Locus 8583

Sequence ID	3L_DroMel_CAF1
Location	22,366,314 – 22,366,413
Length	99
Max. P	0.686782

overview

Window 1

Location	22,366,314 – 22,366,413
Length	99
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	84.96
Mean single sequence MFE	-24.48
Consensus MFE	-18.70
Energy contribution	-18.50
Covariance contribution	-0.20
Combinations/Pair	1.26
Mean z-score	-1.71
Structure conservation index	0.76
SVM decision value	0.32
SVM RNA-class probability	0.686782
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22366314 99 + 23771897
CUUUUCACCGAGUUUCUUCCCUCGGUUAUGCUUAAUUUGAGACAUUAUCCUAACGUCACAGAAAUCGCUUGACUUGGUA-----ACCAUAACUAGCGUGACAAU
......((((((........)))))).((((((.....))).))).........(((((.(....)(((.....(((..-----.))).....))))))))... ( -20.00)
>DroSec_CAF1 17488 99 + 1
CUUUUCACCGAGUUUCCUCCCUCGGUUAUGCUUAAUUUGAGACAUUAUCCUAAUGUCACAGAGAUCGCUUGCCUUGGCA-----GCCAUAACUAGCGUGACAAU
........((((........))))((((((((...((((.(((((((...))))))).))))....(((.((....)))-----)).......))))))))... ( -27.20)
>DroSim_CAF1 31836 99 + 1
CUUUUCACCGAGUUUCCUCCCUCGGUUAUGCUUAAUUUGAGACAUUAUCCUAAUGUCACAGAGAUCGCUUGCCUUGGCA-----GCCAUAACUAGCGUGACAAU
........((((........))))((((((((...((((.(((((((...))))))).))))....(((.((....)))-----)).......))))))))... ( -27.20)
>DroEre_CAF1 34613 103 + 1
CUUUUCACCGAGUUUCCUCCCCCGGCUAUGCUUAAUUCAGGGCGUUAUCCUAAUGUCA-AGAGAUCGCUUGAGCUGCCAGUCUAGCCCUAACUAGCGUGACAAU
....((((.(((....)))....(((...(((((((((..(((((((...))))))).-.))).....)))))).))).(.((((......))))))))).... ( -23.30)
>DroYak_CAF1 15432 102 + 1
CUUUUCACCGAGUACCCUCCUUCGGCUAUGCAUAAUUCGAGACAUUAUCC-AAUGUCC-GAAGAUCGCUUGAGUUGGCAGAAAAGCCUUAACUAGCGUGACAAA
....((((((((........))))(((..((....((((.((((((....-)))))))-)))....))...(((((((......)))..))))))))))).... ( -24.70)
>consensus
CUUUUCACCGAGUUUCCUCCCUCGGUUAUGCUUAAUUUGAGACAUUAUCCUAAUGUCACAGAGAUCGCUUGACUUGGCA_____GCCAUAACUAGCGUGACAAU
....((((((((........))))((((.((....((((.((((((.....)))))).))))....)).......(((......))).....)))))))).... (-18.70 = -18.50 +  -0.20)

alignment

secondary structure

dotplot

Window 2

Location	22,366,314 – 22,366,413
Length	99
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	84.96
Mean single sequence MFE	-28.46
Consensus MFE	-20.02
Energy contribution	-20.38
Covariance contribution	0.36
Combinations/Pair	1.23
Mean z-score	-1.64
Structure conservation index	0.70
SVM decision value	0.02
SVM RNA-class probability	0.543102
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22366314 99 - 23771897
AUUGUCACGCUAGUUAUGGU-----UACCAAGUCAAGCGAUUUCUGUGACGUUAGGAUAAUGUCUCAAAUUAAGCAUAACCGAGGGAAGAAACUCGGUGAAAAG
....((((....((((((.(-----((..(((((....))))).((.(((((((...))))))).))...))).))))))((((........)))))))).... ( -24.30)
>DroSec_CAF1 17488 99 - 1
AUUGUCACGCUAGUUAUGGC-----UGCCAAGGCAAGCGAUCUCUGUGACAUUAGGAUAAUGUCUCAAAUUAAGCAUAACCGAGGGAGGAAACUCGGUGAAAAG
....((((.((.((((((((-----(((....)).)))......((.(((((((...))))))).)).......))))))..)).(((....))).)))).... ( -28.80)
>DroSim_CAF1 31836 99 - 1
AUUGUCACGCUAGUUAUGGC-----UGCCAAGGCAAGCGAUCUCUGUGACAUUAGGAUAAUGUCUCAAAUUAAGCAUAACCGAGGGAGGAAACUCGGUGAAAAG
....((((.((.((((((((-----(((....)).)))......((.(((((((...))))))).)).......))))))..)).(((....))).)))).... ( -28.80)
>DroEre_CAF1 34613 103 - 1
AUUGUCACGCUAGUUAGGGCUAGACUGGCAGCUCAAGCGAUCUCU-UGACAUUAGGAUAACGCCCUGAAUUAAGCAUAGCCGGGGGAGGAAACUCGGUGAAAAG
....((((.(((((....))))).(((((.((....)).....((-(((..(((((.......))))).)))))....)))))..(((....))).)))).... ( -30.40)
>DroYak_CAF1 15432 102 - 1
UUUGUCACGCUAGUUAAGGCUUUUCUGCCAACUCAAGCGAUCUUC-GGACAUU-GGAUAAUGUCUCGAAUUAUGCAUAGCCGAAGGAGGGUACUCGGUGAAAAG
((..((.((((((((..(((......)))))))..))))..((((-((....(-(.(((((.......))))).))...))))))(((....)))))..))... ( -30.00)
>consensus
AUUGUCACGCUAGUUAUGGC_____UGCCAAGUCAAGCGAUCUCUGUGACAUUAGGAUAAUGUCUCAAAUUAAGCAUAACCGAGGGAGGAAACUCGGUGAAAAG
..(((..((((.(...((((......))))...).)))).....((.((((((.....)))))).))......)))..((((((........))))))...... (-20.02 = -20.38 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:19:34 2006