Locus 5662

Sequence ID	3R_DroMel_CAF1
Location	14,873,328 – 14,873,475
Length	147
Max. P	0.886406

overview

Window 5

Location	14,873,328 – 14,873,435
Length	107
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.44
Mean single sequence MFE	-22.05
Consensus MFE	-15.65
Energy contribution	-15.85
Covariance contribution	0.20
Combinations/Pair	1.08
Mean z-score	-1.82
Structure conservation index	0.71
SVM decision value	0.23
SVM RNA-class probability	0.643931
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14873328 107 - 27905053
CACGGUAUAAAUAUCGAGCACCUAACGCACAAGCAACGUAAGUGACUUGUUUAGCUAAAGCAUAAAAAUCACAAUCAUAAGUCACUUUUUUC-------------UUGAUCGUGCUAAUU
..(((((....)))))((((((....)..((((.((...((((((((((((((((....)).)))...........)))))))))))..)))-------------)))...))))).... ( -22.80)
>DroSec_CAF1 991 107 - 1
CACGGUAUAAAUAUCGAGAACCUAACGCACAAGCAACGUAAGUGACUUGUUUAGCUAAAGCAUAAAACUCACAAUCAUAAGUCACUUUUUUC-------------UUGAUCGUGCUAUUU
...(((((....((((((((......((....)).....((((((((((((((((....)).)))...........)))))))))))..)))-------------))))).))))).... ( -22.40)
>DroSim_CAF1 993 107 - 1
CACGGUAUAAAUAUCGAGCACCUAACGCACAAGCAACGUAAGUGACUUAUUCAGCUAAAGCAUAAAAAUCACAAUCAUAAGUCACUUUUUUC-------------UUGAUCGUGCUAUUU
..(((((....)))))((((((....)..((((.((...(((((((((((...((....))...............)))))))))))..)))-------------)))...))))).... ( -21.47)
>DroEre_CAF1 987 119 - 1
CACGGUAUAAAAAUCGAGCUCCUAACGCACAAGCAACGUAAGUGACUUGUUUAGCUAAAGCAUACAAAUCACAAUCAUAAGUCACUUUUUUCAA-UUGUUAAAAGAUUGUCGUGCUCUUU
..((((......))))..........((((..((((.....((((.((((...((....))..)))).))))............(((((..(..-..)..))))).)))).))))..... ( -20.90)
>DroYak_CAF1 988 120 - 1
CACGGUAUAAAUAUCGAGCCCCAAGCGCACACGAAAAGUAAGUGACUUGUUUAGCUAAAGCAUACAAAUCACAAUCAUAAGUCACUUUUUUCAAAAUAUUACUAGUUUGUCGUGCUAUUU
..(((((....))))).((.....))(((((((((.(((((((((.((((...((....))..)))).))))......(((...)))...........)))))..))))).))))..... ( -22.70)
>consensus
CACGGUAUAAAUAUCGAGCACCUAACGCACAAGCAACGUAAGUGACUUGUUUAGCUAAAGCAUAAAAAUCACAAUCAUAAGUCACUUUUUUC_____________UUGAUCGUGCUAUUU
..(((((....)))))..........((((...(((...(((((((((((...((....))...............)))))))))))..................)))...))))..... (-15.65 = -15.85 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	14,873,355 – 14,873,475
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.25
Mean single sequence MFE	-30.55
Consensus MFE	-26.04
Energy contribution	-26.52
Covariance contribution	0.48
Combinations/Pair	1.05
Mean z-score	-1.62
Structure conservation index	0.85
SVM decision value	0.94
SVM RNA-class probability	0.886406
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14873355 120 + 27905053
UUAUGAUUGUGAUUUUUAUGCUUUAGCUAAACAAGUCACUUACGUUGCUUGUGCGUUAGGUGCUCGAUAUUUAUACCGUGGCUGUGUUUAACCUGGGGUAUGCCGAAAUAAUUAUCAUAU
.((((((....(((((((((((((((.((((((((((((..((((.......))))..((((...........)))))))))).))))))..))))))))))..)))))....)))))). ( -31.10)
>DroSec_CAF1 1018 120 + 1
UUAUGAUUGUGAGUUUUAUGCUUUAGCUAAACAAGUCACUUACGUUGCUUGUGCGUUAGGUUCUCGAUAUUUAUACCGUGGCUGUGUUUAACCUGGGGUAUGCCGAAAUAAUUAUCAUAU
.((((((.((...(((((((((((((.((((((((((((..((((.......))))..(((.............))))))))).))))))..))))))))))..)))...)).)))))). ( -29.02)
>DroSim_CAF1 1020 120 + 1
UUAUGAUUGUGAUUUUUAUGCUUUAGCUGAAUAAGUCACUUACGUUGCUUGUGCGUUAGGUGCUCGAUAUUUAUACCGUGGCUGUGUUUAACCUGGGGUAUGCCGAAAUAAUUAUCAUAU
.((((((....(((((((((((((((.((((((((((((..((((.......))))..((((...........)))))))))).))))))..))))))))))..)))))....)))))). ( -29.30)
>DroEre_CAF1 1026 120 + 1
UUAUGAUUGUGAUUUGUAUGCUUUAGCUAAACAAGUCACUUACGUUGCUUGUGCGUUAGGAGCUCGAUUUUUAUACCGUGGCUGUGUUUAACCUGGGGUAUGCCGAAAUAAUUAUCAUAU
.((((((....(((((((((((((((.((((((((((((...((..((((.((...)).)))).))((....))...)))))).))))))..)))))))))))..))))....)))))). ( -30.80)
>DroYak_CAF1 1028 120 + 1
UUAUGAUUGUGAUUUGUAUGCUUUAGCUAAACAAGUCACUUACUUUUCGUGUGCGCUUGGGGCUCGAUAUUUAUACCGUGGCUGUGUUUAACCUGGGGUAUGCCGAAAUAAGUAUCAUAU
.(((((..(((((((((..((....))...))))))))).((((((((((((((.((..((....(((((.............)))))...))..))))))).))))..)))))))))). ( -32.52)
>consensus
UUAUGAUUGUGAUUUUUAUGCUUUAGCUAAACAAGUCACUUACGUUGCUUGUGCGUUAGGUGCUCGAUAUUUAUACCGUGGCUGUGUUUAACCUGGGGUAUGCCGAAAUAAUUAUCAUAU
.((((((....(((((((((((((((.((((((((((((......(((....)))...((...............)))))))).))))))..))))))))))..)))))....)))))). (-26.04 = -26.52 +   0.48)

alignment

secondary structure

dotplot

Window 7

Location	14,873,355 – 14,873,475
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.25
Mean single sequence MFE	-23.54
Consensus MFE	-18.26
Energy contribution	-18.86
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.31
Structure conservation index	0.78
SVM decision value	0.86
SVM RNA-class probability	0.867637
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14873355 120 - 27905053
AUAUGAUAAUUAUUUCGGCAUACCCCAGGUUAAACACAGCCACGGUAUAAAUAUCGAGCACCUAACGCACAAGCAACGUAAGUGACUUGUUUAGCUAAAGCAUAAAAAUCACAAUCAUAA
.((((((....((((..(((((((...((((......))))..)))))........(((..(....).(((((..((....))..)))))...)))...))....))))....)))))). ( -22.40)
>DroSec_CAF1 1018 120 - 1
AUAUGAUAAUUAUUUCGGCAUACCCCAGGUUAAACACAGCCACGGUAUAAAUAUCGAGAACCUAACGCACAAGCAACGUAAGUGACUUGUUUAGCUAAAGCAUAAAACUCACAAUCAUAA
.((((((............(((((...((((......))))..))))).......(((..........(((((..((....))..)))))...((....))......)))...)))))). ( -24.00)
>DroSim_CAF1 1020 120 - 1
AUAUGAUAAUUAUUUCGGCAUACCCCAGGUUAAACACAGCCACGGUAUAAAUAUCGAGCACCUAACGCACAAGCAACGUAAGUGACUUAUUCAGCUAAAGCAUAAAAAUCACAAUCAUAA
.((((((..((((((((((........((((......)))).(((((....))))).)).......((....))..)).))))))........((....))............)))))). ( -19.40)
>DroEre_CAF1 1026 120 - 1
AUAUGAUAAUUAUUUCGGCAUACCCCAGGUUAAACACAGCCACGGUAUAAAAAUCGAGCUCCUAACGCACAAGCAACGUAAGUGACUUGUUUAGCUAAAGCAUACAAAUCACAAUCAUAA
.((((((..((((....(((((((...((((......))))..))))).........((.......))....))...))))((((.((((...((....))..)))).)))).)))))). ( -24.60)
>DroYak_CAF1 1028 120 - 1
AUAUGAUACUUAUUUCGGCAUACCCCAGGUUAAACACAGCCACGGUAUAAAUAUCGAGCCCCAAGCGCACACGAAAAGUAAGUGACUUGUUUAGCUAAAGCAUACAAAUCACAAUCAUAA
.((((((((((..(((((((((((...((((......))))..))))).........((.....))))...))))))))).((((.((((...((....))..)))).))))..))))). ( -27.30)
>consensus
AUAUGAUAAUUAUUUCGGCAUACCCCAGGUUAAACACAGCCACGGUAUAAAUAUCGAGCACCUAACGCACAAGCAACGUAAGUGACUUGUUUAGCUAAAGCAUAAAAAUCACAAUCAUAA
.((((((......(((((.(((((...((((......))))..))))).....)))))........(((((((..((....))..)))))...))..................)))))). (-18.26 = -18.86 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:01:07 2006