Locus 2012

Sequence ID	X_DroMel_CAF1
Location	5,518,207 – 5,518,321
Length	114
Max. P	0.636409

overview

Window 2

Location	5,518,207 – 5,518,321
Length	114
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	78.85
Mean single sequence MFE	-31.71
Consensus MFE	-19.21
Energy contribution	-21.10
Covariance contribution	1.89
Combinations/Pair	1.09
Mean z-score	-1.58
Structure conservation index	0.61
SVM decision value	0.21
SVM RNA-class probability	0.636409
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5518207 114 + 22224390
UGCCCGUUUGUUUGUGCU---CCCGUCCAGGUGAAGGUUAAGUGCUCCGAGCUGAGGAUCAAGGACAAGAAGGAACUCACCAAGCAAUUGGAUGAGCUCAAGAAUGAGUUGCUCAGC
.....((((.(((.((.(---((.((((.(((...((.........))..)))..))))...))))).))).))))...((((....)))).((((((((....)))...))))).. ( -28.10)
>DroVir_CAF1 9854 111 + 1
------UUCCAUUUGGCUCUAUUCUCACAGGUGAAGAUCAAGUGCUCAGAGCUGAGAACCAAGGACAAGAAGGAGCUCACCAAGCAAUUGGAUGAGCUCAAGAAUGAGCUGCUCAAU
------........(((((.(((((....(((............((((....)))).)))............(((((((((((....)))).))))))).))))))))))....... ( -33.72)
>DroPse_CAF1 23089 98 + 1
---------------G-C---CUCACUCAGGUAAAGGUCAAGUGCUCCGAGCUGAGAACCAAGGACAAGAAGGAGCUCACCAAGCAAUUGGAUGAGCUCAAGAAUGAGCUCCUCAAU
---------------(-(---.((((((((.(...((.........)).).)))))................(((((((((((....)))).))))))).....)))))........ ( -29.50)
>DroMoj_CAF1 8669 111 + 1
------AUUGUUUUUGCUCUUCUCGCAUAGGUGAAGAUCAAGUGCUCAGAAUUGAGAACGAAGGACAAGAAGGAGCUCACCAAGCAAUUGGAUGAGCUCAAGAAUGAGCUGCUCAAU
------....((((((..((((((((....)))).......((.(((......))).))))))..)))))).(((((((((((....)))).))))))).....((((...)))).. ( -35.90)
>DroAna_CAF1 7419 109 + 1
UGUACUCUUUUU-----U---GCCGCGCAGGUGAAGGUUAAGUGCUCCGAGCUGAGGACGAAGGACAAGAAGGAGCUGACCAAGCAGCUGGAUGAGCUCAAGAACGAGCUCCUCAAU
.....(((((((-----(---(((((((.............))))(((.......)))....)).)))))))))((((......))))..((.((((((......)))))).))... ( -33.52)
>DroPer_CAF1 25604 98 + 1
---------------G-C---CUCACUCAGGUAAAGGUCAAGUGCUCCGAGCUGAGAACCAAGGACAAGAAGGAGCUCACCAAGCAAUUGGAUGAGCUCAAGAAUGAGCUCCUCAAU
---------------(-(---.((((((((.(...((.........)).).)))))................(((((((((((....)))).))))))).....)))))........ ( -29.50)
>consensus
_______UU_UU___G_U___CUCGCACAGGUGAAGGUCAAGUGCUCCGAGCUGAGAACCAAGGACAAGAAGGAGCUCACCAAGCAAUUGGAUGAGCUCAAGAAUGAGCUCCUCAAU
....................................(((..((.(((......))).))....)))......(((((((((((....)))).))))))).....((((...)))).. (-19.21 = -21.10 +   1.89)

alignment

secondary structure

dotplot

Window 3

Location	5,518,207 – 5,518,321
Length	114
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	78.85
Mean single sequence MFE	-30.39
Consensus MFE	-18.55
Energy contribution	-18.42
Covariance contribution	-0.14
Combinations/Pair	1.17
Mean z-score	-1.55
Structure conservation index	0.61
SVM decision value	0.19
SVM RNA-class probability	0.626227
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5518207 114 - 22224390
GCUGAGCAACUCAUUCUUGAGCUCAUCCAAUUGCUUGGUGAGUUCCUUCUUGUCCUUGAUCCUCAGCUCGGAGCACUUAACCUUCACCUGGACGGG---AGCACAAACAAACGGGCA
((((((...)))......(((((((.((((....))))))))))).((((((((((((.....)))...((((........))))....)))))))---))............))). ( -28.50)
>DroVir_CAF1 9854 111 - 1
AUUGAGCAGCUCAUUCUUGAGCUCAUCCAAUUGCUUGGUGAGCUCCUUCUUGUCCUUGGUUCUCAGCUCUGAGCACUUGAUCUUCACCUGUGAGAAUAGAGCCAAAUGGAA------
...((((.(((((....)))))(((.((((....))))))))))).......(((((((((((...(((...(((..((.....))..))))))...))))))))..))).------ ( -34.20)
>DroPse_CAF1 23089 98 - 1
AUUGAGGAGCUCAUUCUUGAGCUCAUCCAAUUGCUUGGUGAGCUCCUUCUUGUCCUUGGUUCUCAGCUCGGAGCACUUGACCUUUACCUGAGUGAG---G-C---------------
...((((((((((((...((((..........))))))))))))))))...(((....(((((......)))))....)))((((((....)))))---)-.--------------- ( -30.80)
>DroMoj_CAF1 8669 111 - 1
AUUGAGCAGCUCAUUCUUGAGCUCAUCCAAUUGCUUGGUGAGCUCCUUCUUGUCCUUCGUUCUCAAUUCUGAGCACUUGAUCUUCACCUAUGCGAGAAGAGCAAAAACAAU------
........((((......(((((((.((((....))))))))))).(((((((.....((.((((....)))).)).((.....)).....))))))))))).........------ ( -30.90)
>DroAna_CAF1 7419 109 - 1
AUUGAGGAGCUCGUUCUUGAGCUCAUCCAGCUGCUUGGUCAGCUCCUUCUUGUCCUUCGUCCUCAGCUCGGAGCACUUAACCUUCACCUGCGCGGC---A-----AAAAAGAGUACA
...((.(((((((....))))))).))..(((((..(((..(((((...(((...........)))...)))))...........)))...)))))---.-----............ ( -27.12)
>DroPer_CAF1 25604 98 - 1
AUUGAGGAGCUCAUUCUUGAGCUCAUCCAAUUGCUUGGUGAGCUCCUUCUUGUCCUUGGUUCUCAGCUCGGAGCACUUGACCUUUACCUGAGUGAG---G-C---------------
...((((((((((((...((((..........))))))))))))))))...(((....(((((......)))))....)))((((((....)))))---)-.--------------- ( -30.80)
>consensus
AUUGAGCAGCUCAUUCUUGAGCUCAUCCAAUUGCUUGGUGAGCUCCUUCUUGUCCUUGGUUCUCAGCUCGGAGCACUUGACCUUCACCUGAGCGAG___A_C___AA_AA_______
.(((((..((((......(((((((.((((....)))))))))))....(((...........)))....)))).)))))..................................... (-18.55 = -18.42 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:07 2006