Locus 843

Sequence ID	3R_DroMel_CAF1
Location	2,879,561 – 2,879,654
Length	93
Max. P	0.942562

overview

Window 3

Location	2,879,561 – 2,879,654
Length	93
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	66.34
Mean single sequence MFE	-25.73
Consensus MFE	-18.49
Energy contribution	-18.88
Covariance contribution	0.39
Combinations/Pair	1.27
Mean z-score	-1.41
Structure conservation index	0.72
SVM decision value	1.33
SVM RNA-class probability	0.942562
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2879561 93 + 27905053
---------------------------AUCUUAUAUCUUUUAUCCCACAGGCUGCUCAAGCCAUGGGUGCGUCUGAGAUCCUCAUUACGGAUCUUGUGCAGCAACGCCUCGAUGUAGCUA
---------------------------...(((((((......((((..((((.....)))).))))(((((..(((((((.......)))))))..)).))).......)))))))... ( -29.20)
>DroVir_CAF1 729 99 + 1
-----------UAAAUCCAACAAAAUGUUAUUAU----------UUAAAGGUCGCGCAAUCUUUGGGUGCUACGGAGAUUUUGAUUACGGAUCUAGUGCAACAGCGCUUGGAUGUUGCCA
-----------...((((((((((((.((..(((----------((((((((......))))))))))).....)).))))))............((((....))))))))))....... ( -21.60)
>DroSec_CAF1 1243 93 + 1
---------------------------AUCUUAUAUCUUUUAUCCUAAAGGCUGCUCAAGCCAUGGGUGCGUCUGAGAUCCUGAUUACGGAUCUAGUGCAGCAACGCCUCGAUGUAGCUA
---------------------------...(((((((............((((.....))))..(((.(((((((((((((.......))))))....)))..))))))))))))))... ( -27.70)
>DroSim_CAF1 1 70 + 1
--------------------------------------------------GCUGCUCAAGCCAUGGGUGCGUCUGAGAUCCUGAUUACGGAUCUAGUGCAGCAACGCCUCGAUGUAGCUA
--------------------------------------------------(((((((.((.(...(.((((.((.((((((.......)))))))))))).)...).)).)).))))).. ( -23.60)
>DroEre_CAF1 1208 119 + 1
AAUCGUAUUUUUAAAUAAGACAAAUUGUUUUUAUUCCUUUUAA-CUACAGGCUGCUCAAGCCAUGGGUGCGUCGGAGAUCCUGAUUACGGAUCUAGUGCAGCAACGCCUCGAUGUAGCCA
....(((...(((((.(((((.....))))).......)))))-.))).((((.....)))).(((.((((((((((((((.......)))))).(((......))).)))))))).))) ( -30.40)
>DroYak_CAF1 1 70 + 1
--------------------------------------------------GCUGCUCAAGCCAUGGGAGCAUCGGAGAUCCUGAUUACGGAUCUAGUGCAGCAACGCCUCGACGUAGCUA
--------------------------------------------------(((((.(...(((((....))).))((((((.......)))))).).))))).(((......)))..... ( -21.90)
>consensus
____________________________U_UUAU__________CUA_AGGCUGCUCAAGCCAUGGGUGCGUCGGAGAUCCUGAUUACGGAUCUAGUGCAGCAACGCCUCGAUGUAGCUA
.................................................((((((((.((.(...(.((((....((((((.......))))))..)))).)...).)).)).)))))). (-18.49 = -18.88 +   0.39)

alignment

secondary structure

dotplot

Window 4

Location	2,879,561 – 2,879,654
Length	93
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	66.34
Mean single sequence MFE	-24.48
Consensus MFE	-15.60
Energy contribution	-17.43
Covariance contribution	1.83
Combinations/Pair	1.00
Mean z-score	-1.28
Structure conservation index	0.64
SVM decision value	0.72
SVM RNA-class probability	0.831856
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2879561 93 - 27905053
UAGCUACAUCGAGGCGUUGCUGCACAAGAUCCGUAAUGAGGAUCUCAGACGCACCCAUGGCUUGAGCAGCCUGUGGGAUAAAAGAUAUAAGAU---------------------------
.......(((...((((..(((....((((((.......))))))))))))).(((((((((.....)))).)))))......))).......--------------------------- ( -28.00)
>DroVir_CAF1 729 99 - 1
UGGCAACAUCCAAGCGCUGUUGCACUAGAUCCGUAAUCAAAAUCUCCGUAGCACCCAAAGAUUGCGCGACCUUUAA----------AUAAUAACAUUUUGUUGGAUUUA-----------
..((((((.(.....).))))))..(((((((((((((.....................))))))..........(----------((((.......))))))))))))----------- ( -17.30)
>DroSec_CAF1 1243 93 - 1
UAGCUACAUCGAGGCGUUGCUGCACUAGAUCCGUAAUCAGGAUCUCAGACGCACCCAUGGCUUGAGCAGCCUUUAGGAUAAAAGAUAUAAGAU---------------------------
..(((...(((((.(((.(.(((.((((((((.......)))))).))..))).).))).)))))..)))((((......)))).........--------------------------- ( -24.70)
>DroSim_CAF1 1 70 - 1
UAGCUACAUCGAGGCGUUGCUGCACUAGAUCCGUAAUCAGGAUCUCAGACGCACCCAUGGCUUGAGCAGC--------------------------------------------------
..(((...(((((.(((.(.(((.((((((((.......)))))).))..))).).))).)))))..)))-------------------------------------------------- ( -23.50)
>DroEre_CAF1 1208 119 - 1
UGGCUACAUCGAGGCGUUGCUGCACUAGAUCCGUAAUCAGGAUCUCCGACGCACCCAUGGCUUGAGCAGCCUGUAG-UUAAAAGGAAUAAAAACAAUUUGUCUUAUUUAAAAAUACGAUU
.((((...(((((.(((.(.(((...((((((.......)))))).....))).).))).)))))..))))((((.-(((((((((.((((.....)))))))).)))))...))))... ( -31.10)
>DroYak_CAF1 1 70 - 1
UAGCUACGUCGAGGCGUUGCUGCACUAGAUCCGUAAUCAGGAUCUCCGAUGCUCCCAUGGCUUGAGCAGC--------------------------------------------------
..(((.(.(((((.(((.(..(((..((((((.......))))))....)))..).))).)))))).)))-------------------------------------------------- ( -22.30)
>consensus
UAGCUACAUCGAGGCGUUGCUGCACUAGAUCCGUAAUCAGGAUCUCAGACGCACCCAUGGCUUGAGCAGCCU_UAG__________AUAA_A____________________________
..(((...(((((.(((.(.(((...((((((.......)))))).....))).).))).)))))..))).................................................. (-15.60 = -17.43 +   1.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:34 2006