Locus 4674

Sequence ID	3L_DroMel_CAF1
Location	13,216,096 – 13,216,216
Length	120
Max. P	0.877397

overview

Window 0

Location	13,216,096 – 13,216,216
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.03
Mean single sequence MFE	-37.38
Consensus MFE	-33.50
Energy contribution	-32.88
Covariance contribution	-0.62
Combinations/Pair	1.18
Mean z-score	-1.87
Structure conservation index	0.90
SVM decision value	0.90
SVM RNA-class probability	0.877397
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13216096 120 + 23771897
ACAAAGGCCCGAAAGUGUCGGGGAAUUUGAGUGCAGAUAGUGCGGACAGCGAGCAGAUAACUGAUUCAAAUGAUUCUACAGCGAGUGACUGGGAAGCAUUUGGAUUUUUCGCAGAUGGAA
.((((..(((((.....)))))...)))).(..(.....)..).....((((((((....)))(((((((((.((((.(((.......))))))).)))))))))..)))))........ ( -32.10)
>DroSec_CAF1 9437 119 + 1
ACAAAGGCCCGAAAGUGUCGGGGAAUUUGAGUGCAGAUAGUGCGGACAGCGAGCAGAUAACUGAUUCAAAUGAUUCCACAGCGAGUGGCUGGGGAGCAUUUGGGUU-UUCGCAGCUGGAA
.((((..(((((.....)))))...)))).(..(.....)..)...((((..((.((.....((((((((((.((((.((((.....)))).))))))))))))))-.)))).))))... ( -41.20)
>DroSim_CAF1 14517 120 + 1
ACAAAGGCCCGAAAGUGUCGGGGAAUUUGAGUGCAGAUAGUGCGGACAGCGAGCAGAUAACUGAUUCAAAUGAUUCCACAGCGAGUGGCUGGGGAGCAUUUGGGUUUUUCGCAGCUGGAA
.((((..(((((.....)))))...)))).(..(.....)..)...((((..((.((.....((((((((((.((((.((((.....)))).))))))))))))))..)))).))))... ( -41.50)
>DroYak_CAF1 9386 120 + 1
ACAAAGGCCCGAAAGUGUCGGGGAAUUUGAGUGCAGAUAGUGCGGACAGCGAGCAGAUAACUGAUUCAAAUGAUUUCACAGCGAGUCUCUGGAAAGCACUUGGGUUUCUCCCAAAUGGAA
.....(((.(....).)))((((((((..(((((...(((...((((.((((((((....))).)))...((....))..))..)))))))....)))))..))))))))((....)).. ( -34.70)
>consensus
ACAAAGGCCCGAAAGUGUCGGGGAAUUUGAGUGCAGAUAGUGCGGACAGCGAGCAGAUAACUGAUUCAAAUGAUUCCACAGCGAGUGGCUGGGAAGCAUUUGGGUUUUUCGCAGAUGGAA
.....(((.(....).)))((((((((..(((((.......((.....))((((((....))).)))......((((.((((.....)))))))))))))..)))))))).......... (-33.50 = -32.88 +  -0.62)

alignment

secondary structure

dotplot

Window 1

Location	13,216,096 – 13,216,216
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.03
Mean single sequence MFE	-28.12
Consensus MFE	-24.49
Energy contribution	-25.05
Covariance contribution	0.56
Combinations/Pair	1.09
Mean z-score	-1.73
Structure conservation index	0.87
SVM decision value	0.48
SVM RNA-class probability	0.754412
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13216096 120 - 23771897
UUCCAUCUGCGAAAAAUCCAAAUGCUUCCCAGUCACUCGCUGUAGAAUCAUUUGAAUCAGUUAUCUGCUCGCUGUCCGCACUAUCUGCACUCAAAUUCCCCGACACUUUCGGGCCUUUGU
........((((......((((((.(((.((((.....))))..))).))))))...(((....))).)))).....(((.....)))...((((...(((((.....)))))..)))). ( -24.90)
>DroSec_CAF1 9437 119 - 1
UUCCAGCUGCGAA-AACCCAAAUGCUCCCCAGCCACUCGCUGUGGAAUCAUUUGAAUCAGUUAUCUGCUCGCUGUCCGCACUAUCUGCACUCAAAUUCCCCGACACUUUCGGGCCUUUGU
...((((.((((.-(((.((((((.(((.((((.....)))).)))..)))))).....))).)).))..))))...(((.....)))...((((...(((((.....)))))..)))). ( -30.50)
>DroSim_CAF1 14517 120 - 1
UUCCAGCUGCGAAAAACCCAAAUGCUCCCCAGCCACUCGCUGUGGAAUCAUUUGAAUCAGUUAUCUGCUCGCUGUCCGCACUAUCUGCACUCAAAUUCCCCGACACUUUCGGGCCUUUGU
.....((.((((......((((((.(((.((((.....)))).)))..))))))...(((....))).)))).))..(((.....)))...((((...(((((.....)))))..)))). ( -29.90)
>DroYak_CAF1 9386 120 - 1
UUCCAUUUGGGAGAAACCCAAGUGCUUUCCAGAGACUCGCUGUGAAAUCAUUUGAAUCAGUUAUCUGCUCGCUGUCCGCACUAUCUGCACUCAAAUUCCCCGACACUUUCGGGCCUUUGU
...((((((((.....)))))))).....(((((.((((..(((.....((((((..((((.........))))...(((.....)))..)))))).......)))...)))).))))). ( -27.20)
>consensus
UUCCAGCUGCGAAAAACCCAAAUGCUCCCCAGCCACUCGCUGUGGAAUCAUUUGAAUCAGUUAUCUGCUCGCUGUCCGCACUAUCUGCACUCAAAUUCCCCGACACUUUCGGGCCUUUGU
........((((......((((((.((((((((.....)))).)))).))))))...(((....))).)))).....(((.....)))...((((...(((((.....)))))..)))). (-24.49 = -25.05 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:24 2006