Locus 1970

Sequence ID	3L_DroMel_CAF1
Location	5,447,296 – 5,447,455
Length	159
Max. P	0.789883

overview

Window 5

Location	5,447,296 – 5,447,416
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.14
Mean single sequence MFE	-26.96
Consensus MFE	-23.44
Energy contribution	-22.88
Covariance contribution	-0.56
Combinations/Pair	1.09
Mean z-score	-1.54
Structure conservation index	0.87
SVM decision value	-0.01
SVM RNA-class probability	0.526683
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5447296 120 - 23771897
GUGAAUAUUAAUGCCUAAUAUUUUAUUCGGCAACCACUUCAUGGUUUUUAGUUCUUACUUCAUGACCCUGGACGCGAUUCGUGAUGCUCUCAGACCACUUAGGCAAAUGUUUAUGAUUUU
(((((((((..(((((((..........((((.....((((.((((...(((....)))....)))).))))((((...)))).))))..........))))))))))))))))...... ( -27.15)
>DroSec_CAF1 8836 120 - 1
GUGAAUAUUAAUGCUUAAUAUUUUAUUCGGCAACCACUUCAUGGUUUUUAGUUCCUACUUCAUGACCCUGGACGCGAUUCGGUAUGCCCUCAGACCACUUAAGCAAAUGUUUAUGAUUUU
(((((((((..(((((((..........(((((((....((.((((...(((....)))....)))).))((......))))).))))..........))))))))))))))))...... ( -25.85)
>DroSim_CAF1 8887 120 - 1
GUGAAUAUUAAUGCCUAAUAUUUUAUUCGGCAACCACUUCAUGGUUUUUAGUUCUUACUGCAUGACCCUGGACGCGAUUCGGUAUGCCCUCAGACCACUUAGGCAAAUGUUUAUGAUUUU
(((((((((..(((((((..........(((((((....((.((((..((((....))))...)))).))((......))))).))))..........))))))))))))))))...... ( -28.95)
>DroEre_CAF1 8636 120 - 1
GUGAAUAUUAAUGCCAAAUAUUUUAUUCGGCAACCACUUCAUGGUUUUUAGUUUUUGCUCCAUGACCCUGGACGCGAUUCGCUAUGCUCUCAGACCACUUAGGCAAAUGUUUAUGAUUUU
(((((((((..((((.............((((((((.....))))...((((..((((((((......)))).))))...)))))))).............)))))))))))))...... ( -25.87)
>consensus
GUGAAUAUUAAUGCCUAAUAUUUUAUUCGGCAACCACUUCAUGGUUUUUAGUUCUUACUUCAUGACCCUGGACGCGAUUCGGUAUGCCCUCAGACCACUUAGGCAAAUGUUUAUGAUUUU
(((((((((..(((((((..........((((.....((((.((((...(((....)))....)))).))))((.....))...))))..........))))))))))))))))...... (-23.44 = -22.88 +  -0.56)

alignment

secondary structure

dotplot

Window 6

Location	5,447,336 – 5,447,455
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.61
Mean single sequence MFE	-33.75
Consensus MFE	-25.77
Energy contribution	-26.28
Covariance contribution	0.50
Combinations/Pair	1.03
Mean z-score	-1.88
Structure conservation index	0.76
SVM decision value	0.13
SVM RNA-class probability	0.597755
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5447336 119 + 23771897
GAAUCGCGUCCAGGGUCAUGAAGUAAGAACUAAAAACCAUGAAGUGGUUGCCGAAUAAAAUAUUAGGCAUUAAUAUUCACACCCUUAGAGGGCUCACGACGACGGGGUCAUGACC-CAUC
............(((((((((.....(((.....((((((...))))))(((.((((...)))).))).......)))...(((.....)))(((.((....)))))))))))))-)... ( -31.20)
>DroSec_CAF1 8876 117 + 1
GAAUCGCGUCCAGGGUCAUGAAGUAGGAACUAAAAACCAUGAAGUGGUUGCCGAAUAAAAUAUUAAGCAUUAAUAUUCACACCCUUCGAGGACUCACGACG---GGGUCAUGACCCCACC
............(((((((((.((.(((......((((((...))))))((..((((...))))..)).......))))).(((.(((........))).)---)).))))))))).... ( -30.10)
>DroSim_CAF1 8927 120 + 1
GAAUCGCGUCCAGGGUCAUGCAGUAAGAACUAAAAACCAUGAAGUGGUUGCCGAAUAAAAUAUUAGGCAUUAAUAUUCACACCCUUCGAGGACUCACGACGGUGGGGUCAUGACCCCACC
...(((.(((((((((..((.((((.........((((((...))))))(((.((((...)))).))).....)))))).)))))....))))...))).((((((((....)))))))) ( -37.60)
>DroEre_CAF1 8676 116 + 1
GAAUCGCGUCCAGGGUCAUGGAGCAAAAACUAAAAACCAUGAAGUGGUUGCCGAAUAAAAUAUUUGGCAUUAAUAUUCACACCCUUCGAGGGCUCACGACG---GGGUCAUGACCCGAC-
.......(((..(((((((((((...........((((((...))))))((((((((...)))))))).......)))..((((((((........))).)---)))))))))))))))- ( -36.10)
>consensus
GAAUCGCGUCCAGGGUCAUGAAGUAAGAACUAAAAACCAUGAAGUGGUUGCCGAAUAAAAUAUUAGGCAUUAAUAUUCACACCCUUCGAGGACUCACGACG___GGGUCAUGACCCCACC
............((((((((................((.(((((.(((((((.((((...)))).))))...........)))))))).))((((.........)))))))))))).... (-25.77 = -26.28 +   0.50)

alignment

secondary structure

dotplot

Window 7

Location	5,447,336 – 5,447,455
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.61
Mean single sequence MFE	-37.27
Consensus MFE	-29.24
Energy contribution	-30.43
Covariance contribution	1.19
Combinations/Pair	1.14
Mean z-score	-2.17
Structure conservation index	0.78
SVM decision value	0.58
SVM RNA-class probability	0.789883
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5447336 119 - 23771897
GAUG-GGUCAUGACCCCGUCGUCGUGAGCCCUCUAAGGGUGUGAAUAUUAAUGCCUAAUAUUUUAUUCGGCAACCACUUCAUGGUUUUUAGUUCUUACUUCAUGACCCUGGACGCGAUUC
((((-((.......))))))(((((((((((.....))))((((..(((((((((.((((...)))).))))((((.....))))..)))))..)))).))))))).............. ( -34.40)
>DroSec_CAF1 8876 117 - 1
GGUGGGGUCAUGACCC---CGUCGUGAGUCCUCGAAGGGUGUGAAUAUUAAUGCUUAAUAUUUUAUUCGGCAACCACUUCAUGGUUUUUAGUUCCUACUUCAUGACCCUGGACGCGAUUC
...(((((....))))---)(((((..((((..((((((((((((((..((((.....)))).))))).)).))).))))..((((...(((....)))....))))..))))))))).. ( -34.90)
>DroSim_CAF1 8927 120 - 1
GGUGGGGUCAUGACCCCACCGUCGUGAGUCCUCGAAGGGUGUGAAUAUUAAUGCCUAAUAUUUUAUUCGGCAACCACUUCAUGGUUUUUAGUUCUUACUGCAUGACCCUGGACGCGAUUC
((((((((....))))))))(((((..((((..((((((((((((((..((((.....)))).))))).)).))).))))..((((..((((....))))...))))..))))))))).. ( -43.20)
>DroEre_CAF1 8676 116 - 1
-GUCGGGUCAUGACCC---CGUCGUGAGCCCUCGAAGGGUGUGAAUAUUAAUGCCAAAUAUUUUAUUCGGCAACCACUUCAUGGUUUUUAGUUUUUGCUCCAUGACCCUGGACGCGAUUC
-(((((((((((((((---..(((.(....).))).))))(..((.(((((((((.((((...)))).))))((((.....))))..))))).))..)..))))))))..)))....... ( -36.60)
>consensus
GGUGGGGUCAUGACCC___CGUCGUGAGCCCUCGAAGGGUGUGAAUAUUAAUGCCUAAUAUUUUAUUCGGCAACCACUUCAUGGUUUUUAGUUCUUACUUCAUGACCCUGGACGCGAUUC
((((((((....))))))))((((((.((((.....))))...........((((.((((...)))).)))).....((((.((((...(((....)))....)))).)))))))))).. (-29.24 = -30.43 +   1.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:26 2006