Locus 7846

Sequence ID	3L_DroMel_CAF1
Location	20,994,161 – 20,994,251
Length	90
Max. P	0.773132

overview

Window 3

Location	20,994,161 – 20,994,251
Length	90
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	78.43
Mean single sequence MFE	-27.98
Consensus MFE	-17.09
Energy contribution	-17.97
Covariance contribution	0.88
Combinations/Pair	1.19
Mean z-score	-1.73
Structure conservation index	0.61
SVM decision value	0.23
SVM RNA-class probability	0.644918
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20994161 90 + 23771897
UUCCACUUCCUCUUCCGUUCGGAGAGAA-ACGGAGAGACUGAGAGAGCGAGACAGAGAG---CAACUGGUGCCGGAGAAGGAGAGGGAGUGUAU----
...((((((((((((..(((.(......-.(((.....))).....(((...(((....---...))).)))).)))..))))))))))))...---- ( -27.90)
>DroSec_CAF1 11808 90 + 1
UUCCAUUUCCUCUUCCGUUCGGAGAGAA-ACGGAGACACUGAGAGAGCGAGAUAGAGAG---CGACUGGUGCCGGAGAAGGAGAGGGAGUGUAU----
...((((((((((((..(((((......-..(....)(((.((...((..........)---)..))))).)))))...))))))))))))...---- ( -26.50)
>DroSim_CAF1 19212 90 + 1
UUCCACUUCCUCUUCCGUUCGGAGAGAA-ACGGAGACACUGAGAGAGCGAGACAGAGAG---CGACUGGUGCCGGAGAAGGAGAGGGAGUGUAU----
...(((((((((((((((((........-..(....).(((...........))).)))---)).(((....)))....))))))))))))...---- ( -30.30)
>DroYak_CAF1 18079 91 + 1
UUCCACUUCCUCUUCCGUUCGGAGAGAAAACGGAGACACUGAGAGGGAGAGACAGAGAG---CGACUGGUGCCGGAGAAAGAGAGGGAGUAUAU----
....((((((((((.(((((...........(....).((....))..........)))---)).(((....))).....))))))))))....---- ( -26.50)
>DroAna_CAF1 10504 82 + 1
UUCCACUUCCUCUUCCGCUCUUAG------------CUCUUA--AAGCCGGAGAGAGAGUUGAGUCUGGCUU--GGAAAAGAGAGAGAGGGUGUGAGA
(((((((..((((((((..(((((------------(((((.--..........))))))))))..)))(((--....))).)))))..)))).))). ( -28.70)
>consensus
UUCCACUUCCUCUUCCGUUCGGAGAGAA_ACGGAGACACUGAGAGAGCGAGACAGAGAG___CGACUGGUGCCGGAGAAGGAGAGGGAGUGUAU____
...((((((((((((..(((((..............(.(((...........))).)..............)))))...))))))))))))....... (-17.09 = -17.97 +   0.88)

alignment

secondary structure

dotplot

Window 4

Location	20,994,161 – 20,994,251
Length	90
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	78.43
Mean single sequence MFE	-22.54
Consensus MFE	-11.36
Energy contribution	-11.96
Covariance contribution	0.60
Combinations/Pair	1.29
Mean z-score	-2.04
Structure conservation index	0.50
SVM decision value	0.54
SVM RNA-class probability	0.773132
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20994161 90 - 23771897
----AUACACUCCCUCUCCUUCUCCGGCACCAGUUG---CUCUCUGUCUCGCUCUCUCAGUCUCUCCGU-UUCUCUCCGAACGGAAGAGGAAGUGGAA
----...((((.(((((........(((..(((...---....)))....)))...........(((((-((......)))))))))))).))))... ( -22.10)
>DroSec_CAF1 11808 90 - 1
----AUACACUCCCUCUCCUUCUCCGGCACCAGUCG---CUCUCUAUCUCGCUCUCUCAGUGUCUCCGU-UUCUCUCCGAACGGAAGAGGAAAUGGAA
----......(((...((((..((((((((.((..(---(..........))...))..)))))...((-((......)))))))..))))...))). ( -21.20)
>DroSim_CAF1 19212 90 - 1
----AUACACUCCCUCUCCUUCUCCGGCACCAGUCG---CUCUCUGUCUCGCUCUCUCAGUGUCUCCGU-UUCUCUCCGAACGGAAGAGGAAGUGGAA
----...((((.(((((........(((((.((..(---(..........))...))..)))))(((((-((......)))))))))))).))))... ( -25.50)
>DroYak_CAF1 18079 91 - 1
----AUAUACUCCCUCUCUUUCUCCGGCACCAGUCG---CUCUCUGUCUCUCCCUCUCAGUGUCUCCGUUUUCUCUCCGAACGGAAGAGGAAGUGGAA
----......(((....(((((((.((((((((...---....))).............)))))(((((((.......))))))).))))))).))). ( -21.71)
>DroAna_CAF1 10504 82 - 1
UCUCACACCCUCUCUCUCUUUUCC--AAGCCAGACUCAACUCUCUCUCCGGCUU--UAAGAG------------CUAAGAGCGGAAGAGGAAGUGGAA
((.(((..(((((((((((((((.--(((((.((............)).)))))--...)))------------..))))).)).)))))..))))). ( -22.20)
>consensus
____AUACACUCCCUCUCCUUCUCCGGCACCAGUCG___CUCUCUGUCUCGCUCUCUCAGUGUCUCCGU_UUCUCUCCGAACGGAAGAGGAAGUGGAA
.......((((.((((((((((..((((....)))).......(((...........)))..................))).)).))))).))))... (-11.36 = -11.96 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:58:31 2006