Locus 6080

Sequence ID	2R_DroMel_CAF1
Location	19,136,744 – 19,136,869
Length	125
Max. P	0.859150

overview

Window 4

Location	19,136,744 – 19,136,844
Length	100
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	83.93
Mean single sequence MFE	-26.42
Consensus MFE	-20.44
Energy contribution	-21.13
Covariance contribution	0.69
Combinations/Pair	1.05
Mean z-score	-2.68
Structure conservation index	0.77
SVM decision value	0.82
SVM RNA-class probability	0.859150
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19136744 100 - 20766785
---CUCGAAAAUAGAAUAUCAAUUUGGGCAGAAAGCAUAACGGAUGCCGCUGUCAAUAUUUUGACAGUUCUCGCUGCCUAACAGGAACCAGCAAACAACACCC
---...............((...((((((((...((((.....)))).((((((((....)))))))).....))))))))...))................. ( -25.30)
>DroSec_CAF1 20802 97 - 1
---CUCGAAAAUAGAAUAUCAAUUUGGGCAGAAAGCAUAACGGAUGCCGCUGUCAAUAUUUUGACAGUUCUCGCUGCCUAACAGGAACCGGCAAG---CACCC
---...............((...((((((((...((((.....)))).((((((((....)))))))).....))))))))...))...((....---..)). ( -25.40)
>DroEre_CAF1 25416 91 - 1
---CUCCAAAAUAGAAUAUCAAUUUGGGCAGCAGGCAUAACGGAUGCCGCUGUCAAUAUUUUGACAGUUCUCGCUGCCUAACAGGAACCAGCAA---------
---.(((......(.....)...(((((((((.(((((.....)))))((((((((....))))))))....)))))))))..)))........--------- ( -34.20)
>DroWil_CAF1 41861 94 - 1
CCAGUUAAAAAUAGAAUAUCAAUUUGGGCAAAAAGCAUAACGGAUGCGGCUGUCAAUAUUUUGACAGUUCUCCCUACAUAAAGAGGAGCCCCAC---------
.........................((((.....((((.....))))(((((((((....))))))))).(((((......)).)))))))...--------- ( -24.20)
>DroYak_CAF1 26714 100 - 1
---CUCGAAAAUAGAAUAUCAAUUUGGGCAGAAAGCAUAACGGAUGCCGCUGUCAAUAUUUUGACAGUUCUCGCUGCCUAACAGGAACCAGCGAAACACACCC
---...............((...((((((((...((((.....)))).((((((((....)))))))).....))))))))...))................. ( -25.30)
>DroAna_CAF1 29143 103 - 1
GCAUUCAAAAAUAGAAUAUCAAUUUGGGCAAAAAGCAUAACGGAUGCCGCUGUCAAUAUUUUGACAGUUCUCGCUGCCUAACGCAAACCACCGAACCACCGCC
((((((.......))))......(((((((....((((.....)))).((((((((....))))))))......))))))).))................... ( -24.10)
>consensus
___CUCGAAAAUAGAAUAUCAAUUUGGGCAGAAAGCAUAACGGAUGCCGCUGUCAAUAUUUUGACAGUUCUCGCUGCCUAACAGGAACCAGCAAA___CACCC
..................((...((((((((...((((.....)))).((((((((....)))))))).....))))))))...))................. (-20.44 = -21.13 +   0.69)

alignment

secondary structure

dotplot

Window 5

Location	19,136,778 – 19,136,869
Length	91
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	78.24
Mean single sequence MFE	-24.29
Consensus MFE	-13.81
Energy contribution	-14.28
Covariance contribution	0.47
Combinations/Pair	1.10
Mean z-score	-1.86
Structure conservation index	0.57
SVM decision value	0.49
SVM RNA-class probability	0.758240
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19136778 91 - 20766785
-UCGGAGGAGCCUGGGAGCGGG--AGUG--------------CUC-GAAAAUAGAAUAUCAAUUUGGGCAGAAAGCAUAACGGAUGCCGCUGUCAAUAUUUUGACAGUU
-.........((((....))))--..((--------------(((-(((.............))))))))....((((.....)))).((((((((....)))))))). ( -24.42)
>DroPse_CAF1 29556 89 - 1
------GGAGUCUGGGAGCGAGCGAGAA--------------CUCUUAAAAUAGAAUAUCAAUUUGGGCAAAAAGCAUAACGGAUGCCGCUGUCAAUAUUUUGACAGUU
------((.(((((..((((((......--------------)))........(..((......))..).....)).)..))))).))((((((((....)))))))). ( -21.60)
>DroEre_CAF1 25441 86 - 1
------GGAGCCUGGGAGCGGC--AGUG--------------CUC-CAAAAUAGAAUAUCAAUUUGGGCAGCAGGCAUAACGGAUGCCGCUGUCAAUAUUUUGACAGUU
------...((((.((((((..--..))--------------)))-).((((.(.....).))))))))....(((((.....)))))((((((((....)))))))). ( -30.80)
>DroWil_CAF1 41886 78 - 1
------GAAGUC-------G-----------------CCCCAGUU-AAAAAUAGAAUAUCAAUUUGGGCAAAAAGCAUAACGGAUGCGGCUGUCAAUAUUUUGACAGUU
------......-------(-----------------(((.((((-..............)))).)))).....((((.....))))(((((((((....))))))))) ( -20.84)
>DroAna_CAF1 29177 106 - 1
GUCAGAAAAGUCUGGGAGCGGG--AGCGGGAGCAGCAACGCAUUC-AAAAAUAGAAUAUCAAUUUGGGCAAAAAGCAUAACGGAUGCCGCUGUCAAUAUUUUGACAGUU
(((((((.(...(((.((((..--.((....))......((((((-..((((.(.....).))))..((.....)).....)))))))))).))).).))))))).... ( -26.50)
>DroPer_CAF1 29643 89 - 1
------GGAGUCUGGGAGCGAGCGAGAA--------------CUCUUAAAAUAGAAUAUCAAUUUGGGCAAAAAGCAUAACGGAUGCCGCUGUCAAUAUUUUGACAGUU
------((.(((((..((((((......--------------)))........(..((......))..).....)).)..))))).))((((((((....)))))))). ( -21.60)
>consensus
______GGAGUCUGGGAGCGGG__AGAG______________CUC_AAAAAUAGAAUAUCAAUUUGGGCAAAAAGCAUAACGGAUGCCGCUGUCAAUAUUUUGACAGUU
.........(((..((.((......))..........................(.....)..))..))).....((((.....)))).((((((((....)))))))). (-13.81 = -14.28 +   0.47)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:19 2006