Locus 4799

Sequence ID	3L_DroMel_CAF1
Location	13,429,691 – 13,429,929
Length	238
Max. P	0.800461

overview

Window 7

Location	13,429,691 – 13,429,809
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.58
Mean single sequence MFE	-19.32
Consensus MFE	-16.68
Energy contribution	-15.76
Covariance contribution	-0.92
Combinations/Pair	1.17
Mean z-score	-1.28
Structure conservation index	0.86
SVM decision value	0.22
SVM RNA-class probability	0.640158
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13429691 118 + 23771897
--UUUCCAUGGUAUUCCCCUUGUUUCAAUAAAAACCAUUUAAUAAUACGAUUUAUCUGAAGUUAUCACGAAGCUCACGCACUCCCCAUUGAGUUCUCCUUCAGUGGCAUAAAUCUGCCUC
--.......((((........((((......)))).............(((((((((((((..........((....))((((......))))....))))))....))))))))))).. ( -17.30)
>DroSec_CAF1 26835 120 + 1
UAUUUCCAUGGUAUUCCCCUUGUUUUAAUAAAAACCAUUUAAUAAUACGAUUUAUCUGAAUUUAUCACGAAGCUCACGCACUCCCCAUUGAGUUCUCCUUCAGUGGCAUAAAUCUGCCUC
.........((((........((.(((.((((.....)))).))).))(((((((................((....)).....((((((((......)))))))).))))))))))).. ( -18.00)
>DroSim_CAF1 28704 120 + 1
UAUUUCCAUGGUAUUCCCCUUGGUUUAAUAAAAACCAUUUAAUAAUACGAUUUAUCUGAAGUUAUCACGAAGCUCACGCACUCCCCAUUGAGUUCUCCUUCAGUGGCAUAAAUCUGCCUC
.......((.(((((.....((((((.....))))))......))))).))....((((((..........((....))((((......))))....)))))).((((......)))).. ( -22.60)
>DroEre_CAF1 27869 120 + 1
UAUUACCAUGGUAUUCCCCUUGAUUUAACGAAAUCCAUUUAAUAACAAGAUUUAUCUGAAGUUAUCACGAAGCUCACGCACUCCCCAUUGAGUUCUCCUUCAAUGGCAUAAAUCUGCCUC
.........(((.........(((((....)))))............((((((((................((....)).....((((((((......)))))))).))))))))))).. ( -18.70)
>DroYak_CAF1 27076 120 + 1
GAUUACCAUGGUAUUCCCCUGGCUUUAACCAAAUCCAUUAAAUAAUAAGAUUUAUCUGAAGUUAUCACGAAGCUCACGCACUCCCCAUUGAGUUCUCCUUCAAUGGCAUAAAUCUGCCUC
((.(((....))).))....((((((((.........))))).....((((((((................((....)).....((((((((......)))))))).))))))))))).. ( -20.00)
>consensus
UAUUUCCAUGGUAUUCCCCUUGUUUUAAUAAAAACCAUUUAAUAAUACGAUUUAUCUGAAGUUAUCACGAAGCUCACGCACUCCCCAUUGAGUUCUCCUUCAGUGGCAUAAAUCUGCCUC
.........((((......(((......))).................(((((((................((....)).....((((((((......)))))))).))))))))))).. (-16.68 = -15.76 +  -0.92)

alignment

secondary structure

dotplot

Window 8

Location	13,429,691 – 13,429,809
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.58
Mean single sequence MFE	-28.80
Consensus MFE	-22.78
Energy contribution	-23.22
Covariance contribution	0.44
Combinations/Pair	1.08
Mean z-score	-1.47
Structure conservation index	0.79
SVM decision value	-0.01
SVM RNA-class probability	0.525976
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13429691 118 - 23771897
GAGGCAGAUUUAUGCCACUGAAGGAGAACUCAAUGGGGAGUGCGUGAGCUUCGUGAUAACUUCAGAUAAAUCGUAUUAUUAAAUGGUUUUUAUUGAAACAAGGGGAAUACCAUGGAAA--
((((((......)))).((((((....((((......))))((....))..........)))))).....))......((..(((((.(((.(((...)))...))).)))))..)).-- ( -27.90)
>DroSec_CAF1 26835 120 - 1
GAGGCAGAUUUAUGCCACUGAAGGAGAACUCAAUGGGGAGUGCGUGAGCUUCGUGAUAAAUUCAGAUAAAUCGUAUUAUUAAAUGGUUUUUAUUAAAACAAGGGGAAUACCAUGGAAAUA
..((((......)))).(((((.....((((......))))((....))...........)))))..(((((((........))))))).........((.((......)).))...... ( -24.20)
>DroSim_CAF1 28704 120 - 1
GAGGCAGAUUUAUGCCACUGAAGGAGAACUCAAUGGGGAGUGCGUGAGCUUCGUGAUAACUUCAGAUAAAUCGUAUUAUUAAAUGGUUUUUAUUAAACCAAGGGGAAUACCAUGGAAAUA
..((((......)))).((((((....((((......))))((....))..........))))))..(((((((........)))))))........(((.((......)).)))..... ( -30.60)
>DroEre_CAF1 27869 120 - 1
GAGGCAGAUUUAUGCCAUUGAAGGAGAACUCAAUGGGGAGUGCGUGAGCUUCGUGAUAACUUCAGAUAAAUCUUGUUAUUAAAUGGAUUUCGUUAAAUCAAGGGGAAUACCAUGGUAAUA
..(((((((((((.(((((((.(.....))))))))(((((((....)).........)))))..))))))).))))((((.(((((((((.((......)).))))).))))..)))). ( -31.00)
>DroYak_CAF1 27076 120 - 1
GAGGCAGAUUUAUGCCAUUGAAGGAGAACUCAAUGGGGAGUGCGUGAGCUUCGUGAUAACUUCAGAUAAAUCUUAUUAUUUAAUGGAUUUGGUUAAAGCCAGGGGAAUACCAUGGUAAUC
..((((......)))).((((((....((((......))))((....))..........)))))).(((((((...........)))))))......((((.((.....)).)))).... ( -30.30)
>consensus
GAGGCAGAUUUAUGCCACUGAAGGAGAACUCAAUGGGGAGUGCGUGAGCUUCGUGAUAACUUCAGAUAAAUCGUAUUAUUAAAUGGUUUUUAUUAAAACAAGGGGAAUACCAUGGAAAUA
..((((......)))).((((((....((((......))))((....))..........)))))).................(((((.(((.((.......)).))).)))))....... (-22.78 = -23.22 +   0.44)

alignment

secondary structure

dotplot

Window 9

Location	13,429,729 – 13,429,849
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.00
Mean single sequence MFE	-31.18
Consensus MFE	-29.42
Energy contribution	-29.58
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-1.19
Structure conservation index	0.94
SVM decision value	0.08
SVM RNA-class probability	0.572281
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13429729 120 - 23771897
CUUUGAGUGUGCUUCAAGGAUUUGCUUAUAUAUCCGAAUUGAGGCAGAUUUAUGCCACUGAAGGAGAACUCAAUGGGGAGUGCGUGAGCUUCGUGAUAACUUCAGAUAAAUCGUAUUAUU
...(((((.((((((((((((..........))))...)))))))).))))).....((((((....((((......))))((....))..........))))))............... ( -31.80)
>DroSec_CAF1 26875 120 - 1
CUUUGAGUGUGCUUCAAGGAUUUGCUUAUAUAUCCGAAUUGAGGCAGAUUUAUGCCACUGAAGGAGAACUCAAUGGGGAGUGCGUGAGCUUCGUGAUAAAUUCAGAUAAAUCGUAUUAUU
...(((((.((((((((((((..........))))...)))))))).))))).....(((((.....((((......))))((....))...........)))))............... ( -28.50)
>DroSim_CAF1 28744 120 - 1
CUUUGAGUGUGCUUCAAGGAUUUGCUUAUAUAUCCGAAUUGAGGCAGAUUUAUGCCACUGAAGGAGAACUCAAUGGGGAGUGCGUGAGCUUCGUGAUAACUUCAGAUAAAUCGUAUUAUU
...(((((.((((((((((((..........))))...)))))))).))))).....((((((....((((......))))((....))..........))))))............... ( -31.80)
>DroEre_CAF1 27909 120 - 1
CUUUGAGUGUGCUUCAAGGAUUUGCUUAUAUAUCCGAAUUGAGGCAGAUUUAUGCCAUUGAAGGAGAACUCAAUGGGGAGUGCGUGAGCUUCGUGAUAACUUCAGAUAAAUCUUGUUAUU
...(((((.((((((((((((..........))))...)))))))).)))))..(((((((.(.....)))))))).(((.((....)))))..((((((...(((....))).)))))) ( -33.50)
>DroYak_CAF1 27116 120 - 1
CUUUGAGUGUGCUUCAAGGAUUUGCUUAUAUAUCCGAAUCGAGGCAGAUUUAUGCCAUUGAAGGAGAACUCAAUGGGGAGUGCGUGAGCUUCGUGAUAACUUCAGAUAAAUCUUAUUAUU
....((((.(.((((((((((..........)))).......((((......)))).)))))).)..))))(((((((((.((....))))).(((.....))).......))))))... ( -30.30)
>consensus
CUUUGAGUGUGCUUCAAGGAUUUGCUUAUAUAUCCGAAUUGAGGCAGAUUUAUGCCACUGAAGGAGAACUCAAUGGGGAGUGCGUGAGCUUCGUGAUAACUUCAGAUAAAUCGUAUUAUU
...(((((.(((((((.((((..........))))....))))))).))))).....((((((....((((......))))((....))..........))))))............... (-29.42 = -29.58 +   0.16)

alignment

secondary structure

dotplot

Window 0

Location	13,429,809 – 13,429,929
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.50
Mean single sequence MFE	-32.24
Consensus MFE	-30.60
Energy contribution	-30.68
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-1.30
Structure conservation index	0.95
SVM decision value	0.62
SVM RNA-class probability	0.800461
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13429809 120 - 23771897
CCUUUCCAUAUGCCAGAUGUUGUCUGAAGUGACGAUCCAGUCAACGUAUGGAAAAGGAAAACUUUAUCGGCAAUCGGCUCCUUUGAGUGUGCUUCAAGGAUUUGCUUAUAUAUCCGAAUU
((((((((((((.(((((...)))))...((((......)))).))))))).))))).........((((..((.((((((((.(((....))).)))))...))).))....))))... ( -34.20)
>DroSec_CAF1 26955 120 - 1
CCUUUCCAUAUGCCAGAUGUUGUCUGAAGUGACGAUCCAGUCAACGUAUGGAAAAGGAAAAGUUUAUCGGCAAUCGGCUCCUUUGAGUGUGCUUCAAGGAUUUGCUUAUAUAUCCGAAUU
((((((((((((.(((((...)))))...((((......)))).))))))).))))).........((((..((.((((((((.(((....))).)))))...))).))....))))... ( -34.20)
>DroSim_CAF1 28824 120 - 1
CCUUUCCAUAUGCCAGAUGUUGUCUGAAGUGACGAUCCAGUCAACGUAUGGAAAAGGAAAAGUUUAUCGGCAAUCGGCUCCUUUGAGUGUGCUUCAAGGAUUUGCUUAUAUAUCCGAAUU
((((((((((((.(((((...)))))...((((......)))).))))))).))))).........((((..((.((((((((.(((....))).)))))...))).))....))))... ( -34.20)
>DroEre_CAF1 27989 120 - 1
CCUUUCCAUAUGCCAGAUGUUGUCUGAAGUGACGAUCCAGUCAACGCACGGAAGAAGAAAAGUUUAUCGGCAAUCGGCUCCUUUGAGUGUGCUUCAAGGAUUUGCUUAUAUAUCCGAAUU
..(((((...((((((((...)))))...((((......))))..))).)))))............((((..((.((((((((.(((....))).)))))...))).))....))))... ( -26.60)
>DroYak_CAF1 27196 120 - 1
CCUUUCCAUAUGCCAGAUGUUGUCUGAAGUGACGAUCCAGUCAACGUAUGGAGAAAGAAAAGUUUAUCGGCAAUCGGCUCCUUUGAGUGUGCUUCAAGGAUUUGCUUAUAUAUCCGAAUC
..((((((((((.(((((...)))))...((((......)))).))))))))))............((((..((.((((((((.(((....))).)))))...))).))....))))... ( -32.00)
>consensus
CCUUUCCAUAUGCCAGAUGUUGUCUGAAGUGACGAUCCAGUCAACGUAUGGAAAAGGAAAAGUUUAUCGGCAAUCGGCUCCUUUGAGUGUGCUUCAAGGAUUUGCUUAUAUAUCCGAAUU
..((((((((((.(((((...)))))...((((......)))).))))))))))............((((..((.((((((((.(((....))).)))))...))).))....))))... (-30.60 = -30.68 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:39 2006