Locus 7868

Sequence ID	3R_DroMel_CAF1
Location	21,064,104 – 21,064,197
Length	93
Max. P	0.959269

overview

Window 6

Location	21,064,104 – 21,064,197
Length	93
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	77.61
Mean single sequence MFE	-34.23
Consensus MFE	-21.93
Energy contribution	-22.60
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.19
Structure conservation index	0.64
SVM decision value	1.50
SVM RNA-class probability	0.959269
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21064104 93 + 27905053
GCAGCGCAAUGGACGCACCUACCUGAGCGUGGAUAAGCUCAAGGUUCUGGUGGAGCCACAAAAGUAGGUGC--AGUUCGGA---U------U---------UUAGCUGAGAUA
.((((....(((((((((((((.(((((........))))).(((((.....)))))......))))))))--.)))))..---.------.---------...))))..... ( -38.20)
>DroVir_CAF1 18138 93 + 1
GUCGCGCAACGGACGCACCUAUCUGAGCGUGGACAAGCUCAAGGUGCUCGUGGAGCCACAGAAGUAAGUUG--AGAGCGGA---U------C---------AAAGGUUAUACA
.((((.((((..((((((((...(((((........)))))))))))..(((....)))....))..))))--...)))).---.------.---------............ ( -32.60)
>DroSec_CAF1 17460 93 + 1
GCAGCGCAAUGGACGCACCUACCUGAGCGUGGAUAAGCUCAAGGUGCUGGUGGAGCCACAAAAGUGGGUGC--AGUUCGGA---U------U---------UUAGCUGACUCA
.((((....(((((((((((((((((((........)))).))))(((.(((....)))...)))))))))--.)))))..---.------.---------...))))..... ( -36.40)
>DroSim_CAF1 16752 93 + 1
GCAGCGCAAUGGACGCACCUAUUUGAGCGUGGAUAAGCUCAAGGUGCUGGUGGAGCCACAAAAGUGGGUGC--AGUUCGGA---U------U---------UUAGCUGACUCA
.((((....(((((((((((...(((((........)))))))))))...((.(.((((....)))).).)--))))))..---.------.---------...))))..... ( -35.10)
>DroEre_CAF1 18090 103 + 1
GGUGCGCAAUGGACGCACCUACCUGAGCGUGGAUAAGCUCAAGGUGCUGGUGGAGCCACAAAAGUAAGUGC--AGCUCAGA---UUGGUGUCCUUUCAUGUUAAGCUG-----
(((..(((..((((((((((((((((((........)))).)))))..))).(((((((........))).--.))))...---...)))))).....)))...))).----- ( -33.10)
>DroAna_CAF1 17359 95 + 1
GCAGCGCAACGGUCGCACCUUCCUGAGCGUGGACAAGCUCAAGGUGCUUGUGGAGCCCCAAAAGUAAGUGCCAAGCUGGGGGAGA------U---------UUAGAGAA---A
...((((....).)))..((((((.(((.(((((((((.......))))))((....))...........))).))).)))))).------.---------........---. ( -30.00)
>consensus
GCAGCGCAAUGGACGCACCUACCUGAGCGUGGAUAAGCUCAAGGUGCUGGUGGAGCCACAAAAGUAAGUGC__AGUUCGGA___U______U_________UUAGCUGA__CA
...((((.......((((((...(((((........)))))))))))..(((....)))........)))).......................................... (-21.93 = -22.60 +   0.67)

alignment

secondary structure

dotplot

Window 7

Location	21,064,104 – 21,064,197
Length	93
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	77.61
Mean single sequence MFE	-27.85
Consensus MFE	-18.54
Energy contribution	-18.73
Covariance contribution	0.19
Combinations/Pair	1.11
Mean z-score	-1.73
Structure conservation index	0.67
SVM decision value	1.00
SVM RNA-class probability	0.897813
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21064104 93 - 27905053
UAUCUCAGCUAA---------A------A---UCCGAACU--GCACCUACUUUUGUGGCUCCACCAGAACCUUGAGCUUAUCCACGCUCAGGUAGGUGCGUCCAUUGCGCUGC
.....((((...---------.------.---........--(((((((((((.(((....))).)))...((((((........))))))))))))))((.....)))))). ( -28.40)
>DroVir_CAF1 18138 93 - 1
UGUAUAACCUUU---------G------A---UCCGCUCU--CAACUUACUUCUGUGGCUCCACGAGCACCUUGAGCUUGUCCACGCUCAGAUAGGUGCGUCCGUUGCGCGAC
............---------.------.---..(((...--((((..((...((((....)))).(((((((((((........)))))...))))))))..)))).))).. ( -27.00)
>DroSec_CAF1 17460 93 - 1
UGAGUCAGCUAA---------A------A---UCCGAACU--GCACCCACUUUUGUGGCUCCACCAGCACCUUGAGCUUAUCCACGCUCAGGUAGGUGCGUCCAUUGCGCUGC
.....((((...---------.------.---........--((((((((....)))(((.....)))((((.((((........)))))))).)))))((.....)))))). ( -26.70)
>DroSim_CAF1 16752 93 - 1
UGAGUCAGCUAA---------A------A---UCCGAACU--GCACCCACUUUUGUGGCUCCACCAGCACCUUGAGCUUAUCCACGCUCAAAUAGGUGCGUCCAUUGCGCUGC
.....((((...---------.------.---........--....((((....))))........(((((((((((........)))))...)))))).........)))). ( -26.30)
>DroEre_CAF1 18090 103 - 1
-----CAGCUUAACAUGAAAGGACACCAA---UCUGAGCU--GCACUUACUUUUGUGGCUCCACCAGCACCUUGAGCUUAUCCACGCUCAGGUAGGUGCGUCCAUUGCGCACC
-----...............((((.....---...((((.--.((........))..)))).....(((((((((((........)))))...)))))))))).......... ( -33.60)
>DroAna_CAF1 17359 95 - 1
U---UUCUCUAA---------A------UCUCCCCCAGCUUGGCACUUACUUUUGGGGCUCCACAAGCACCUUGAGCUUGUCCACGCUCAGGAAGGUGCGACCGUUGCGCUGC
.---........---------.------.......((((.((((.........(((....)))...(((((((((((........)))))...))))))....)))).)))). ( -25.10)
>consensus
UG__UCAGCUAA_________A______A___UCCGAACU__GCACCUACUUUUGUGGCUCCACCAGCACCUUGAGCUUAUCCACGCUCAGGUAGGUGCGUCCAUUGCGCUGC
..........................................(((.((((....))))........(((((((((((........)))))...))))))......)))..... (-18.54 = -18.73 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:56:45 2006