Locus 5

Sequence ID	X_DroMel_CAF1
Location	21,759 – 21,998
Length	239
Max. P	0.598632

overview

Window 5

Location	21,759 – 21,878
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.58
Mean single sequence MFE	-36.15
Consensus MFE	-34.44
Energy contribution	-33.50
Covariance contribution	-0.94
Combinations/Pair	1.17
Mean z-score	-1.35
Structure conservation index	0.95
SVM decision value	0.13
SVM RNA-class probability	0.598632
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21759 119 - 22224390
UGAUCAUAUAUGUCUCCCUUUUGGGCGAAGACGAUAGCUGCUGGCUGGGAAUGGUAGGGGGCUCAACUCGCCGAAUAUUCUUUGGCGGAGGUCUGAGAAAAGAAGAAUA-AGAGGCAUAA
........((((((((.(((((...(..((((...((((.((.(((......))).)).))))...(((((((((.....)))))).)))))))..)...)))))....-.)))))))). ( -36.40)
>DroSec_CAF1 9079 119 - 1
UGAUCAAAUAUGUCUCCCUUUUUGGCGAAGACGAUAGCUGCUGGCUGGGAAUGGUAGGGGGCUCAACUCGCCGAAUGUUCUUUGGCGGAGGUCUGGGAAAAAAAGAAUA-AGAGGCAUAA
........((((((((.((((((..(..((((...((((.((.(((......))).)).))))...(((((((((.....)))))).)))))))..)..))))))....-.)))))))). ( -37.30)
>DroSim_CAF1 9172 119 - 1
UGAUCAAAUAUGUCUCCCUUUUUGGCGAAGACGAUAGCUGCUGGCUGGGAAUGGUAGGGGGCUCAACUCGCCGAAUGUUCUUUGGCGGAGGUCUGGGAAAAAAAGAAUA-AGAGGCAUAA
........((((((((.((((((..(..((((...((((.((.(((......))).)).))))...(((((((((.....)))))).)))))))..)..))))))....-.)))))))). ( -37.30)
>DroYak_CAF1 3858 120 - 1
UGAUCAGAUAUGUUUCCCUUUUGGGUGAAGACGACAGCUGCUGGCUGGGAAUGGUAGGGGGCUCAACUCGCCGAAUGUUCUUCGGCGGAGGUCUGGGAAAAGAAGAAGAAAGGGACAUUA
..............((((((((......((((...((((.((.(((......))).)).))))...(((((((((.....)))))).))))))).............))))))))..... ( -33.61)
>consensus
UGAUCAAAUAUGUCUCCCUUUUGGGCGAAGACGAUAGCUGCUGGCUGGGAAUGGUAGGGGGCUCAACUCGCCGAAUGUUCUUUGGCGGAGGUCUGGGAAAAAAAGAAUA_AGAGGCAUAA
........((((((((.(((((...(..((((...((((.((.(((......))).)).))))...(((((((((.....)))))).)))))))..)...)))))......)))))))). (-34.44 = -33.50 +  -0.94)

alignment

secondary structure

dotplot

Window 6

Location	21,878 – 21,998
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.92
Mean single sequence MFE	-35.08
Consensus MFE	-32.28
Energy contribution	-33.02
Covariance contribution	0.75
Combinations/Pair	1.12
Mean z-score	-1.31
Structure conservation index	0.92
SVM decision value	-0.03
SVM RNA-class probability	0.517048
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21878 120 + 22224390
ACACGAUGCCAAGCAGUUCAAGCGGCAGUCUCUGCAUUGACAGCCUGGGCAAUUCGCUGGAGCGGAACAUCAAGCCGUCUGAUAUACUACGUCAGAAAUCAUCUGAUAAUUUGGAUUCCA
....((..(((((.((((((..((((.((((..((.......))..))))..(((((....))))).......))))..)))...)))..((((((.....))))))..)))))..)).. ( -33.40)
>DroSec_CAF1 9198 120 + 1
ACACGAUAGCGAGCAGUUCAAGCGGCAGUCUCUCCAUUGACAGUUUGGGCAAUUCGUUGGAGCGGAACAUCAAGCCGUCUGAUAUACUGCGUCAGAAAUCAUCUGAUAAUUUGGAUUCCA
...(((......((((((((..((((.(((........))).((((.(((.....))).))))..........))))..)))...)))))((((((.....))))))...)))....... ( -33.90)
>DroSim_CAF1 9291 120 + 1
ACACGAUACCGAGCAGUUCAAGCGGCAGUCUCUCCAUUGACAGUUUGGGCAAUUCGCUGGAGCGGAACAUCAAGCCGUCUGAUAUACUGCGUCAGAAAUCAUCUGAUAAUUUGGAUUCCA
........((((((((((((..((((.(((........))).((((.(((.....))).))))..........))))..)))...)))))((((((.....))))))...))))...... ( -39.70)
>DroYak_CAF1 3978 120 + 1
ACACGAUGCCGAGCAGUUCAAGCGGCAAUCUCGCCUUCGACAGUAUGGGCAAUUCGCUGGAGCGGAACAUUAAGCCGUCUGAUAUAUUGCGUCAAAAGUCAUCUGAUAAUUUGGAUUCCA
....(((((.((.....(((..((((......((((.(....)...))))..(((((....))))).......))))..)))....)))))))....(..(((..(....)..)))..). ( -33.30)
>consensus
ACACGAUACCGAGCAGUUCAAGCGGCAGUCUCUCCAUUGACAGUUUGGGCAAUUCGCUGGAGCGGAACAUCAAGCCGUCUGAUAUACUGCGUCAGAAAUCAUCUGAUAAUUUGGAUUCCA
....((..((((((((((((..((((.(((........))).((((.(((.....))).))))..........))))..)))...)))))((((((.....))))))...))))..)).. (-32.28 = -33.02 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:58 2006