Locus 5686

Sequence ID	2L_DroMel_CAF1
Location	16,168,619 – 16,168,759
Length	140
Max. P	0.789455

overview

Window 8

Location	16,168,619 – 16,168,722
Length	103
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	75.45
Mean single sequence MFE	-31.68
Consensus MFE	-18.39
Energy contribution	-17.67
Covariance contribution	-0.72
Combinations/Pair	1.40
Mean z-score	-1.57
Structure conservation index	0.58
SVM decision value	0.37
SVM RNA-class probability	0.708669
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16168619 103 + 22407834
UCCGCAUCAUUCAGGAUUGCUGCGGCGGCAACAACGACUCACUCGAAGACGUUGGCGAGGUGGACGACAACGCCGACGUUGUCGUGAGAAAGAACUCAAGG---AA
((((((.((........)).))).((((((((..(((.....))).....(((((((..((.....))..)))))))))))))))(((......)))..))---). ( -35.20)
>DroPse_CAF1 131431 97 + 1
UGCGGAUCGUGCGGGCUAG------UGGCAACAAUGAUUCACUCGAGGAUGUCGGCGAAGUGGAUGACAAUGCCGACGUGGUUGUAAGGAAAAAUACGCGC---AA
........(((((......------((....))....(((...(((..(((((((((...((.....)).)))))))))..)))....))).....)))))---.. ( -28.90)
>DroEre_CAF1 88960 103 + 1
UCCGCAUCAUUCAGGAUAGCUGCGGUGGCAACAACGACUCUCUCGAAGACGUUGGUGAGGUGGACGACAACGCCGACGUUGUUGUGAGAAAGAACUCGAGG---AA
((((((((......))).))..((.((....)).))..((((.(((.((((((((((..((.....))..)))))))))).))).))))..........))---). ( -33.50)
>DroWil_CAF1 125952 103 + 1
UACGAAUUAUUCGCUGUAGAAGCGGUGG---CAAUGAUUCCCUUGAAGACGUUGGCGAUGUGGAUGACAAUGCCGAUGUUGUUGUAAAAAAGAAUACACGCAAUAA
...((((((((((((((....)))))))---..))))))).......((((((((((.(((.....))).))))))))))((((((........)))).))..... ( -28.00)
>DroAna_CAF1 82343 100 + 1
UACGGAUCAUCCAAGAAAG---UGGUGGGAACAACGACUCACUCGAGGACGUCGGCGAGGUCGAUGACAACGCCGAUGUUGUGGUGAGAAAGAAUUCGCGC---AA
...((.....)).......---..(((.(((......((((((..(.((((((((((..(((...)))..)))))))))).)))))))......))).)))---.. ( -35.60)
>DroPer_CAF1 120461 97 + 1
UGCGGAUCGUGCGGGCUAG------UGGCAACAAUGAUUCACUCGAGGAUGUCGGCGAAGUGGAUGACAAUGCCGACGUGGUUGUAAGGAAAAAUACGCGC---AA
........(((((......------((....))....(((...(((..(((((((((...((.....)).)))))))))..)))....))).....)))))---.. ( -28.90)
>consensus
UACGGAUCAUUCAGGAUAG___CGGUGGCAACAACGACUCACUCGAAGACGUCGGCGAGGUGGAUGACAACGCCGACGUUGUUGUAAGAAAGAAUACGCGC___AA
.........................((....))....((..((((..((((((((((..((.....))..))))))))))....))))..)).............. (-18.39 = -17.67 +  -0.72)

alignment

secondary structure

dotplot

Window 9

Location	16,168,645 – 16,168,759
Length	114
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.02
Mean single sequence MFE	-36.35
Consensus MFE	-23.69
Energy contribution	-23.12
Covariance contribution	-0.58
Combinations/Pair	1.46
Mean z-score	-1.79
Structure conservation index	0.65
SVM decision value	0.58
SVM RNA-class probability	0.789455
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16168645 114 + 22407834
GGCAACAACGACUCACUCGAAGACGUUGGCGAGGUGGACGACAACGCCGACGUUGUCGUGAGAAAGAACUCAAGG---AAU---CGUCCCUCGAUCAGAAGGACAUGCAGGAUAACCGAG
.(((.....((.((...(((.((((((((((..((.....))..)))))))))).)))((((......))))..)---).)---)((((.((.....)).)))).))).((....))... ( -37.70)
>DroPse_CAF1 131451 114 + 1
GGCAACAAUGAUUCACUCGAGGAUGUCGGCGAAGUGGAUGACAAUGCCGACGUGGUUGUAAGGAAAAAUACGCGC---AAC---CGGCCCUCCAUCAGGAGGACAUGUAGGAUCACCGAG
(....).........((((..((((((((((...((.....)).)))))))((((((((..(........)..))---)))---)...(((((....))))))).......)))..)))) ( -38.70)
>DroGri_CAF1 94713 114 + 1
GG---CAACGAUUCGCUCGAAGAUGUUGGUGAUGUGGACGACAAUGCCGAUGUCAUUGUAAGAAGGAAUACGCGA---AAUAAACGGCCCUCCAUACGGAGGACAUGUAGAAUCACUGAG
(.---...)(((((((.((..((((((((((.(((.....))).))))))))))...(((........)))....---......))))(((((....))))).......)))))...... ( -31.50)
>DroWil_CAF1 125978 114 + 1
GG---CAAUGAUUCCCUUGAAGACGUUGGCGAUGUGGAUGACAAUGCCGAUGUUGUUGUAAAAAAGAAUACACGCAAUAAU---CGUCCUUCGAUAAGAAGGACAUGUAGAAUCACCGAG
((---...((((((....((.((((((((((.(((.....))).))))))))))((((((........)))).)).....)---)(((((((.....))))))).....))))))))... ( -35.20)
>DroAna_CAF1 82366 114 + 1
GGGAACAACGACUCACUCGAGGACGUCGGCGAGGUCGAUGACAACGCCGAUGUUGUGGUGAGAAAGAAUUCGCGC---AAC---CGACCCUCGAUCAGGAGGACAUGUAGGAUUACAGAA
....(((....(((..((((((..(((((((..(((...)))..)))))))((((((.((((......)))))))---)))---....))))))....)))....)))............ ( -36.30)
>DroPer_CAF1 120481 114 + 1
GGCAACAAUGAUUCACUCGAGGAUGUCGGCGAAGUGGAUGACAAUGCCGACGUGGUUGUAAGGAAAAAUACGCGC---AAC---CGGCCCUCCAUCAGGAGGACAUGUAGGAUCACCGAG
(....).........((((..((((((((((...((.....)).)))))))((((((((..(........)..))---)))---)...(((((....))))))).......)))..)))) ( -38.70)
>consensus
GGCAACAACGAUUCACUCGAAGACGUCGGCGAAGUGGAUGACAAUGCCGACGUUGUUGUAAGAAAGAAUACGCGC___AAC___CGGCCCUCCAUCAGGAGGACAUGUAGGAUCACCGAG
.........(((((...(((.((((((((((..((.....))..)))))))))).)))..............................((((......)))).......)))))...... (-23.69 = -23.12 +  -0.58)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:10 2006