Locus 3938

Sequence ID	3L_DroMel_CAF1
Location	11,420,751 – 11,420,884
Length	133
Max. P	0.999479

overview

Window 0

Location	11,420,751 – 11,420,844
Length	93
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	98.07
Mean single sequence MFE	-21.28
Consensus MFE	-20.18
Energy contribution	-20.02
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-2.50
Structure conservation index	0.95
SVM decision value	3.64
SVM RNA-class probability	0.999479
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11420751 93 + 23771897
AACAA-AAACUGGGAGAAAAAUGCAAAGCAAACAAGCACCAAAUUGCAUUGCUGUAAAGCAUGUUUUGUGUUUGCUUUUUUGUAGAAUUUUUAA
.....-...(((.(((((((((((((((((.....(((......)))..((((....)))))))))))))))...)))))).)))......... ( -21.40)
>DroSec_CAF1 140476 93 + 1
AACAA-AAACUGGGAGAAAAAUGCAAAGCAAACAAGCACCAAAUUGCAUUGCUGUAAAGCAUGUUUUGUGUUUGCUUUUUUGUAGAAUUUUUAA
.....-...(((.(((((((((((((((((.....(((......)))..((((....)))))))))))))))...)))))).)))......... ( -21.40)
>DroSim_CAF1 151958 93 + 1
AACAA-AAACCGGGAGAAAAAUGCAAAGCAAACAAGCACCAAAUUGCAUUGCUGUAAAGCAUGUUUUGUGUUUGCUUUUUUGUAGAAUUUUUAA
.((((-(((...((....((((((((((((.....(((......)))..((((....)))))))))))))))).)))))))))........... ( -20.90)
>DroEre_CAF1 148051 92 + 1
AACAA-AAACUGGGGGAAAAAUGCAAAGCAAACAAGCACCAAAUUGCAUUGCUGUAAAGCAUGUUUUGUGUUUGCUU-UUUGUAGAAUUUUUAA
.....-...(((.(((((((((((((((((.....(((......)))..((((....))))))))))))))))..))-))).)))......... ( -20.90)
>DroYak_CAF1 138900 93 + 1
AACAAAAAACUGGGAGAAAAAUGCAAAGCAAACAAGCACCAAAUUGCAUUGCUGUAAAGCAUGUUUUGUGUUUGCUU-UUUGUAGAAUUUUUAA
.........(((.(((((((((((((((((.....(((......)))..((((....))))))))))))))))..))-))).)))......... ( -21.80)
>consensus
AACAA_AAACUGGGAGAAAAAUGCAAAGCAAACAAGCACCAAAUUGCAUUGCUGUAAAGCAUGUUUUGUGUUUGCUUUUUUGUAGAAUUUUUAA
.............(((((...(((((((((((((.(((......)))..((((....)))).......))))))))...)))))...))))).. (-20.18 = -20.02 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	11,420,751 – 11,420,844
Length	93
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	98.07
Mean single sequence MFE	-16.00
Consensus MFE	-14.74
Energy contribution	-15.14
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.45
Structure conservation index	0.92
SVM decision value	0.73
SVM RNA-class probability	0.836596
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11420751 93 - 23771897
UUAAAAAUUCUACAAAAAAGCAAACACAAAACAUGCUUUACAGCAAUGCAAUUUGGUGCUUGUUUGCUUUGCAUUUUUCUCCCAGUUU-UUGUU
................((((((((((.......((((....))))..(((......))).))))))))))..................-..... ( -15.90)
>DroSec_CAF1 140476 93 - 1
UUAAAAAUUCUACAAAAAAGCAAACACAAAACAUGCUUUACAGCAAUGCAAUUUGGUGCUUGUUUGCUUUGCAUUUUUCUCCCAGUUU-UUGUU
................((((((((((.......((((....))))..(((......))).))))))))))..................-..... ( -15.90)
>DroSim_CAF1 151958 93 - 1
UUAAAAAUUCUACAAAAAAGCAAACACAAAACAUGCUUUACAGCAAUGCAAUUUGGUGCUUGUUUGCUUUGCAUUUUUCUCCCGGUUU-UUGUU
................((((((((((.......((((....))))..(((......))).))))))))))..................-..... ( -15.90)
>DroEre_CAF1 148051 92 - 1
UUAAAAAUUCUACAAA-AAGCAAACACAAAACAUGCUUUACAGCAAUGCAAUUUGGUGCUUGUUUGCUUUGCAUUUUUCCCCCAGUUU-UUGUU
...............(-(((((((((.......((((....))))..(((......))).))))))))))..................-..... ( -15.90)
>DroYak_CAF1 138900 93 - 1
UUAAAAAUUCUACAAA-AAGCAAACACAAAACAUGCUUUACAGCAAUGCAAUUUGGUGCUUGUUUGCUUUGCAUUUUUCUCCCAGUUUUUUGUU
...........(((((-((((......((((.((((.....(((((.(((......)))....)))))..))))))))......))))))))). ( -16.40)
>consensus
UUAAAAAUUCUACAAAAAAGCAAACACAAAACAUGCUUUACAGCAAUGCAAUUUGGUGCUUGUUUGCUUUGCAUUUUUCUCCCAGUUU_UUGUU
................((((((((((.......((((....))))..(((......))).))))))))))........................ (-14.74 = -15.14 +   0.40)

alignment

secondary structure

dotplot

Window 2

Location	11,420,774 – 11,420,884
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	99.09
Mean single sequence MFE	-20.20
Consensus MFE	-18.92
Energy contribution	-19.32
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.31
Structure conservation index	0.94
SVM decision value	0.13
SVM RNA-class probability	0.597474
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11420774 110 - 23771897
ACGGCCUAGAAGUUUUGCUCGCCAAACAGAAAAAAAUUGUUUAAAAAUUCUACAAAAAAGCAAACACAAAACAUGCUUUACAGCAAUGCAAUUUGGUGCUUGUUUGCUUU
..(((..((........)).)))((((((.......))))))..............((((((((((.......((((....))))..(((......))).)))))))))) ( -19.80)
>DroSec_CAF1 140499 109 - 1
ACGGCCUAGAAGUUUUGCUCGCCAAACAGAAA-AAAUUGUUUAAAAAUUCUACAAAAAAGCAAACACAAAACAUGCUUUACAGCAAUGCAAUUUGGUGCUUGUUUGCUUU
..(((..((........)).)))((((((...-...))))))..............((((((((((.......((((....))))..(((......))).)))))))))) ( -20.30)
>DroSim_CAF1 151981 109 - 1
ACGGCCUAGAAGUUUUGCUCGCCAAACAGAAA-AAAUUGUUUAAAAAUUCUACAAAAAAGCAAACACAAAACAUGCUUUACAGCAAUGCAAUUUGGUGCUUGUUUGCUUU
..(((..((........)).)))((((((...-...))))))..............((((((((((.......((((....))))..(((......))).)))))))))) ( -20.30)
>DroEre_CAF1 148074 108 - 1
ACGGCCUAGAAGUUUUGCUCGCCAAACAGAAA-AAAUUGUUUAAAAAUUCUACAAA-AAGCAAACACAAAACAUGCUUUACAGCAAUGCAAUUUGGUGCUUGUUUGCUUU
..(((..((........)).)))((((((...-...)))))).............(-(((((((((.......((((....))))..(((......))).)))))))))) ( -20.30)
>DroYak_CAF1 138924 108 - 1
ACGGCCUAGAAGUUUUGCUCGCCAAACAGAAA-AAAUUGUUUAAAAAUUCUACAAA-AAGCAAACACAAAACAUGCUUUACAGCAAUGCAAUUUGGUGCUUGUUUGCUUU
..(((..((........)).)))((((((...-...)))))).............(-(((((((((.......((((....))))..(((......))).)))))))))) ( -20.30)
>consensus
ACGGCCUAGAAGUUUUGCUCGCCAAACAGAAA_AAAUUGUUUAAAAAUUCUACAAAAAAGCAAACACAAAACAUGCUUUACAGCAAUGCAAUUUGGUGCUUGUUUGCUUU
..(((..((........)).)))((((((.......))))))..............((((((((((.......((((....))))..(((......))).)))))))))) (-18.92 = -19.32 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:29 2006