Locus 580

Sequence ID	2L_DroMel_CAF1
Location	1,774,582 – 1,774,722
Length	140
Max. P	0.774678

overview

Window 6

Location	1,774,582 – 1,774,683
Length	101
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	67.38
Mean single sequence MFE	-25.18
Consensus MFE	-12.72
Energy contribution	-12.76
Covariance contribution	0.04
Combinations/Pair	1.30
Mean z-score	-1.59
Structure conservation index	0.51
SVM decision value	0.21
SVM RNA-class probability	0.633535
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1774582 101 + 22407834
ACUUGAAACGGGGUACC-------------CAUAUGCCACCCUCUUCUCACUUCACACAUUUUAAACCAAUUGCGAACUUGGCCCA-----GGCGACAAACACUUAAUUGGUUUAAAGG
....(((..((((((..-------------....)))).))...)))............((((((((((((((.(...(((((...-----.))..)))...).)))))))))))))). ( -20.50)
>DroPse_CAF1 36186 113 + 1
--AUGGUAUGUUGUGUUCAACAUGGAGCUCUACCAGUCAUCCCCCUCUGA----CAACAGUUAAAUCCAAUUACGAACUUGGCCCAAACUGAGCAUCAAACAGGUUAUUGAGUUUGAGG
--....(((((((....)))))))((((((.(((.((((........)))----)..(((((....((((........))))....)))))...........)))....)))))).... ( -25.70)
>DroSec_CAF1 31582 100 + 1
-CUUGAAACGGGGUACC-------------CAUACGCCACCCUCUUCUCAGUUCACACACUUUAAACCAAUUACGAACUUGGCCCA-----GGCGACAAACACUUAAUUGGUUUAAAGG
-.((((((.(((((...-------------........))))).)).))))........((((((((((((((.(...(((((...-----.))..)))...).)))))))))))))). ( -23.90)
>DroYak_CAF1 40763 100 + 1
ACUUGAAACGGGGUAAC-------------CGUAUGCCACCCU-UUCACACUUCACACACUUUAAACCAAUUACGAACUUGGCCCA-----GGCGACAAGCACUUAAUUGGUUUAAAGG
...(((((.((((((..-------------....)))).)).)-))))...........((((((((((((((.(..((((((...-----.))..))))..).)))))))))))))). ( -31.20)
>DroPer_CAF1 35033 113 + 1
--AUGGUAUGGUGUGUUCAACAUGGAGCUCUACCAGUCAUCCCCCUCUGA----CAACAGUUAAAUCCAAUUACGAACUUGGCCCAAACUGAGCAUCAAACAGGUUAUUGAGUUUGAGG
--..((..(((((.((((......)))).).)))).....)).((((.((----(..(((((....((((........))))....)))))....((((........))))))).)))) ( -24.60)
>consensus
_CUUGAAACGGGGUACC_____________CAUAAGCCACCCUCUUCUCA_UUCACACACUUUAAACCAAUUACGAACUUGGCCCA_____GGCGACAAACACUUAAUUGGUUUAAAGG
....((...(((((........................)))))..))............((((((((((((((.....((((((.......)))..))).....)))))))))))))). (-12.72 = -12.76 +   0.04)

alignment

secondary structure

dotplot

Window 7

Location	1,774,609 – 1,774,722
Length	113
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	71.87
Mean single sequence MFE	-27.37
Consensus MFE	-11.36
Energy contribution	-11.56
Covariance contribution	0.20
Combinations/Pair	1.27
Mean z-score	-1.93
Structure conservation index	0.42
SVM decision value	0.54
SVM RNA-class probability	0.774678
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1774609 113 + 22407834
CCUCUUCUCACUUCACACAUUUUAAACCAAUUGCGAACUUGGCCCA------GGCGACAAACACUUAAUUGGUUUAAAGGCCUUGACACAAAGUUUUCACUGGCAAUUUGUGAUGG-CUG
..........(.(((((..((((((((((((((.(...(((((...------.))..)))...).))))))))))))))(((.(((..........)))..)))....))))).).-... ( -24.30)
>DroPse_CAF1 36224 112 + 1
CCCCCUCUGA----CAACAGUUAAAUCCAAUUACGAACUUGGCCCA-AACUGAGCAUCAAACAGGUUAUUGAGUUUGAGGCCUUGGUAUAAAGUUUUACCUGGCAAUUAG--GUGG-GAU
.(((.(((((----...(((.((((......(((.((...((((((-((((.((.(((.....)))..)).)))))).)))))).)))......)))).)))....))))--).))-).. ( -29.20)
>DroSec_CAF1 31608 113 + 1
CCUCUUCUCAGUUCACACACUUUAAACCAAUUACGAACUUGGCCCA------GGCGACAAACACUUAAUUGGUUUAAAGGCCUUGACACAAAGUUUUCACUGGCAAUUUGUGAUGG-CUG
........(((((((((..((((((((((((((.(...(((((...------.))..)))...).))))))))))))))(((.(((..........)))..)))....)))))..)-))) ( -29.60)
>DroYak_CAF1 40790 112 + 1
CCU-UUCACACUUCACACACUUUAAACCAAUUACGAACUUGGCCCA------GGCGACAAGCACUUAAUUGGUUUAAAGGCCUUGACACAAAGUUUUCACUGGCAAUUUGCGAUGG-CUG
((.-.((.((.........((((((((((((((.(..((((((...------.))..))))..).))))))))))))))(((.(((..........)))..)))....)).)).))-... ( -28.00)
>DroAna_CAF1 31831 103 + 1
--------CUGGU-CUACACUUUAAACCAAUUACGAACUUGGCCCACAACCGAGUGACAAUCAUUUAAUUCGUUUAAAGUCCUCGCCACAAAGUAUUGACUUUCAAUUCAAG--------
--------.((((-....(((((((((.(((((...((((((.......))))))(.....)...))))).)))))))))....))))....(.((((.....)))).)...-------- ( -20.00)
>DroPer_CAF1 35071 113 + 1
CCCCCUCUGA----CAACAGUUAAAUCCAAUUACGAACUUGGCCCA-AACUGAGCAUCAAACAGGUUAUUGAGUUUGAGGCCUUGGUAUAAAGUUUUACCUGGCACUUAG--AUGGGGAU
((((.(((((----...(((.((((......(((.((...((((((-((((.((.(((.....)))..)).)))))).)))))).)))......)))).)))....))))--).)))).. ( -33.10)
>consensus
CCUCUUCUCA_UU_ACACACUUUAAACCAAUUACGAACUUGGCCCA______AGCGACAAACACUUAAUUGGUUUAAAGGCCUUGACACAAAGUUUUCACUGGCAAUUUG_GAUGG_CUG
...................((((((((((((((.....(((((..........))..))).....))))))))))))))(((...................)))................ (-11.36 = -11.56 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:12 2006