Locus 1793

Sequence ID	3L_DroMel_CAF1
Location	5,072,281 – 5,072,473
Length	192
Max. P	0.653821

overview

Window 1

Location	5,072,281 – 5,072,393
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.92
Mean single sequence MFE	-24.24
Consensus MFE	-18.57
Energy contribution	-19.81
Covariance contribution	1.24
Combinations/Pair	1.03
Mean z-score	-1.67
Structure conservation index	0.77
SVM decision value	-0.02
SVM RNA-class probability	0.525928
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5072281 112 + 23771897
GUUCAGCUUGAUUGCAGCAAUUAAACUGUGAUUGUUUGUCCAAUUAGAAACAAAGUAUUUUCAAAUGAAUGUAUGCACAAACAGUGCAAUAUUCCACAUUUGACGUGCA--------ACU
(..(((..((((..(((........)))..)))).)))..).............((((..((((((((((((.(((((.....)))))))))))...)))))).)))).--------... ( -24.40)
>DroSec_CAF1 278785 112 + 1
GUUCAGCUUGAUUGCAGCAAUUAAACUGUGAUUGUUUGUCCAAUUAGAAACAAAGUAUUUUCAAAUGAAAGUAUGGACAAACAGUGCAAUAUUCCACAUUUGACGUGCA--------ACU
.....((......)).(((.(((((.((((((((((((((((.............(((((((....))))))))))))))))))).........)))))))))..))).--------... ( -26.41)
>DroSim_CAF1 300074 112 + 1
GUUCAGCUUGAUUGCAGCAAUUAAACUGUGAUUGUUUGUCCAAUUAGAAACAAAGUAUUUUCAAAUGAAAGUAUGGACAAACAGUGCAAUAUUCCACAUUUGACGUGCA--------ACU
.....((......)).(((.(((((.((((((((((((((((.............(((((((....))))))))))))))))))).........)))))))))..))).--------... ( -26.41)
>DroEre_CAF1 285714 111 + 1
GUUCAGCUUGAUUGCAGCAAUUAAACUCUGAUUGUUUGUCCAAUUAGAAACAAAGUAUUU-CAAAUGAAAGUAUGGACAAAUAGUGCAAUAUUCCACAUUUGAUGUGCA--------ACU
(((....(((((((...)))))))..((((((((......)))))))))))...((((.(-((((((..((((((.((.....)).).)))))...))))))).)))).--------... ( -22.40)
>DroYak_CAF1 289683 120 + 1
GUUCAGCUUGAUUGCAGCAAUUAAACUCUGAUUGUUUGUCCAAUUAGAAACAAAGUAUUUCCAAAUGAAAGUAUGAACAAACAGUGCAAUAUUCCACAUUUGAUGUGCACAUUCCACAUU
((((((((((((((...)))))....((((((((......))))))))....................)))).))))).....(((((.((((........))))))))).......... ( -21.60)
>consensus
GUUCAGCUUGAUUGCAGCAAUUAAACUGUGAUUGUUUGUCCAAUUAGAAACAAAGUAUUUUCAAAUGAAAGUAUGGACAAACAGUGCAAUAUUCCACAUUUGACGUGCA________ACU
.....((......)).(((....((.((((((((((((((((.............(((((((....))))))))))))))))))).........)))).))....)))............ (-18.57 = -19.81 +   1.24)

alignment

secondary structure

dotplot

Window 2

Location	5,072,361 – 5,072,473
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.80
Mean single sequence MFE	-28.44
Consensus MFE	-22.06
Energy contribution	-22.30
Covariance contribution	0.24
Combinations/Pair	1.10
Mean z-score	-1.60
Structure conservation index	0.78
SVM decision value	0.25
SVM RNA-class probability	0.653821
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5072361 112 - 23771897
GGCGCAAAACCAAAGUGAAUUAUAUGGCUAAGCAACGGAGUCAAAAUGUGAAGCCGCUUGAUGAACUAUGAGGCGACUCAAGU--------UGCACGUCAAAUGUGGAAUAUUGCACUGU
((.((((......(((..((((..(((((..(((............)))..)))))..))))..))).((((....)))).((--------(.(((((...))))).))).)))).)).. ( -27.70)
>DroSec_CAF1 278865 112 - 1
GGCGCAAAACCAAAGUGAAUUAUAUGGCUAAGCAACGGAGUCAAAAUGUGAAGCCACUUGAUGAACUAUGAGGCGACUCAAGU--------UGCACGUCAAAUGUGGAAUAUUGCACUGU
((.((((......(((..((((..(((((..(((............)))..)))))..))))..))).((((....)))).((--------(.(((((...))))).))).)))).)).. ( -28.40)
>DroSim_CAF1 300154 112 - 1
GGCGCAAAAACAAAGUGAAUUAUAUGGCUAAGCAACGGAGUCAAAAUGUGAAGCCACUUGAUGAACUAUGAGGCGACUCAAGU--------UGCACGUCAAAUGUGGAAUAUUGCACUGU
((.((((......(((..((((..(((((..(((............)))..)))))..))))..))).((((....)))).((--------(.(((((...))))).))).)))).)).. ( -28.40)
>DroEre_CAF1 285793 112 - 1
GGCGCAUAGCCAAAGUGAAUUAUAUAGCUAAGCAACGAAGAUAAAGUUUGAAGCCACUUGAUGAACAAUGAGACGACUCAAGU--------UGCACAUCAAAUGUGGAAUAUUGCACUAU
(((.....)))..((((....((((...(((((............)))))...((((((((((..(((((((....))))..)--------))..))))))..)))).))))..)))).. ( -23.90)
>DroYak_CAF1 289763 120 - 1
GGCGCAAAACCAAAGUGAAUUAUAUGGCUAAGCAACGGAGACGAAAUGCGAAGCCACUUGAUGAACUAUGAGACGACUCAAAUGUGGAAUGUGCACAUCAAAUGUGGAAUAUUGCACUGU
((.......))..(((..((((..(((((..(((.((....))...)))..)))))..))))..))).((((....))))...(((.(((((.(((((...)))))..))))).)))... ( -33.80)
>consensus
GGCGCAAAACCAAAGUGAAUUAUAUGGCUAAGCAACGGAGUCAAAAUGUGAAGCCACUUGAUGAACUAUGAGGCGACUCAAGU________UGCACGUCAAAUGUGGAAUAUUGCACUGU
((.((((......(((..((((..(((((..(((............)))..)))))..))))..))).((((....)))).............(((((...))))).....)))).)).. (-22.06 = -22.30 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:37 2006