Locus 15

Sequence ID	2R_DroMel_CAF1
Location	1,026,734 – 1,026,921
Length	187
Max. P	0.671220

overview

Window 8

Location	1,026,734 – 1,026,848
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.57
Mean single sequence MFE	-33.64
Consensus MFE	-23.04
Energy contribution	-24.10
Covariance contribution	1.06
Combinations/Pair	1.09
Mean z-score	-1.76
Structure conservation index	0.68
SVM decision value	0.29
SVM RNA-class probability	0.671220
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1026734 114 + 20766785
GUGUGUUUAAAAGUUCGUUUACCCUGGUGAAAGUGUGCUAACGGUUUCGUAUAGCUCCAUAUACUGUCGUGAACAAACACAGUCACAGCAGUAGCAUUACUGCUG------GCCCUCAGA
.(((((((....((((((((((....)))))((((((((((((....))).)))).....)))))....))))))))))))....((((((((....))))))))------......... ( -30.70)
>DroSec_CAF1 29163 120 + 1
GUGUGUUUAAAAGUUCGUUUACCCUGGUGAAAGUGUGCUAACGGUUUCGUAUAGCUUUAUAUACUGACGUGAACACACACAGUCACAGCAGUAGCAUUACUGUUGUUUCUGUUACUCAGA
(((((((((...(((..(((((....)))))((((((((((((....))).)))).....)))))))).)))))))))((((..(((((((((....)))))))))..))))........ ( -37.70)
>DroSim_CAF1 10654 119 + 1
GUGUGUUUA-AAGUUCGUUUACCCUGGUGAAAGUGUGCUAACGGUUUCGUGUAGCUUUAUAUACUGCCGUGAACAAACACAGACGCAGCAGUAGCAUUACUGUUGUUUCUGUUACUCAGA
(.(((....-..(((.((((((...(((((((.(((....))).))))(((((......))))).))))))))).)))(((((.(((((((((....))))))))).)))))))).)... ( -36.20)
>DroEre_CAF1 86875 114 + 1
GGGAGUUUAAAAGUUCGUUUACUCUGGUGAAAGUGUGCUAACGGUUUUGUAUGCCUUCAAAUACUGCCGUGACGAAACACAGUCUCAGCAAUAGCAAUACUGCUG------GGCCUCAGA
.(((((..............)))))(((((..((((....(((((...((((........)))).)))))......))))..))((((((.((....)).)))))------))))..... ( -29.94)
>consensus
GUGUGUUUAAAAGUUCGUUUACCCUGGUGAAAGUGUGCUAACGGUUUCGUAUAGCUUCAUAUACUGCCGUGAACAAACACAGUCACAGCAGUAGCAUUACUGCUG______GUACUCAGA
..((((((...(((...(((((....))))).....))).(((((...(((((......))))).)))))....)))))).....((((((((....))))))))............... (-23.04 = -24.10 +   1.06)

alignment

secondary structure

dotplot

Window 9

Location	1,026,774 – 1,026,888
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	84.31
Mean single sequence MFE	-28.05
Consensus MFE	-18.62
Energy contribution	-19.00
Covariance contribution	0.38
Combinations/Pair	1.16
Mean z-score	-1.54
Structure conservation index	0.66
SVM decision value	-0.03
SVM RNA-class probability	0.516899
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1026774 114 + 20766785
ACGGUUUCGUAUAGCUCCAUAUACUGUCGUGAACAAACACAGUCACAGCAGUAGCAUUACUGCUG------GCCCUCAGAAAGAUCAUCUCACUGCAAUGCAUAUGCAUAGAGUAUUAAA
(((....)))...((((((((((((((.((......)))))))..((((((((....))))))))------((...(((..((.....))..)))....)))))))....))))...... ( -25.10)
>DroSec_CAF1 29203 120 + 1
ACGGUUUCGUAUAGCUUUAUAUACUGACGUGAACACACACAGUCACAGCAGUAGCAUUACUGUUGUUUCUGUUACUCAGAAAGAUUAUCUCACUGCAAUGCAUAUGCAUAGGGUAUUAAA
...(((..(((((......))))).)))(((....)))((((..(((((((((....)))))))))..))))(((((((..((.....))..))...((((....)))).)))))..... ( -28.10)
>DroSim_CAF1 10693 120 + 1
ACGGUUUCGUGUAGCUUUAUAUACUGCCGUGAACAAACACAGACGCAGCAGUAGCAUUACUGUUGUUUCUGUUACUCAGAAAGAUUAUCUCACUGCAAUGCAUAUGCAUAGGGUAUUAAA
(((((...(((((......))))).)))))........(((((.(((((((((....))))))))).)))))(((((((..((.....))..))...((((....)))).)))))..... ( -33.60)
>DroEre_CAF1 86915 113 + 1
ACGGUUUUGUAUGCCUUCAAAUACUGCCGUGACGAAACACAGUCUCAGCAAUAGCAAUACUGCUG------GGCCUCAGAAAACUUAUCUCACUGCAAGUCAUAUGCAUAGGGUAUUA-A
(((((...((((........)))).)))))..........((.(((((((.((....)).)))))------)).)).........(((((...((((.......))))..)))))...-. ( -25.40)
>consensus
ACGGUUUCGUAUAGCUUCAUAUACUGCCGUGAACAAACACAGUCACAGCAGUAGCAUUACUGCUG______GUACUCAGAAAGAUUAUCUCACUGCAAUGCAUAUGCAUAGGGUAUUAAA
(((((...(((((......))))).)))))...............((((((((....)))))))).......................(((..((((.......))))..)))....... (-18.62 = -19.00 +   0.38)

alignment

secondary structure

dotplot

Window 0

Location	1,026,814 – 1,026,921
Length	107
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	82.91
Mean single sequence MFE	-22.87
Consensus MFE	-14.34
Energy contribution	-14.84
Covariance contribution	0.50
Combinations/Pair	1.12
Mean z-score	-1.66
Structure conservation index	0.63
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1026814 107 + 20766785
AGUCACAGCAGUAGCAUUACUGCUG------GCCCUCAGAAAGAUCAUCUCACUGCAAUGCAUAUGCAUAGAGUAUUAAAGUGCAAAAAAAUA-------AAAUUAACAUGAUACUUUAA
.....((((((((....))))))))------........(((((((((.........((((....))))...((((....)))).........-------........))))).)))).. ( -21.50)
>DroSec_CAF1 29243 120 + 1
AGUCACAGCAGUAGCAUUACUGUUGUUUCUGUUACUCAGAAAGAUUAUCUCACUGCAAUGCAUAUGCAUAGGGUAUUAAAGUGCAACAAAAUAAAUACAAAAAUUAACGUGAUACUUUAA
.(((((.(((((((((....)))).((((((.....)))))).........)))))..(((((((((.....))))....))))).......................)))))....... ( -24.10)
>DroSim_CAF1 10733 120 + 1
AGACGCAGCAGUAGCAUUACUGUUGUUUCUGUUACUCAGAAAGAUUAUCUCACUGCAAUGCAUAUGCAUAGGGUAUUAAAGUGCAACAAAAUAAAUACAAAAAUUAACGUGAUACUUUAA
(((.(((((((((....))))))))).)))..(((((((..((.....))..))...((((....)))).)))))((((((((..((.....................))..)))))))) ( -24.10)
>DroEre_CAF1 86955 113 + 1
AGUCUCAGCAAUAGCAAUACUGCUG------GGCCUCAGAAAACUUAUCUCACUGCAAGUCAUAUGCAUAGGGUAUUA-AGUGCAACACAAUAUAUUUAAAAAUUAACAUGCGGCUUUAA
.....(((((.((....)).)))))------((((.......(((((.(((..((((.......))))..)))...))-)))(((........................))))))).... ( -21.76)
>consensus
AGUCACAGCAGUAGCAUUACUGCUG______GUACUCAGAAAGAUUAUCUCACUGCAAUGCAUAUGCAUAGGGUAUUAAAGUGCAACAAAAUAAAUACAAAAAUUAACAUGAUACUUUAA
.....((((((((....))))))))............................((((.......))))((((((((((..((........................)).)))))))))). (-14.34 = -14.84 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:23:29 2006