Locus 4844

Sequence ID	X_DroMel_CAF1
Location	12,595,405 – 12,595,645
Length	240
Max. P	0.580115

overview

Window 4

Location	12,595,405 – 12,595,525
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.97
Mean single sequence MFE	-36.55
Consensus MFE	-28.40
Energy contribution	-29.02
Covariance contribution	0.63
Combinations/Pair	1.19
Mean z-score	-1.48
Structure conservation index	0.78
SVM decision value	0.09
SVM RNA-class probability	0.580115
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12595405 120 + 22224390
UUCAUUCAUAAGCUUCUUGAUGAGAUUAGCGAUAUCCUCACGCUUCUUGGUUACUGUGAGCAGGUCAAACCAAUUGCUCAGCUCCUUAAUGGGCAGUGUAUAGUCGUUGAUGGGUUUUGU
(((((.((.........)))))))(((((((((.....(((((...((((((.(((....)))....))))))..))...((.((.....)))).)))....)))))))))......... ( -28.30)
>DroSec_CAF1 3497 120 + 1
UUCAUUCAUCAGAUUCUGGAUGAGAUUGGCGAUAUCCUCGCGCUUCUUGGUUACUGUGAGCAGGUCAAACCAAUCGAUCAGCUCCGUAAUGGGCAGCUUAUAGUUAACGAUGGGUUUUGU
((((((((........))))))))....((((.....))))(((..(((...(((((((((.((((.........)))).((((......)))).)))))))))...)))..)))..... ( -34.70)
>DroEre_CAF1 4730 120 + 1
CUCAUCCAUCAGAUUCUGGAUGAGAUUGGCGAUAUCCUCGCGCUUCUUGGUUACCGUGAGCGGCUCAAACCAAUUUCUCAGCUCCCUAAUGGGCAGUCUAUAGUCUCUGAUGGGUUUCGU
...((((((((((..(((..(((((...((((.....)))).....((((((.(((....)))....))))))..)))))((((((....))).)))...)))..))))))))))..... ( -40.50)
>DroYak_CAF1 3746 120 + 1
CUCAUCCAUCAGAUGCUGGAUGAGUUUGGCGAUAUCCUCGCGCUUCUUGGUCACCGUCAGUGGAUCGAACCAAUUUCUCAGCUCCCUAAUGGGCAGUCUAUAGUCUCUGAUGGGUGUGGU
(.(((((((((((.((((..((((.(((((((.....)))).....((((((..(....)..))))))..)))...))))((((((....))).)))...)))).))))))))))).).. ( -42.70)
>consensus
CUCAUCCAUCAGAUUCUGGAUGAGAUUGGCGAUAUCCUCGCGCUUCUUGGUUACCGUGAGCAGGUCAAACCAAUUGCUCAGCUCCCUAAUGGGCAGUCUAUAGUCUCUGAUGGGUUUUGU
...((((((((((..(((..((((....((((.....)))).....((((((.(((....)))....))))))...))))((((((....))).)))...)))..))))))))))..... (-28.40 = -29.02 +   0.63)

alignment

secondary structure

dotplot

Window 5

Location	12,595,525 – 12,595,645
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.33
Mean single sequence MFE	-40.90
Consensus MFE	-32.67
Energy contribution	-34.05
Covariance contribution	1.38
Combinations/Pair	1.14
Mean z-score	-1.42
Structure conservation index	0.80
SVM decision value	0.03
SVM RNA-class probability	0.547522
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12595525 120 - 22224390
AAUGCGCUGGCGCAUGUCUUUAACAAGGAUAAUAUGCCCGGUCAUAGUGUGGAGGUGCCGCAACAGCAGAAUCUUACAGAUUGCGGCCUCUAUCUGCUGCAAUAUGUGGAGCAAUUCUUC
..((((((((.((((((..((......))..))))))))))).....(((((.....)))))...)))((((((((((.((((((((........)))))))).))).)))..))))... ( -37.20)
>DroSec_CAF1 3617 120 - 1
AGACAGCGGGCGCGCAUCUUCAACAGGGAUAAUAUGCCCGGUCUUAUUGUGGAGGUGCCGCAGCAGGAGAAUCUCACCGAUUGCGGCCUCUAUCUGCUGCAGUAUGCGGAGCAAUUCUUC
.....((..(((.(((((((((((.(((........))).)).......)))))))))))).)).((((((((((..((((((((((........)))))))).))..)))..))))))) ( -43.91)
>DroEre_CAF1 4850 120 - 1
AAUGCGCAGGCGCAUGUCUUCAACAAGCACAAUAUGCCCGCUCAUAGAGUGGAGGUGCCGCAGCAGGAGAAUCUCACUGAUUGCGGCCUCUAUCUGCUGCAAUAUGUGGAGCAAUUCUUC
..(((((.(((((.((((((....))).)))......((((((...))))))..))))))).)))((((((((((((..((((((((........))))))))..)).)))..))))))) ( -41.70)
>DroYak_CAF1 3866 120 - 1
AAUGCGCAGGCGCAUAUCUUCACCAAGGACAACAUGCCCGCUCAUCGAGUGGAGGUGCCGCAGCAGGAGAAUCUCACCGAUUGCGGCCUCUAUCUGCUGCAGUAUGUGGAGCAAUUCUUC
..(((((.(((((...((((.....))))........((((((...))))))..))))))).)))((((((((((..((((((((((........)))))))).))..)))..))))))) ( -40.80)
>consensus
AAUGCGCAGGCGCAUAUCUUCAACAAGGACAAUAUGCCCGCUCAUAGAGUGGAGGUGCCGCAGCAGGAGAAUCUCACCGAUUGCGGCCUCUAUCUGCUGCAAUAUGUGGAGCAAUUCUUC
.....((.(((((.((((((.....))))))......((((((...))))))..)))))))....((((((((((....((((((((........)))))))).....)))..))))))) (-32.67 = -34.05 +   1.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:24 2006