Locus 4557

Sequence ID	X_DroMel_CAF1
Location	11,981,347 – 11,981,458
Length	111
Max. P	0.904702

overview

Window 1

Location	11,981,347 – 11,981,458
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.70
Mean single sequence MFE	-39.94
Consensus MFE	-32.44
Energy contribution	-32.48
Covariance contribution	0.04
Combinations/Pair	1.11
Mean z-score	-1.44
Structure conservation index	0.81
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11981347 111 + 22224390
GUCGUUCCACU--------GGAG-CCAUGGCCACAGAUAUGACGACCACUCAGCAAGGUCACCAAAUGGGUGGGGGAGUUGGGCGGCAUUUGGAGUGCUGUGGGCAGCAAGGUGAGAGGC
(((.(..((((--------...(-(..((.((((((.(((..(((((.((((((....(((((.....)))))....)))))).))...)))..))))))))).))))..))))..)))) ( -39.30)
>DroSec_CAF1 21108 98 + 1
-------------------GGAG-ACAUGGCCACAGAUAUGCCGACCACUCAGCAAGGUCACCAAAUGGGUGG--GAGUUGGGCGGCACUCGGAGUGCUGUGGGCAGCAAGGUGAGAGGC
-------------------(...-.)...(((.......(((((.((((((.......(((((.....)))))--))).))).)))))((((...(((((....)))))...)))).))) ( -36.21)
>DroSim_CAF1 21166 98 + 1
-------------------GGAG-CCAUGGCCACAGAUAUGCCGACCACUCAGCAAGGUCACCAAAUGGGUGG--GAGUUGGGCGGCAUUCGGAGUGCUGUGGGCAGCAAGGUGAGAGGC
-------------------...(-((.((.((((((.(((.((((((.((((((....(((((.....)))))--..)))))).))...)))).))))))))).))....)))....... ( -37.50)
>DroEre_CAF1 19792 99 + 1
-----------------GUGGAA-CCCUGGCCACAGAUAUGCCGACCACUCAGCAAGGUCACCA-AUGGGUGC--GAGUUGGUCGGCAUUUGGAGUGCUGUGGGCGGCAAGGUGAGAGGC
-----------------......-((((.(((.((((..((((((((((((.(((...(((...-.))).)))--))).)))))))))))))...(((((....))))).))).)).)). ( -40.70)
>DroYak_CAF1 20790 115 + 1
G---UUCCACUGCAGCCAUGGAAGCCAUGGCCACAGAUAUGCCGACCACUCAGCAAGGUCACCAAAUGGGUGG--GAGUUGGGCGGCAUUUGGAAUGCUGUGGGCAGCAAGGUGAGAGGC
(---((((((((..(((((((...)))))))..)))..((((((.((((((.......(((((.....)))))--))).))).)))))).))))))((((....))))............ ( -46.01)
>consensus
___________________GGAG_CCAUGGCCACAGAUAUGCCGACCACUCAGCAAGGUCACCAAAUGGGUGG__GAGUUGGGCGGCAUUUGGAGUGCUGUGGGCAGCAAGGUGAGAGGC
...........................((.((((((.(((.((((((.((((((....(((((.....)))))....)))))).))...)))).))))))))).)).............. (-32.44 = -32.48 +   0.04)

alignment

secondary structure

dotplot

Window 2

Location	11,981,347 – 11,981,458
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.70
Mean single sequence MFE	-34.90
Consensus MFE	-26.08
Energy contribution	-26.32
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-2.20
Structure conservation index	0.75
SVM decision value	1.04
SVM RNA-class probability	0.904702
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11981347 111 - 22224390
GCCUCUCACCUUGCUGCCCACAGCACUCCAAAUGCCGCCCAACUCCCCCACCCAUUUGGUGACCUUGCUGAGUGGUCGUCAUAUCUGUGGCCAUGG-CUCC--------AGUGGAACGAC
.((.((((.(.(((((....)))))(.(((((((..................))))))).).....).)))).))((((..((.(((..((....)-)..)--------))))..)))). ( -29.77)
>DroSec_CAF1 21108 98 - 1
GCCUCUCACCUUGCUGCCCACAGCACUCCGAGUGCCGCCCAACUC--CCACCCAUUUGGUGACCUUGCUGAGUGGUCGGCAUAUCUGUGGCCAUGU-CUCC-------------------
(((.(......((((((((.(((((....((((........))))--.((((.....))))....))))).).)).))))).....).))).....-....------------------- ( -29.50)
>DroSim_CAF1 21166 98 - 1
GCCUCUCACCUUGCUGCCCACAGCACUCCGAAUGCCGCCCAACUC--CCACCCAUUUGGUGACCUUGCUGAGUGGUCGGCAUAUCUGUGGCCAUGG-CUCC-------------------
(((..((((..(((((....)))))....((((((((.(((.(((--.((((.....))))........)))))).)))))).)).))))....))-)...------------------- ( -30.90)
>DroEre_CAF1 19792 99 - 1
GCCUCUCACCUUGCCGCCCACAGCACUCCAAAUGCCGACCAACUC--GCACCCAU-UGGUGACCUUGCUGAGUGGUCGGCAUAUCUGUGGCCAGGG-UUCCAC-----------------
.......((((((..(((.((((........((((((((((.(((--(((((...-.)))).......))))))))))))))..))))))))))))-).....----------------- ( -36.91)
>DroYak_CAF1 20790 115 - 1
GCCUCUCACCUUGCUGCCCACAGCAUUCCAAAUGCCGCCCAACUC--CCACCCAUUUGGUGACCUUGCUGAGUGGUCGGCAUAUCUGUGGCCAUGGCUUCCAUGGCUGCAGUGGAA---C
...........(((((....)))))(((((.((((((.(((.(((--.((((.....))))........)))))).))))))..(((..(((((((...)))))))..))))))))---. ( -47.40)
>consensus
GCCUCUCACCUUGCUGCCCACAGCACUCCAAAUGCCGCCCAACUC__CCACCCAUUUGGUGACCUUGCUGAGUGGUCGGCAUAUCUGUGGCCAUGG_CUCC___________________
(((.(......(((((....)))))......((((((.(((.(((...((((.....))))........)))))).))))))....).)))............................. (-26.08 = -26.32 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:04 2006