Locus 1001

Sequence ID	X_DroMel_CAF1
Location	2,902,706 – 2,902,806
Length	100
Max. P	0.990623

overview

Window 0

Location	2,902,706 – 2,902,806
Length	100
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	77.26
Mean single sequence MFE	-35.42
Consensus MFE	-18.18
Energy contribution	-19.90
Covariance contribution	1.72
Combinations/Pair	1.11
Mean z-score	-2.58
Structure conservation index	0.51
SVM decision value	2.22
SVM RNA-class probability	0.990623
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2902706 100 + 22224390
CAAAUAUGGAAUCAUAUGAAGCGCCAGUGGUCGCUGCUAGUUGAUGUUGCUGCUUGCUG---------UUUGCAAUAGUUGCUGGUUAGCUG-CAACUGUUGCAGCUGCC
...(((((....)))))..((((((...)).))))((((((...((((((.((.....)---------)..))))))...))))))((((((-((.....)))))))).. ( -32.50)
>DroSec_CAF1 289467 96 + 1
CAAAUAUGGAAUCAUAUGAAGCGCCAGUGGUUGCUGCUAGUUGAUGUUGCUGCUUGCU-------------GCAAUAGUUGCUGGUUAGCUG-CAACUGUUGCAGCUGCC
...(((((....))))).((((((.(((....))))).(((.......)))))))(((-------------(((((((((((.((....)))-))))))))))))).... ( -33.20)
>DroEre_CAF1 313268 94 + 1
CAAAUAUGGAAUCAUAUGAAGCGCCAGUGGUUGCGGCCAGUUGAUGUUGCUGGUUG----------------CAAUAGUUGCUGGUUAGCUGGCAACUGUUGCAGCUGCC
...(((((....)))))..((((.(((((((....)))).))).))))((.(((((----------------((((((((((..(....)..))))))))))))))))). ( -38.20)
>DroYak_CAF1 297907 102 + 1
CAAAUAUGGAAUCAUAUGGAGCGCCAGUGGUUGCUGCCAGUUGAUGUUGCUGGUUGCAA-------GAGUUGCAAUAGUUGCUGGUUAGCUG-CAACUGUUGCAGCUGCC
.........((((((.(((....)))))))))((.((((((.......)))))).))..-------.(((((((((((((((.((....)))-))))))))))))))... ( -40.90)
>DroAna_CAF1 457472 91 + 1
CAAAUAUGGAAUCAUAUGUAGCGCCAGUUG---------GCUGCUGCUGCUGCUUGCAACUAGCCAGGCUUGCAACAAACGGCGGC----------GCGUUGCAGCUGCC
...(((((....)))))((((((((....)---------)).)))))(((.((((((.....).)))))..)))......((((((----------........)))))) ( -32.30)
>consensus
CAAAUAUGGAAUCAUAUGAAGCGCCAGUGGUUGCUGCCAGUUGAUGUUGCUGCUUGCA___________UUGCAAUAGUUGCUGGUUAGCUG_CAACUGUUGCAGCUGCC
...(((((....)))))...(((.((((....(((((((((...((((((.....................))))))...))))).)))).....)))).)))....... (-18.18 = -19.90 +   1.72)

alignment

secondary structure

dotplot

Window 1

Location	2,902,706 – 2,902,806
Length	100
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	77.26
Mean single sequence MFE	-27.80
Consensus MFE	-10.97
Energy contribution	-12.42
Covariance contribution	1.45
Combinations/Pair	1.00
Mean z-score	-2.27
Structure conservation index	0.39
SVM decision value	1.25
SVM RNA-class probability	0.936133
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2902706 100 - 22224390
GGCAGCUGCAACAGUUG-CAGCUAACCAGCAACUAUUGCAAA---------CAGCAAGCAGCAACAUCAACUAGCAGCGACCACUGGCGCUUCAUAUGAUUCCAUAUUUG
....(((((...(((((-(.........)))))).((((...---------..)))))))))...........(.((((.((...)))))).)(((((....)))))... ( -26.70)
>DroSec_CAF1 289467 96 - 1
GGCAGCUGCAACAGUUG-CAGCUAACCAGCAACUAUUGC-------------AGCAAGCAGCAACAUCAACUAGCAGCAACCACUGGCGCUUCAUAUGAUUCCAUAUUUG
(((.(((((((.(((((-(.........)))))).))))-------------)))..((.((...........)).))..........)))..(((((....)))))... ( -26.40)
>DroEre_CAF1 313268 94 - 1
GGCAGCUGCAACAGUUGCCAGCUAACCAGCAACUAUUG----------------CAACCAGCAACAUCAACUGGCCGCAACCACUGGCGCUUCAUAUGAUUCCAUAUUUG
((((((((...))))))))(((...((((......(((----------------(..((((.........))))..))))...)))).)))..(((((....)))))... ( -26.20)
>DroYak_CAF1 297907 102 - 1
GGCAGCUGCAACAGUUG-CAGCUAACCAGCAACUAUUGCAACUC-------UUGCAACCAGCAACAUCAACUGGCAGCAACCACUGGCGCUCCAUAUGAUUCCAUAUUUG
((.((((((((.(((((-(.........)))))).)))))....-------((((..((((.........))))..))))........)))))(((((....)))))... ( -28.00)
>DroAna_CAF1 457472 91 - 1
GGCAGCUGCAACGC----------GCCGCCGUUUGUUGCAAGCCUGGCUAGUUGCAAGCAGCAGCAGCAGC---------CAACUGGCGCUACAUAUGAUUCCAUAUUUG
(((...(((((((.----------((....)).))))))).((((((((.(((((........))))))))---------))...))))))..(((((....)))))... ( -31.70)
>consensus
GGCAGCUGCAACAGUUG_CAGCUAACCAGCAACUAUUGCAA___________AGCAAGCAGCAACAUCAACUAGCAGCAACCACUGGCGCUUCAUAUGAUUCCAUAUUUG
(((.(((((...........(((....))).....((((..............)))))))))..............((........)))))..(((((....)))))... (-10.97 = -12.42 +   1.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:05 2006