Locus 7442

Sequence ID	2L_DroMel_CAF1
Location	20,652,648 – 20,652,777
Length	129
Max. P	0.939853

overview

Window 2

Location	20,652,648 – 20,652,747
Length	99
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	79.41
Mean single sequence MFE	-20.63
Consensus MFE	-11.43
Energy contribution	-11.52
Covariance contribution	0.09
Combinations/Pair	1.38
Mean z-score	-2.65
Structure conservation index	0.55
SVM decision value	1.28
SVM RNA-class probability	0.939853
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20652648 99 - 22407834
AUUAGUUU------UAUGGCUACUACAUUCGCCCUGUCAGAUUUUCUUUGACACAGGCAUCCCGAAAUC-AUUUUUAGCCAAACAUUCAACAUAAUUGCAAAACUG
..((((((------(.((((((........(((.(((((((.....)))))))..))).....(....)-.....)))))).........((....)).))))))) ( -20.10)
>DroSec_CAF1 5452 99 - 1
AUUAGUUU------UAUGACUACUGCAUUCGCCCUGUCAGAUUUUCUUUGACACAGGCAUCCCAAAAUC-AUUUUUAGGCAAACAUUCAACAUAAUUGCAAAACUG
..(((((.------...))))).((((...(((.(((((((.....)))))))..)))..((.((((..-..)))).)).................))))...... ( -18.00)
>DroSim_CAF1 5455 99 - 1
AUUAGUUU------UAUGGCUACUGCAUUCGCCCUGUCAGAUUUUCUUUGACACAGGCAUCCCGAAAUC-AUUUUUAGCCAAACAUUCAACAUAAUUGCAAAACUG
..((((((------(.((((((........(((.(((((((.....)))))))..))).....(....)-.....)))))).........((....)).))))))) ( -20.10)
>DroEre_CAF1 5489 99 - 1
AUUAGUUU------UAUGGCUACUGCACUCGCCCUGUCAGAUUUUCUCUGACACAGGUAUUCUGAAAUC-AUUUUCAGACAAACACUCAACAUAAUUGCAAAACUG
....((.(------((((((....))....(((.(((((((.....)))))))..)))..(((((((..-..)))))))...........)))))..))....... ( -23.20)
>DroYak_CAF1 5507 105 - 1
AUUAGUUUGCUUAUUAGUUAUACUGCAUUCAGCCUGUCAAAUUUUCUUUGACACAGGUAUUUUAAAAUC-UUUUUUAAGCAAACAUUCAACAUAAUUGCAAAACUG
....(((((((((...((......)).....((((((((((.....))))))..))))...........-.....)))))))))...................... ( -19.50)
>DroAna_CAF1 5417 90 - 1
AUUAGUUU------GAUGACUUUUGCAUUUGGCUUGUCAGAAAUCCUCUGACACUGGCAUCUUUCGAUCCAUUUUCAAACCAA----AAGCAUAA------GAAUA
........------.....(((.(((.(((((..(((((((.....))))))).(((.(((....))))))........))))----).))).))------).... ( -22.90)
>consensus
AUUAGUUU______UAUGGCUACUGCAUUCGCCCUGUCAGAUUUUCUUUGACACAGGCAUCCCGAAAUC_AUUUUUAGACAAACAUUCAACAUAAUUGCAAAACUG
..((((((......((((............(((.(((((((.....)))))))..))).....((((.....))))..............))))......)))))) (-11.43 = -11.52 +   0.09)

alignment

secondary structure

dotplot

Window 3

Location	20,652,678 – 20,652,777
Length	99
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	82.48
Mean single sequence MFE	-19.04
Consensus MFE	-14.18
Energy contribution	-13.78
Covariance contribution	-0.40
Combinations/Pair	1.21
Mean z-score	-1.82
Structure conservation index	0.74
SVM decision value	0.55
SVM RNA-class probability	0.779178
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20652678 99 - 22407834
A---GUAUAUUAUAUA-GCUUUUCAGUUUGCUUAAUUAGUUUUAUGGCUACUACAUUCGCCCUGUCAGAUUUUCUUUGACACAGGCAUCCCGAAAUC-AUUUUU
.---............-...((((.(..(((((............(((..........))).(((((((.....))))))).)))))..).))))..-...... ( -16.30)
>DroSec_CAF1 5482 99 - 1
A---GUAUAUUAUAUA-GCUUUUCAGUCUGCUUAAUUAGUUUUAUGACUACUGCAUUCGCCCUGUCAGAUUUUCUUUGACACAGGCAUCCCAAAAUC-AUUUUU
(---(((..(((((.(-(((.((.((....)).))..)))).))))).))))......(((.(((((((.....)))))))..)))...........-...... ( -16.50)
>DroSim_CAF1 5485 99 - 1
A---GUAUAUUAUAUA-GCUUUUCAGUCUGCUUAAUUAGUUUUAUGGCUACUGCAUUCGCCCUGUCAGAUUUUCUUUGACACAGGCAUCCCGAAAUC-AUUUUU
.---............-...((((.(..(((.....(((((....)))))..)))..)(((.(((((((.....)))))))..))).....))))..-...... ( -17.50)
>DroEre_CAF1 5519 93 - 1
A---G--UAUACUAUA-GC----CAGUCUGCUUAAUUAGUUUUAUGGCUACUGCACUCGCCCUGUCAGAUUUUCUCUGACACAGGUAUUCUGAAAUC-AUUUUC
(---(--.(((((.((-((----((....(((.....)))....))))))............(((((((.....)))))))..))))).))......-...... ( -22.30)
>DroAna_CAF1 5437 104 - 1
AAUAAUAUAAACUAUAUGCACUUUAGUCUGCUUAAUUAGUUUGAUGACUUUUGCAUUUGGCUUGUCAGAAAUCCUCUGACACUGGCAUCUUUCGAUCCAUUUUC
...........(((.(((((....((((.(((.....))).....))))..))))).)))..(((((((.....))))))).(((.(((....))))))..... ( -22.60)
>consensus
A___GUAUAUUAUAUA_GCUUUUCAGUCUGCUUAAUUAGUUUUAUGGCUACUGCAUUCGCCCUGUCAGAUUUUCUUUGACACAGGCAUCCCGAAAUC_AUUUUU
.................((.....((((.(((.....))).....))))...))....(((.(((((((.....)))))))..))).................. (-14.18 = -13.78 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:36:57 2006