Locus 2750

Sequence ID	2R_DroMel_CAF1
Location	9,628,553 – 9,628,670
Length	117
Max. P	0.955281

overview

Window 9

Location	9,628,553 – 9,628,649
Length	96
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	74.07
Mean single sequence MFE	-31.85
Consensus MFE	-15.36
Energy contribution	-14.83
Covariance contribution	-0.53
Combinations/Pair	1.27
Mean z-score	-2.23
Structure conservation index	0.48
SVM decision value	1.45
SVM RNA-class probability	0.955281
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9628553 96 + 20766785
GAAGA------CUCCGUUUUCCGC----GCUG-AC--UG----CUCUCGGUGCAUUG--UUGCAUGUGCCGGAAACGGAAAUGCGCACAUAAUUCUGUUAGGAAGCAUG-CAACAA---
(((((------(...)))))).((----((((-(.--..----...))))))).(((--((((((((.(((....)))..............((((....)))))))))-))))))--- ( -35.60)
>DroVir_CAF1 31365 105 + 1
GAAU-------CGCCAUUUUGUUUGCGCUCUGCUC--GG----CUCUUGGUGCACUGUGUUGUGUGUACCGGAAACGGAAAUGCGCACAUAAUUCUGUUAGAAAACGUG-GUACAGUCC
....-------.(((((.((((.(((((....(.(--(.----.(((.(((((((........))))))))))..)))....))))).))))(((.....)))...)))-))....... ( -31.50)
>DroEre_CAF1 27643 96 + 1
GAAGA------CGCCAUUUUCCGC----GCUG-AC--GG----CACUCGGUGCAUUG--UUGCAUGUGCCGGAAACGGAAACGCGCACAUAAUUCUGUUAGGAAGCAUG-CAACAA---
(((((------.....))))).((----((((-(.--..----...))))))).(((--((((((((.(((....)))..............((((....)))))))))-))))))--- ( -33.60)
>DroWil_CAF1 28894 83 + 1
GAAGACG---ACGCCAUUUUGU---------------------------GUGCAGCG--UUGCGUGUGCCGGAAACGGAAAUGCGCACAUAAUUCUGUUAGAAAACAUG-CAACAA---
.......---..((....((((---------------------------((((.(((--((.......(((....))).)))))))))))))...((((....)))).)-).....--- ( -22.70)
>DroYak_CAF1 37057 83 + 1
GAAAG------CGCCAUUUUCUGC------------------------GGUGCACUG--UUGCAUGUGCCGGAAACGGAAAUGCGCACAUAAUUCUGUUAGGAAGCAUG-CAACAA---
....(------((((.........------------------------)))))..((--((((((((.(((....)))..............((((....)))))))))-))))).--- ( -30.40)
>DroPer_CAF1 21618 109 + 1
GAAGAAGAAUAUGCCAUUUUGCUC----GCUG-AUGCUGCGCUCUCUUGGUGCAGUG--UUGCGUGUGCCGGAAACGGAAAUGCGCACAUAAUUCUGUUAGGAAACAUGCCAACAA---
..((((..((.((((((((.((.(----((.(-((((((((((.....)))))))))--))))).)).(((....)))))))).))).))..))))(((.((.......)))))..--- ( -37.30)
>consensus
GAAGA______CGCCAUUUUCCGC____GCUG_AC___G____CUCU_GGUGCACUG__UUGCAUGUGCCGGAAACGGAAAUGCGCACAUAAUUCUGUUAGGAAACAUG_CAACAA___
.................................................((((........((((...(((....)))..)))))))).......((((....))))............ (-15.36 = -14.83 +  -0.53)

alignment

secondary structure

dotplot

Window 0

Location	9,628,579 – 9,628,670
Length	91
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	85.05
Mean single sequence MFE	-33.03
Consensus MFE	-22.27
Energy contribution	-22.72
Covariance contribution	0.44
Combinations/Pair	1.14
Mean z-score	-3.06
Structure conservation index	0.67
SVM decision value	0.21
SVM RNA-class probability	0.635495
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9628579 91 + 20766785
----CUCUCGGUGCAUUGUUGCAUGUGCCGGAAACGGAAAUGCGCACAUAAUUCUGUUAGGAAGCAUG-CAACAAAAUGGCGCCCGGACCACAUCA
----.(((.(((((.(((((((((((.(((....)))..............((((....)))))))))-))))))....))))).)))........ ( -34.50)
>DroPse_CAF1 26874 96 + 1
CGCUCUCUUGGUGCAGUGUUGCGUGGGCCGGAAACGGAAAUGCGCACAUAAUUCUGUUAGGAAACAUGCCAACAAAAUGGCGCCCGCACCGCAGAC
.....(((((((((.((((.((((...(((....)))..))))))))............(....)..((((......))))....)))))).))). ( -35.80)
>DroEre_CAF1 27669 90 + 1
----CACUCGGUGCAUUGUUGCAUGUGCCGGAAACGGAAACGCGCACAUAAUUCUGUUAGGAAGCAUG-CAACAAAAUGGCGC-CGGACCACAAAC
----...(((((((.(((((((((((.(((....)))..............((((....)))))))))-))))))....))))-)))......... ( -35.30)
>DroWil_CAF1 28913 85 + 1
----------GUGCAGCGUUGCGUGUGCCGGAAACGGAAAUGCGCACAUAAUUCUGUUAGAAAACAUG-CAACAAAAUGGUGAAUGGACCACCAAC
----------.......(((((((((.(((....)))..............(((.....))).)))))-))))....(((((.......))))).. ( -26.30)
>DroYak_CAF1 37075 86 + 1
---------GGUGCACUGUUGCAUGUGCCGGAAACGGAAAUGCGCACAUAAUUCUGUUAGGAAGCAUG-CAACAAAAUGGCGCCCGGACCACAACC
---------(((((..((((((((((.(((....)))..............((((....)))))))))-))))).....)))))............ ( -30.50)
>DroPer_CAF1 21652 96 + 1
CGCUCUCUUGGUGCAGUGUUGCGUGUGCCGGAAACGGAAAUGCGCACAUAAUUCUGUUAGGAAACAUGCCAACAAAAUGGCGCCCGCACCGCAGAC
.....(((((((((.((((.((((...(((....)))..))))))))............(....)..((((......))))....)))))).))). ( -35.80)
>consensus
____CUCU_GGUGCAGUGUUGCAUGUGCCGGAAACGGAAAUGCGCACAUAAUUCUGUUAGGAAACAUG_CAACAAAAUGGCGCCCGGACCACAAAC
.........(((((..((((((((((.(((....)))..............((((....))))))))).))))).....)))))............ (-22.27 = -22.72 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:35 2006