Locus 3367

Sequence ID	3L_DroMel_CAF1
Location	9,841,536 – 9,841,718
Length	182
Max. P	0.568283

overview

Window 0

Location	9,841,536 – 9,841,641
Length	105
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	77.05
Mean single sequence MFE	-41.85
Consensus MFE	-26.89
Energy contribution	-26.86
Covariance contribution	-0.03
Combinations/Pair	1.29
Mean z-score	-1.24
Structure conservation index	0.64
SVM decision value	0.07
SVM RNA-class probability	0.568283
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9841536 105 + 23771897
GGCGGCAUGAUGCGCACCGGGAUGCGG---GUGGGAGGAAUGCGCGUUGUGCGCACC---AGGGUCAACGAGUCGAAUGACCUGCGCACCAUGCGCCGCCAGCUGCUCUAU
((((((......(.((((.(....).)---))).).((...((((((.(((((((..---..(((((..........)))))))))))).))))))..)).)))))).... ( -47.30)
>DroVir_CAF1 1504 108 + 1
GGCGGGAUGAUGCGCAACAACAUGCGUGGCGUUGGCAACAUGCGGAUUGUGCGGCCG---CGCAUCAACGAAUCCAAUGAUCUGCGCACCAUGCGCCGCCAACUGCUUUAU
(((((((((.((((((.....(((((((((..((....))((((.....))))))))---)))))....((.((....)))))))))).))).).)))))........... ( -42.10)
>DroPse_CAF1 1632 108 + 1
GGCGGCAUGACACGUGGAAAUAUGCGG---GUUGGAGCCAUGCGCGUUGUGCGUACCCGCAACGUCAACGAGUCCAAUGAUCUGCGCACCAUGCGCCGCCAGUUGCUCUAU
((((((..(((.(((.((....(((((---((.(....)((((((...)))))))))))))...)).))).)))...........((.....))))))))........... ( -40.20)
>DroWil_CAF1 15728 105 + 1
GGCGGGAUUGUACGCAG---CAUGCGUGGCGUUGGUACCAUGCGCAUUGUCCGUGCU---CGGACCAAUGAGUCAAAUGAUUUGCGGACUAUGCGCCGCCAGCUGCUCUAU
.(((........)))((---((.((.(((((.((....)).((((((.(((((((((---((......)))))..........)))))).))))))))))))))))).... ( -41.90)
>DroMoj_CAF1 1485 108 + 1
GGCGGCAUGAUUCGUAACAACAUGCGCGGCGUUGGCACCAUGAGGAUUGUGCGUCCG---CGCCUCAACGAAUCCAAUGAUUUGCGCACCAUGCGCCGCCAGCUGCUCUAC
((((((..(((((((........(((((((((..(((((....))..)))))).)))---)))....)))))))...........((.....))))))))........... ( -39.40)
>DroPer_CAF1 1635 108 + 1
GGCGGCAUGACACGUGGAAAUAUGCGG---GUUGGAGCCAUGCGCGUUGUGCGUACCCGCAACGUCAACGAGUCCAAUGAUCUGCGCACCAUGCGCCGCCAGUUGCUUUAU
((((((..(((.(((.((....(((((---((.(....)((((((...)))))))))))))...)).))).)))...........((.....))))))))........... ( -40.20)
>consensus
GGCGGCAUGAUACGCAGCAACAUGCGG___GUUGGAACCAUGCGCAUUGUGCGUACC___AGCGUCAACGAGUCCAAUGAUCUGCGCACCAUGCGCCGCCAGCUGCUCUAU
((((((......((((......)))).................((((.(((((((...........................))))))).))))))))))........... (-26.89 = -26.86 +  -0.03)

alignment

secondary structure

dotplot

Window 1

Location	9,841,601 – 9,841,718
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.88
Mean single sequence MFE	-27.18
Consensus MFE	-16.80
Energy contribution	-17.50
Covariance contribution	0.70
Combinations/Pair	1.29
Mean z-score	-1.45
Structure conservation index	0.62
SVM decision value	-0.02
SVM RNA-class probability	0.521011
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9841601 117 + 23771897
GUCGAAUGACCUGCGCACCAUGCGCCGCCAGCUGCUCUAUGCACAGCAGAAAGACCGGGCUCGCCUGCUCAAGAUUCAGCAGCUGAAAAGGUAAAUAGACCAAAUUUCAA---AAAAAAA
(((.....((((((((.....))))...((((((((...(((...)))....((.((((....)))).)).......))))))))...)))).....)))..........---....... ( -35.30)
>DroGri_CAF1 1656 115 + 1
AUCCAAUGAUCUGCGCACCAUGCGCCGCCAACUGCUAUAUGCACAGCAAAAAGAUCGCGCUCGCCUCCUCAAGAUUCAACAGCUGAAAAGGUAAUUAGACAAAAACA--AAAAAAAA---
.......(((((((((.....)))).((....(((.....)))..))....)))))......((((..(((............)))..))))...............--........--- ( -19.90)
>DroWil_CAF1 15793 110 + 1
GUCAAAUGAUUUGCGGACUAUGCGCCGCCAGCUGCUCUAUGCUCAGCAGAAAGAUAAAGCUCUAUUGGCUAAAAUAGAGCAGCUGAAAAGGUAAUUAGAUACA-----AA---AACAA--
(((.(((.((((((((........))))((((((((((((....(((.((.(((......))).)).)))...))))))))))))...)))).))).)))...-----..---.....-- ( -33.20)
>DroMoj_CAF1 1553 117 + 1
AUCCAAUGAUUUGCGCACCAUGCGCCGCCAGCUGCUCUACGCACAGCAGAAAGAUCGCGCUCGUCUGCUCAAGAUACAACAGUUGAAAAGGUAAUUAGACAAAAAGUUAAACAAACA---
......((((((((((.....))))...((((((..........((((((.((......))..))))))..........))))))..................))))))........--- ( -21.75)
>DroAna_CAF1 2259 117 + 1
GUCGAAUGACCUGCGUACCAUGCGCCGCCAACUGCUCUAUGCUCAGCAGAAAGAUCGGGCCCGCCUGCUUAAGAUUCAGCAGCUGAAAAGGUAAAUAGACAAAAACGAAA---UAAGAAA
(((.....(((((((((....(((........)))..)))))(((((.........(((....)))(((........))).)))))..)))).....)))..........---....... ( -26.00)
>DroPer_CAF1 1703 117 + 1
GUCCAAUGAUCUGCGCACCAUGCGCCGCCAGUUGCUUUAUGCACAGCAGAAAGAUCGGGCUCGCCUGCUUAAGAUUCAACAGCUGAAAAGGUAAAUAGACAAAAGACAAA---UAGAAAA
(((...((.(((((((.....)))).(((...(((.....)))((((.....((((.(((......)))...)))).....))))....)))....)))))...)))...---....... ( -26.90)
>consensus
GUCCAAUGAUCUGCGCACCAUGCGCCGCCAGCUGCUCUAUGCACAGCAGAAAGAUCGGGCUCGCCUGCUCAAGAUUCAACAGCUGAAAAGGUAAAUAGACAAAAACU_AA___AAAAA__
(((.....((((((((.....))))...((((((..........(((((...((......))..)))))..........))))))...)))).....))).................... (-16.80 = -17.50 +   0.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:21 2006