAUGCCCCAACAAUCACAACAUACAGAAGAAGAAAAAAAA---CUACACAUUGAAAUUACAAACUGAAACGCGCAGGUCUAAUAGU
...((((.(((((......((((((........-.......................))))))...........---.......(((......)))........))))).))))...... ( -20.28)
>DroSec_CAF1 28070 119 - 1
UCAAGACGUGCGCUUUACACUUCUGCGCCCCAA-AAUGCCCCAACAAUAACAACAUUCAAAAGAAGAAAAAAAAACGCUACAGUUUGAAAUUACAAACCGAAACGCGCAGGUCUAAUAGU
...((((.(((((......(((((.........-...........................)))))..............(.(((((......))))).)....))))).))))...... ( -22.02)
>DroEre_CAF1 26714 114 - 1
UCAAGACGUGCGCUUUACACUUCUGCGCCCCAAAAAUGCCCCAACAAUAACAACAUACAGAAAAAAAAA----CACGCUAC--AGUGAAAUUACAAACUGAAACGCGCAGGUCUAAUAAU
...((((.(((((.......(((((...........((......))...........))))).......----.......(--(((..........))))....))))).))))...... ( -20.95)
>DroYak_CAF1 27042 119 - 1
UCAAGACGUGCGCUUUACACUUCUGCGCCCCAA-AAUGCCCCAACAAUAACAACAUACAGAAGAAAAAAAAACCCCGCUACACAUUGAAAUUACAAACCGAAACGCGCAGGUCUAAUAGU
...((((.(((((......((((((........-.......................)))))).....................(((......)))........))))).))))...... ( -20.28)
>consensus
UCAAGACGUGCGCUUUACACUUCUGCGCCCCAA_AAUGCCCCAACAAUAACAACAUACAGAAGAAAAAAAAAAAACGCUACACAUUGAAAUUACAAACCGAAACGCGCAGGUCUAAUAGU
...((((.(((((......((((((...........((......))...........)))))).....................(((......)))........))))).))))...... (-17.20 = -17.95 +   0.75)

alignment

secondary structure

dotplot

Window 0

Location	24,914,949 – 24,915,061
Length	112
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	92.64
Mean single sequence MFE	-23.25
Consensus MFE	-23.05
Energy contribution	-23.18
Covariance contribution	0.13
Combinations/Pair	1.04
Mean z-score	-1.80
Structure conservation index	0.99
SVM decision value	1.42
SVM RNA-class probability	0.952306
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24914949 112 - 27905053
UAUCUGUGUGUUUUGUUAUAUUGACGUAUCUGAGCCUCAAGACGUGCGCUUUACACUUCUGCGCCCCAA-AAUGCCCCAACAAUCACAACAUACAGAAGAAGAAAAAAAA---CUA
..(((((((((((((((......((((...((.....))..))))((((...........)))).....-........)))))....)))))))))).............---... ( -23.20)
>DroSec_CAF1 28110 115 - 1
UAUCUGAGUGUUUUGUUAUAUUGACGUAUCUGAGCCUCAAGACGUGCGCUUUACACUUCUGCGCCCCAA-AAUGCCCCAACAAUAACAACAUUCAAAAGAAGAAAAAAAAACGCUA
....(((((((..((((((.(((((((...((.....))..))))((((...........)))).....-.......)))..)))))))))))))..................... ( -20.00)
>DroEre_CAF1 26752 112 - 1
UAUCUGUGUGUUUUGUUAUAUUGACGUAUCUGAGCCUCAAGACGUGCGCUUUACACUUCUGCGCCCCAAAAAUGCCCCAACAAUAACAACAUACAGAAAAAAAAA----CACGCUA
..(((((((((..((((((.(((((((...((.....))..))))((((...........)))).............)))..)))))))))))))))........----....... ( -24.90)
>DroYak_CAF1 27082 115 - 1
UAUCUGUGUGUUUUGUUAUAUUGACGUAUCUGAGCCUCAAGACGUGCGCUUUACACUUCUGCGCCCCAA-AAUGCCCCAACAAUAACAACAUACAGAAGAAAAAAAAACCCCGCUA
..(((((((((..((((((.(((((((...((.....))..))))((((...........)))).....-.......)))..)))))))))))))))................... ( -24.90)
>consensus
UAUCUGUGUGUUUUGUUAUAUUGACGUAUCUGAGCCUCAAGACGUGCGCUUUACACUUCUGCGCCCCAA_AAUGCCCCAACAAUAACAACAUACAGAAGAAAAAAAAAAAACGCUA
..(((((((((..((((((.(((((((...((.....))..))))((((...........)))).............)))..)))))))))))))))................... (-23.05 = -23.18 +   0.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:33:32 2006