Locus 7257

Sequence ID	3L_DroMel_CAF1
Location	19,419,633 – 19,419,727
Length	94
Max. P	0.987386

overview

Window 0

Location	19,419,633 – 19,419,727
Length	94
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	75.37
Mean single sequence MFE	-28.60
Consensus MFE	-17.22
Energy contribution	-17.50
Covariance contribution	0.28
Combinations/Pair	1.14
Mean z-score	-2.40
Structure conservation index	0.60
SVM decision value	2.08
SVM RNA-class probability	0.987386
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19419633 94 + 23771897
UUUGAGCUGCUGCUUUGCUUUAUUGCUGCUGCAGUAACAGGU-GCAGCAUUGUUCGUUC-------GAA-UUUCCCAUUUUCCAG------CUUUCCAGCUUUCCGCUC
...((((((((((((((..(((((((....))))))))))).-))))))..((((....-------)))-)............((------((....))))....)))) ( -24.90)
>DroVir_CAF1 16525 91 + 1
UUGGAGCUGCUGUUUUGGUUUAUUGCCGCUGCAGCAGACGGUCGCUG-AUGGUGCUGCCGGCCAGGGGAUAAU----------------CAGGGACGGGCCUGAUAAU-
((((..(((((((..((((.....))))..))))))).((((.((..-.....)).)))).))))......((----------------((((......))))))...- ( -35.30)
>DroSec_CAF1 58378 93 + 1
UUUGAGCUGCUGCUUUGCUUUAUUGCUGCUGCAGUAACAGGU-GCAGCAUUGUUCGGGC-------CAA-UUUCCCAUUUC-------CCAUUUUCCAGCUUUCCGCUA
...((((((((((((((..(((((((....))))))))))).-))))))..))))(((.-------...-...))).....-------.........(((.....))). ( -26.30)
>DroSim_CAF1 59550 100 + 1
UUUGAGCUGCUGCUUUGCUUUAUUGCUGCUGCAGUAACAGGU-GCAGCAUUGUUCGGGC-------GAA-UUUCCCAUUUCCCAGUUCCCAUUUUCCAGCUUUCCGCUC
...((((((((((((((..(((((((....))))))))))).-))))))..))))(((.-------(((-(.....)))))))..............(((.....))). ( -26.60)
>DroEre_CAF1 54830 93 + 1
UUUGAGCUGCUGCUUUGCUUUAUUGCUGCUGCAGUAACAGGU-GCAGCAUUGUUCGGGG-------GAA-UUUCCCAUUUC-------CCAUUUUCCAGCUUUCUGCGC
.((((((((((((((((..(((((((....))))))))))).-))))))..))))))((-------(((-........)))-------))........((.....)).. ( -30.80)
>DroYak_CAF1 98453 86 + 1
UUUGAGCUGCUGCUUUGCUUUAUUGCUGCUGCAGUAACAGGU-GCAGCAUUGUUCGGGG-------GAA-UUUCC--------------CAGUUUCCAGCUUUCCACUC
...((((((((((((((..(((((((....))))))))))).-))))))..))))((((-------(..-...))--------------)(((.....)))..)).... ( -27.70)
>consensus
UUUGAGCUGCUGCUUUGCUUUAUUGCUGCUGCAGUAACAGGU_GCAGCAUUGUUCGGGC_______GAA_UUUCCCAUUUC________CAUUUUCCAGCUUUCCGCUC
..(((((((((((...((((((((((....)))))))..))).))))))..)))))..................................................... (-17.22 = -17.50 +   0.28)

alignment

secondary structure

dotplot

Window 1

Location	19,419,633 – 19,419,727
Length	94
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	75.37
Mean single sequence MFE	-25.25
Consensus MFE	-11.48
Energy contribution	-12.62
Covariance contribution	1.14
Combinations/Pair	1.12
Mean z-score	-2.17
Structure conservation index	0.45
SVM decision value	0.86
SVM RNA-class probability	0.868373
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19419633 94 - 23771897
GAGCGGAAAGCUGGAAAG------CUGGAAAAUGGGAAA-UUC-------GAACGAACAAUGCUGC-ACCUGUUACUGCAGCAGCAAUAAAGCAAAGCAGCAGCUCAAA
((((....((((....))------)).............-...-------..........((((((-..((((....))))..((......))...))))))))))... ( -27.30)
>DroVir_CAF1 16525 91 - 1
-AUUAUCAGGCCCGUCCCUG----------------AUUAUCCCCUGGCCGGCAGCACCAU-CAGCGACCGUCUGCUGCAGCGGCAAUAAACCAAAACAGCAGCUCCAA
-...((((((......))))----------------)).......(((.(((..((.....-..))..))).((((((....((.......))....))))))..))). ( -22.30)
>DroSec_CAF1 58378 93 - 1
UAGCGGAAAGCUGGAAAAUGG-------GAAAUGGGAAA-UUG-------GCCCGAACAAUGCUGC-ACCUGUUACUGCAGCAGCAAUAAAGCAAAGCAGCAGCUCAAA
((((.....)))).....(((-------(...((((...-...-------.)))).....((((((-..((((....))))..((......))...)))))).)))).. ( -25.40)
>DroSim_CAF1 59550 100 - 1
GAGCGGAAAGCUGGAAAAUGGGAACUGGGAAAUGGGAAA-UUC-------GCCCGAACAAUGCUGC-ACCUGUUACUGCAGCAGCAAUAAAGCAAAGCAGCAGCUCAAA
((((.....((((...................((((...-...-------.)))).....((((((-(........)))))))((......))....)))).))))... ( -26.60)
>DroEre_CAF1 54830 93 - 1
GCGCAGAAAGCUGGAAAAUGG-------GAAAUGGGAAA-UUC-------CCCCGAACAAUGCUGC-ACCUGUUACUGCAGCAGCAAUAAAGCAAAGCAGCAGCUCAAA
...(((....))).....(((-------(...((((...-...-------.)))).....((((((-..((((....))))..((......))...)))))).)))).. ( -23.60)
>DroYak_CAF1 98453 86 - 1
GAGUGGAAAGCUGGAAACUG--------------GGAAA-UUC-------CCCCGAACAAUGCUGC-ACCUGUUACUGCAGCAGCAAUAAAGCAAAGCAGCAGCUCAAA
((((((......(....).(--------------((...-..)-------))))......((((((-..((((....))))..((......))...))))))))))... ( -26.30)
>consensus
GAGCGGAAAGCUGGAAAAUG________GAAAUGGGAAA_UUC_______GCCCGAACAAUGCUGC_ACCUGUUACUGCAGCAGCAAUAAAGCAAAGCAGCAGCUCAAA
((((.....((((...............................................((((((...........))))))((......))....)))).))))... (-11.48 = -12.62 +   1.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:42:25 2006