Locus 2050

Sequence ID	X_DroMel_CAF1
Location	5,627,621 – 5,627,748
Length	127
Max. P	0.878844

overview

Window 6

Location	5,627,621 – 5,627,711
Length	90
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.16
Mean single sequence MFE	-28.73
Consensus MFE	-16.55
Energy contribution	-17.50
Covariance contribution	0.95
Combinations/Pair	1.14
Mean z-score	-1.95
Structure conservation index	0.58
SVM decision value	0.91
SVM RNA-class probability	0.878844
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5627621 90 + 22224390
CUCGAGCUCCAUUUCCAUACC------GAUCUCG------------AUCU------------GAAUCGCUGAAUCAGCGGGAGCCCCAAUUGAUAAUCGAUGUCAAUUGGCAAUGGUGUG
...............((((((------(.(((((------------((..------------..)))((((...))))))))...((((((((((.....))))))))))...))))))) ( -26.30)
>DroSec_CAF1 17276 90 + 1
CUCGAGCUCCAUUUCCAUAUC------GAUCUCG------------AUCU------------GAAUCGCUGAAUCAGCGGGAGCCCCAAUUGAUAAUCGAUGUCAAUUGGCAAUGGUGUG
.....(((((.....((.(((------(....))------------)).)------------)...(((((...)))))))))).((((((((((.....)))))))))).......... ( -29.80)
>DroSim_CAF1 17621 90 + 1
CUCGAGCUCCAUUUCCAUAUC------GAUCUCG------------AUCU------------GAAUCGCUGAAUCAGCGGGAGCCCCAAUUGAUAAUCGAUGUCAAUUGGCAAUGGUGUG
.....(((((.....((.(((------(....))------------)).)------------)...(((((...)))))))))).((((((((((.....)))))))))).......... ( -29.80)
>DroEre_CAF1 17448 98 + 1
CUGAGGCUCCAUUUCCAUAUC------GAUCUCG------------AUCUGAAUCG----CUGAAGCGCUGAAUCAGCGGGGCCCCCAAUUGAUAAUCGAUGUCAAUUGGCAGUGGCGCG
(((.((((((.....((.(((------(....))------------)).))....(----((((.........))))))))))).((((((((((.....)))))))))))))....... ( -34.20)
>DroYak_CAF1 17176 114 + 1
CUGAAGCUCCAUUUCCAUAUC------GAUCUCGAUCUCGAUCUCGAUCUCAAUCUCGAUCUGAAUCGCUGAAUCAGCGGGGGCCCCAAUUGAUAAACGAUGUCAAUUGGCAAUGGCGUG
.....(((((.....((.(((------((....((..(((....)))..))....))))).))...(((((...)))))))))).((((((((((.....)))))))))).......... ( -33.30)
>DroPer_CAF1 64704 100 + 1
CUGAAUCUCCCUCUCCCACUCCGUCGCAAUCUUC------------AACUGAAUCU------GAAU--CUGAAUCUGAUUCAGCCUCAAUUUAUAAUCGAUGUCAAUUGGCAAUUGCGUG
........................((((((....------------...(((..((------((((--(.......)))))))..)))............((((....)))))))))).. ( -19.00)
>consensus
CUCAAGCUCCAUUUCCAUAUC______GAUCUCG____________AUCU____________GAAUCGCUGAAUCAGCGGGAGCCCCAAUUGAUAAUCGAUGUCAAUUGGCAAUGGCGUG
.....((.(((((.....................................................(((((...)))))......((((((((((.....)))))))))).))))).)). (-16.55 = -17.50 +   0.95)

alignment

secondary structure

dotplot

Window 7

Location	5,627,649 – 5,627,748
Length	99
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	73.55
Mean single sequence MFE	-26.32
Consensus MFE	-16.48
Energy contribution	-16.15
Covariance contribution	-0.33
Combinations/Pair	1.23
Mean z-score	-1.25
Structure conservation index	0.63
SVM decision value	0.22
SVM RNA-class probability	0.641638
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5627649 99 + 22224390
------AUCU------------GAAUCGCUGAAUCAGCGGGAGCCCCAAUUGAUAAUCGAUGUCAAUUGGCAAUGGUGUGUUAAUUGCAAUGCGUAUUGUCAUUGAAAUCGGCGUUC
------....------------(((.((((((....((....))..((((.((((((((.((.(((((((((......)))))))))))...)).))))))))))...))))))))) ( -28.90)
>DroSec_CAF1 17304 84 + 1
------AUCU------------GAAUCGCUGAAUCAGCGGGAGCCCCAAUUGAUAAUCGAUGUCAAUUGGCAAUGGUGUGUUAAUUGCAAUGCGUAUUGUCA---------------
------....------------.....((((...))))(((...)))...(((((((((.((.(((((((((......)))))))))))...)).)))))))--------------- ( -21.80)
>DroSim_CAF1 17649 86 + 1
------AUCU------------GAAUCGCUGAAUCAGCGGGAGCCCCAAUUGAUAAUCGAUGUCAAUUGGCAAUGGUGUGUUAAUUGCAAUGCGUAUUGUCAUU-------------
------....------------.....((((...))))(((...)))...(((((((((.((.(((((((((......)))))))))))...)).)))))))..------------- ( -22.40)
>DroEre_CAF1 17476 95 + 1
------AUCUGAAUCG----CUGAAGCGCUGAAUCAGCGGGGCCCCCAAUUGAUAAUCGAUGUCAAUUGGCAGUGGCGCGUUAACUGUCAUGUGUAUUGUCAUU------------G
------...(((..((----(((...(((((...)))))......((((((((((.....)))))))))))))))((((((........))))))....)))..------------. ( -27.50)
>DroYak_CAF1 17210 117 + 1
AUCUCGAUCUCAAUCUCGAUCUGAAUCGCUGAAUCAGCGGGGGCCCCAAUUGAUAAACGAUGUCAAUUGGCAAUGGCGUGUUAACUGCAAUGCGUAUUGUCAUUGCAAUCGUUUUUG
..(((((((........)))).....(((((...))))))))(((((((((((((.....))))))))))....)))........((((((((.....).))))))).......... ( -32.90)
>DroPer_CAF1 64738 103 + 1
------AACUGAAUCU------GAAU--CUGAAUCUGAUUCAGCCUCAAUUUAUAAUCGAUGUCAAUUGGCAAUUGCGUGUUAACUGCAUUGUUGAUUGUAGCUGGAAUUGUUACUG
------...(((..((------((((--(.......)))))))..)))................(((..(((((.((((....)).)))))))..)))(((((.......))))).. ( -24.40)
>consensus
______AUCU____________GAAUCGCUGAAUCAGCGGGAGCCCCAAUUGAUAAUCGAUGUCAAUUGGCAAUGGCGUGUUAACUGCAAUGCGUAUUGUCAUU____________G
..........................(((((...)))))......((((((((((.....))))))))))(((((((((((.....))).))).))))).................. (-16.48 = -16.15 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:04 2006