Locus 3534

Sequence ID 3L_DroMel_CAF1
Location 10,361,380 – 10,361,541
Length 161
Max. P 0.968634
window5513 window5514 window5515

overview

Window 3

Location 10,361,380 – 10,361,489
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 73.41
Mean single sequence MFE -25.68
Consensus MFE -16.60
Energy contribution -17.60
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.65
SVM decision value 1.07
SVM RNA-class probability 0.909832
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10361380 109 + 23771897
--------GCUCUAUACU-AUAUUUGUACGAAGUAAAUA-UCACCAUAUUU-AUUUUCCAAGUGUACUGACCGCUGUCCACCUUCAGGACAGGAGAAUGCUGGUUGGUAAAACUCCUAUA
--------..........-(((((((...((((((((((-(....))))))-))))).)))))))((..(((.((((((.......)))))).((....)))))..))............ ( -26.00)
>DroSec_CAF1 235047 89 + 1
------------------------------AAGGAUGUAUUCACCAUAUUU-ACUUUCCGAGUGUACUGACCGCUGUCCGCCUUCAGGACAGGAGAAUGCUGGUUGGUAAAACUCCUAUA
------------------------------..(((.(((...........)-))..)))((((.(((..(((.((((((.......)))))).((....)))))..)))..))))..... ( -26.10)
>DroSim_CAF1 245421 89 + 1
------------------------------AAGGAUGUAUUCACCAUAUUU-ACUUUCCGAGUGUACUGACCGCUGUCCGCCUUCAGGACAGGAGAAUGCUGGUUGGUAAAACUCCUAUA
------------------------------..(((.(((...........)-))..)))((((.(((..(((.((((((.......)))))).((....)))))..)))..))))..... ( -26.10)
>DroEre_CAF1 249525 111 + 1
UGAAAUGUGUACUUAACUAUUA------UUGAGUAAAUU-UCAU-ACGAUU-UUUUUCUGAGUGUACUGACCGCUGUCCACCUUCAGGAAAGGAGAAUGCUGGCUGGUAAAACUCCUAUA
((((((...(((((((......------))))))).)))-))).-......-..((((((((((.((........)).)))..)))))))(((((..((((....))))...)))))... ( -26.50)
>DroYak_CAF1 247151 112 + 1
-----UAUACACUUUA-UGUUAUUUGCUUUCAGUAAAUG-UCAU-AUAUUUAAUUUUCCAAGUGUACUGACCGCUGUCCACCUUCAGGAAAGGAGAAUGCUGGUUGGUAAAACUCCGAUA
-----...((((((((-((.(((((((.....)))))))-.)))-).............))))))((..((((((.(((.((....))...))).)..)).)))..))............ ( -23.71)
>consensus
___________CU__A_U__UA________AAGUAAAUA_UCACCAUAUUU_AUUUUCCGAGUGUACUGACCGCUGUCCACCUUCAGGACAGGAGAAUGCUGGUUGGUAAAACUCCUAUA
...........................................................((((.((((((((.((((((.......)))))).((....))))))))))..))))..... (-16.60 = -17.60 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 10,361,410 – 10,361,521
Length 111
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 93.53
Mean single sequence MFE -30.08
Consensus MFE -28.42
Energy contribution -29.22
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.47
Structure conservation index 0.94
SVM decision value 1.63
SVM RNA-class probability 0.968634
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10361410 111 + 23771897
UCACCAUAUUU-AUUUUCCAAGUGUACUGACCGCUGUCCACCUUCAGGACAGGAGAAUGCUGGUUGGUAAAACUCCUAUAUUGGACUUGCCAAUAAUGUCAUUGUGCUGCAA
...........-........((..((.((((..((((((.......))))))..........((((((((...(((......))).))))))))...)))).))..)).... ( -28.40)
>DroSec_CAF1 235057 111 + 1
UCACCAUAUUU-ACUUUCCGAGUGUACUGACCGCUGUCCGCCUUCAGGACAGGAGAAUGCUGGUUGGUAAAACUCCUAUAUUGGAGUUGCCAAUAAUGUCAUUGUGCUGCAA
...........-........((..((.((((..((((((.......))))))..........(((((((..(((((......))))))))))))...)))).))..)).... ( -32.90)
>DroSim_CAF1 245431 111 + 1
UCACCAUAUUU-ACUUUCCGAGUGUACUGACCGCUGUCCGCCUUCAGGACAGGAGAAUGCUGGUUGGUAAAACUCCUAUAUUGGAGUUGCCAAUAAUGUCAUUGUGCUGCAA
...........-........((..((.((((..((((((.......))))))..........(((((((..(((((......))))))))))))...)))).))..)).... ( -32.90)
>DroEre_CAF1 249558 110 + 1
UCAU-ACGAUU-UUUUUCUGAGUGUACUGACCGCUGUCCACCUUCAGGAAAGGAGAAUGCUGGCUGGUAAAACUCCUAUAUUGGAGUUGCCAAUAAUGUCAUUGUGCUGCAA
....-....((-((((((((((((.((........)).)))..)))))))))))...(((.((((((((..(((((......))))))))))(((((...))))))))))). ( -29.30)
>DroYak_CAF1 247184 111 + 1
UCAU-AUAUUUAAUUUUCCAAGUGUACUGACCGCUGUCCACCUUCAGGAAAGGAGAAUGCUGGUUGGUAAAACUCCGAUAUUGGAGUUGCCAAUAAUGUCAUUGUGCUGCAA
((((-((((((........))))))).)))..((..(((.......))).((.(.(((((..(((((((..((((((....)))))))))))))...).)))).).)))).. ( -26.90)
>consensus
UCACCAUAUUU_AUUUUCCGAGUGUACUGACCGCUGUCCACCUUCAGGACAGGAGAAUGCUGGUUGGUAAAACUCCUAUAUUGGAGUUGCCAAUAAUGUCAUUGUGCUGCAA
....................((..((.((((..((((((.......))))))..........(((((((..(((((......))))))))))))...)))).))..)).... (-28.42 = -29.22 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 10,361,449 – 10,361,541
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 97.17
Mean single sequence MFE -25.24
Consensus MFE -22.02
Energy contribution -22.82
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.50
Structure conservation index 0.87
SVM decision value 0.54
SVM RNA-class probability 0.775077
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10361449 92 + 23771897
CCUUCAGGACAGGAGAAUGCUGGUUGGUAAAACUCCUAUAUUGGACUUGCCAAUAAUGUCAUUGUGCUGCAACUGCCAUGCCAAAAGACAGC
.((((......))))...((((((((((((...(((......))).)))))))).......(((.((.((....))...)))))....)))) ( -22.20)
>DroSec_CAF1 235096 92 + 1
CCUUCAGGACAGGAGAAUGCUGGUUGGUAAAACUCCUAUAUUGGAGUUGCCAAUAAUGUCAUUGUGCUGCAACUGCCAUGCCAAAAGACAGC
.((((......))))...(((((((((((..(((((......)))))))))))).......(((.((.((....))...)))))....)))) ( -25.90)
>DroSim_CAF1 245470 91 + 1
CCUUCAGGACAGGAGAAUGCUGGUUGGUAAAACUCCUAUAUUGGAGUUGCCAAUAAUGUCAUUGUGCUGCAACUG-CAUGCCAAAAGACAAC
.((((......)))).......(((((((..(((((......))))))))))))..((((.(((.(((((....)-)).)))))..)))).. ( -27.00)
>DroEre_CAF1 249596 92 + 1
CCUUCAGGAAAGGAGAAUGCUGGCUGGUAAAACUCCUAUAUUGGAGUUGCCAAUAAUGUCAUUGUGCUGCAACUGCCAUGCCAAAAGACAGC
.((((......)))).....(((((((((.((((((......))))))((((((......)))).))......))))).))))......... ( -25.70)
>DroYak_CAF1 247223 92 + 1
CCUUCAGGAAAGGAGAAUGCUGGUUGGUAAAACUCCGAUAUUGGAGUUGCCAAUAAUGUCAUUGUGCUGCAACUGCCAUGCCAAAAGACAGC
.((((......))))...(((((((((((..((((((....))))))))))))).......(((.((.((....))...)))))....)))) ( -25.40)
>consensus
CCUUCAGGACAGGAGAAUGCUGGUUGGUAAAACUCCUAUAUUGGAGUUGCCAAUAAUGUCAUUGUGCUGCAACUGCCAUGCCAAAAGACAGC
....(((..(((.(.(((((..(((((((..(((((......))))))))))))...).)))).).)))...)))................. (-22.02 = -22.82 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:25 2006