Locus 415

Sequence ID	3R_DroMel_CAF1
Location	1,544,047 – 1,544,183
Length	136
Max. P	0.955594

overview

Window 9

Location	1,544,047 – 1,544,159
Length	112
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	82.15
Mean single sequence MFE	-32.58
Consensus MFE	-26.51
Energy contribution	-27.25
Covariance contribution	0.74
Combinations/Pair	1.12
Mean z-score	-2.04
Structure conservation index	0.81
SVM decision value	0.84
SVM RNA-class probability	0.863897
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1544047 112 + 27905053
GCAGAGCAGAGUACAGGCUGCAGGAUCAGGCCUGGAUAUGGUUUGUCACUUGGUUGGCGAAUUGGGAUUGAAGUGGGAUUGGGAUUUACCAAUUGUUGCCAUAAUUGAGUGA
(((((.((.....((((((.........))))))....)).)))))((((..(((((((((((........)))..((((((......)))))).))))))..))..)))). ( -35.30)
>DroSec_CAF1 45595 112 + 1
GUAGAGCAGAGUACAGGCUGCAGGAUCAGGCCAGGAUAUGGUUUGUCACUUGGUUGGCGAAUUGGGAUUGAAGUGGGAUUGGGAUUUACCAAUUGUUGCCAUAAUUGAGUGA
.....((((........)))).....(((((((.....)))))))(((((..(((((((((((........)))..((((((......)))))).))))))..))..))))) ( -33.50)
>DroSim_CAF1 46234 112 + 1
GUAGAGCAGAGUACAGGCUGCAGGAUCAGGCCAGGAUAUGGUUUGUCACUUGGUUGGCGAAUUGGGAUUGAAGUGGGAUUGGGACUUACCAAUUGUUGCCAUAAUUGAGUGA
.....((((........)))).....(((((((.....)))))))(((((..(((((((((((((.....((((.........)))).)))))..))))))..))..))))) ( -33.60)
>DroEre_CAF1 44978 103 + 1
--AGCGCAGGGAUCGGGCGGCAGGAUCAGGCCAGGACAUGGUUUGUCCCUUGGUUGGCGAAUUGGGAUGGAAGUG-------GAUUUACCAAUUGUUGCCAUAAUUGAGUGA
--.((.(((......((((((((((.(((((((.....))))))))))....(((((..((((.(........).-------))))..))))))))))))....))).)).. ( -31.60)
>DroYak_CAF1 40988 103 + 1
--AGAGCAGAGAACAGGCUGCAGGAUCAGACCAGGACAUGGUUUGUCACUUGGUUGGCGAAUUGGGUAUAGAGUG-------GACUUACCAAUUGUUGCCGCAAUUGAGUGA
--...((((........)))).....(((((((.....)))))))(((((..((((((((....((((.((....-------..)))))).....)))))..)))..))))) ( -33.10)
>DroAna_CAF1 43455 87 + 1
------------------GUCCUGAGGCGGCCAGGACUUGGUUUGUCACUUGGUUGGCGAAUUGGGAUUGAAGUG-------GAUUUACCAAUUGUUGCCAUAAUUGAGUGA
------------------((((((.......))))))........(((((..(((((((((((((..........-------......)))))..))))))..))..))))) ( -28.39)
>consensus
__AGAGCAGAGUACAGGCUGCAGGAUCAGGCCAGGACAUGGUUUGUCACUUGGUUGGCGAAUUGGGAUUGAAGUG_______GAUUUACCAAUUGUUGCCAUAAUUGAGUGA
.....((((........)))).....(((((((.....)))))))(((((..(((((((((((((.....((((.........)))).)))))..))))))..))..))))) (-26.51 = -27.25 +   0.74)

alignment

secondary structure

dotplot

Window 0

Location	1,544,087 – 1,544,183
Length	96
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	81.55
Mean single sequence MFE	-25.16
Consensus MFE	-22.51
Energy contribution	-22.43
Covariance contribution	-0.08
Combinations/Pair	1.12
Mean z-score	-2.02
Structure conservation index	0.89
SVM decision value	1.18
SVM RNA-class probability	0.926465
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1544087 96 + 27905053
GUUUGUCACUUGGUUGGCGAAUUGGGAUUGAAGUGGGAUUGGGAUUUACCAAUUGUUGCCAUAAUUGAGUGACAUGGAUAACGCAGC--CAG--AGCAGA
((((((((((..(((((((((((........)))..((((((......)))))).))))))..))..)))))).(((.........)--)))--)))... ( -28.10)
>DroVir_CAF1 55436 87 + 1
GUUUGUCACUUGGUUGGCGAAUUGAGAUUGAAGUG-------GAUUUACCAAUUGUUGCCAUAAUUGAGUGACAUGGAUAAGAGA----AAG--GCCAAG
...(((((((..((((((((.....(((((.....-------.......))))).))))))..))..)))))))(((........----...--.))).. ( -23.00)
>DroEre_CAF1 45016 87 + 1
GUUUGUCCCUUGGUUGGCGAAUUGGGAUGGAAGUG-------GAUUUACCAAUUGUUGCCAUAAUUGAGUGACAUGGAUAACGCAGC--AAG--AGCA--
...((((.((..(((((((((((((....(((...-------..))).)))))..))))))..))..)).))))...........((--...--.)).-- ( -21.30)
>DroWil_CAF1 46386 89 + 1
GUUUGUCACUUGGUUGGCGAAUUGGGAUUGAAGUG-------GAUUUACCAAUUGUUGCCAUAAUUGAGUGACAUGGAUAACACAGACCCAG--GGCU--
...(((((((..(((((((((((((..........-------......)))))..))))))..))..)))))))(((...........))).--....-- ( -25.29)
>DroYak_CAF1 41026 73 + 1
GUUUGUCACUUGGUUGGCGAAUUGGGUAUAGAGUG-------GACUUACCAAUUGUUGCCGCAAUUGAGUGACAUGGAUA--------------------
...(((((((..((((((((....((((.((....-------..)))))).....)))))..)))..)))))))......-------------------- ( -25.00)
>DroAna_CAF1 43477 91 + 1
GUUUGUCACUUGGUUGGCGAAUUGGGAUUGAAGUG-------GAUUUACCAAUUGUUGCCAUAAUUGAGUGACAUGGAUAGCGCGGG--GAGCGAGCGGG
((((((((((..(((((((((((((..........-------......)))))..))))))..))..))))))).......(((...--..))))))... ( -28.29)
>consensus
GUUUGUCACUUGGUUGGCGAAUUGGGAUUGAAGUG_______GAUUUACCAAUUGUUGCCAUAAUUGAGUGACAUGGAUAACGCAG___AAG__AGCA__
...(((((((..(((((((((((((.....((((.........)))).)))))..))))))..))..))))))).......................... (-22.51 = -22.43 +  -0.08)

alignment

secondary structure

dotplot

Window 1

Location	1,544,087 – 1,544,183
Length	96
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	81.55
Mean single sequence MFE	-16.79
Consensus MFE	-14.39
Energy contribution	-14.58
Covariance contribution	0.20
Combinations/Pair	1.06
Mean z-score	-2.59
Structure conservation index	0.86
SVM decision value	1.46
SVM RNA-class probability	0.955594
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1544087 96 - 27905053
UCUGCU--CUG--GCUGCGUUAUCCAUGUCACUCAAUUAUGGCAACAAUUGGUAAAUCCCAAUCCCACUUCAAUCCCAAUUCGCCAACCAAGUGACAAAC
...((.--...--...))........(((((((......((((...((((((.......................)))))).))))....)))))))... ( -17.30)
>DroVir_CAF1 55436 87 - 1
CUUGGC--CUU----UCUCUUAUCCAUGUCACUCAAUUAUGGCAACAAUUGGUAAAUC-------CACUUCAAUCUCAAUUCGCCAACCAAGUGACAAAC
......--...----...........(((((((......((....)).((((..(((.-------.............)))..))))...)))))))... ( -14.44)
>DroEre_CAF1 45016 87 - 1
--UGCU--CUU--GCUGCGUUAUCCAUGUCACUCAAUUAUGGCAACAAUUGGUAAAUC-------CACUUCCAUCCCAAUUCGCCAACCAAGGGACAAAC
--((((--(((--(..(((.......(((((........)))))..((((((......-------..........)))))))))....)))))).))... ( -15.09)
>DroWil_CAF1 46386 89 - 1
--AGCC--CUGGGUCUGUGUUAUCCAUGUCACUCAAUUAUGGCAACAAUUGGUAAAUC-------CACUUCAAUCCCAAUUCGCCAACCAAGUGACAAAC
--....--.(((((.......)))))(((((((......((((...((((((......-------..........)))))).))))....)))))))... ( -19.09)
>DroYak_CAF1 41026 73 - 1
--------------------UAUCCAUGUCACUCAAUUGCGGCAACAAUUGGUAAGUC-------CACUCUAUACCCAAUUCGCCAACCAAGUGACAAAC
--------------------......(((((((.......(((...((((((((((..-------....)).)).)))))).))).....)))))))... ( -15.90)
>DroAna_CAF1 43477 91 - 1
CCCGCUCGCUC--CCCGCGCUAUCCAUGUCACUCAAUUAUGGCAACAAUUGGUAAAUC-------CACUUCAAUCCCAAUUCGCCAACCAAGUGACAAAC
...((.((...--..)).))......(((((((......((((...((((((......-------..........)))))).))))....)))))))... ( -18.89)
>consensus
__UGCU__CUG___CUGCGUUAUCCAUGUCACUCAAUUAUGGCAACAAUUGGUAAAUC_______CACUUCAAUCCCAAUUCGCCAACCAAGUGACAAAC
..........................(((((((......((((...((((((.......................)))))).))))....)))))))... (-14.39 = -14.58 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:39 2006