Locus 5966

Sequence ID	3L_DroMel_CAF1
Location	15,979,322 – 15,979,478
Length	156
Max. P	0.996177

overview

Window 6

Location	15,979,322 – 15,979,442
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.50
Mean single sequence MFE	-30.16
Consensus MFE	-27.02
Energy contribution	-27.30
Covariance contribution	0.28
Combinations/Pair	1.06
Mean z-score	-1.28
Structure conservation index	0.90
SVM decision value	0.09
SVM RNA-class probability	0.578845
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15979322 120 + 23771897
CAAAAUAAAAUACCAUUCAAAGUGGCUGCGAGUUGUUUUUAUCUCGUUAGAGUUGCCAGCGCGCCGAUUUCUUUUCGACUUAAAUGGUUUAUGUGCGUUUGCAACCAGUUUUAUGGACAU
............((((..(((.((.(((((((.((....)).)))).))).(((((.((((((((((.......)))(((.....)))....))))))).))))))).))).)))).... ( -30.10)
>DroSec_CAF1 8524 120 + 1
CAAAAUAAAAUACCAUUCAAAGUGGCUGCGAGUUGUUUUUAUCUCGUUAGAGUUGCCAGCGCGCCGAUUUCUUUUCGGCUUAAAUGGUUUAUGUGCGUUUGUAACCAGUUUUAUGGACAU
............((((..(((.((.(((((((.((....)).)))).))).(((((.((((((((((.......))))).(((.....)))...))))).))))))).))).)))).... ( -29.60)
>DroSim_CAF1 9206 120 + 1
CAAAAUAAAAUACCAUUCAAAGUGGCUGCAAGUUGUUUUUAUCUCGUUAGAGUUGCCAGCGCGCCGAUUUCUUUUCGGCUUAAAUGGUUUAUGUGCGUUUGCAACCAGUUUUAUGGACAU
............((((..(((.(((.((((((..........(((....)))..((((....(((((.......))))).....)))).........)))))).))).))).)))).... ( -29.90)
>DroEre_CAF1 8711 118 + 1
CAAAAUAAAAUACCAUUCAAAGUGGCUCCGAGUUGUU--UAUCUCGUUAGAGUUGCCAGCGCGCCGAUUUCUUUUCGGCUUAAAUGGUUUAUGUGCGUUUGCAACCAGUUUUAUGGACAU
............((((..(((.((((((((((.....--...))))...)))((((.((((((((((.......))))).(((.....)))...))))).))))))).))).)))).... ( -30.60)
>DroYak_CAF1 8649 118 + 1
CAAAAUAAAAUACCAUUCAAAGUGGCUCCGAGUUGUU--UAUCUCGUUAGAGUUGCCAGCGCGCCGAUUUCUUUUCGGCUUAAAUGGUUUAUGUGCGUUUGCAACCAGUUUUAUGGACAU
............((((..(((.((((((((((.....--...))))...)))((((.((((((((((.......))))).(((.....)))...))))).))))))).))).)))).... ( -30.60)
>consensus
CAAAAUAAAAUACCAUUCAAAGUGGCUGCGAGUUGUUUUUAUCUCGUUAGAGUUGCCAGCGCGCCGAUUUCUUUUCGGCUUAAAUGGUUUAUGUGCGUUUGCAACCAGUUUUAUGGACAU
............((((..(((.((.(((((((.((....)).)))).))).(((((.((((((((((.......)))(((.....)))....))))))).))))))).))).)))).... (-27.02 = -27.30 +   0.28)

alignment

secondary structure

dotplot

Window 7

Location	15,979,322 – 15,979,442
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.50
Mean single sequence MFE	-27.90
Consensus MFE	-26.24
Energy contribution	-25.92
Covariance contribution	-0.32
Combinations/Pair	1.07
Mean z-score	-1.91
Structure conservation index	0.94
SVM decision value	2.48
SVM RNA-class probability	0.994490
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15979322 120 - 23771897
AUGUCCAUAAAACUGGUUGCAAACGCACAUAAACCAUUUAAGUCGAAAAGAAAUCGGCGCGCUGGCAACUCUAACGAGAUAAAAACAACUCGCAGCCACUUUGAAUGGUAUUUUAUUUUG
....((((.(((.(((((((.............(((.....(((((.......)))))....)))...(((....))).............))))))).)))..))))............ ( -27.10)
>DroSec_CAF1 8524 120 - 1
AUGUCCAUAAAACUGGUUACAAACGCACAUAAACCAUUUAAGCCGAAAAGAAAUCGGCGCGCUGGCAACUCUAACGAGAUAAAAACAACUCGCAGCCACUUUGAAUGGUAUUUUAUUUUG
.((((((......)))..)))...........((((((((((((((.......)))))....((((..(((....))).......(.....)..))))..)))))))))........... ( -25.80)
>DroSim_CAF1 9206 120 - 1
AUGUCCAUAAAACUGGUUGCAAACGCACAUAAACCAUUUAAGCCGAAAAGAAAUCGGCGCGCUGGCAACUCUAACGAGAUAAAAACAACUUGCAGCCACUUUGAAUGGUAUUUUAUUUUG
....((((.(((.(((((((((...........(((.....(((((.......)))))....)))...(((....)))...........))))))))).)))..))))............ ( -31.20)
>DroEre_CAF1 8711 118 - 1
AUGUCCAUAAAACUGGUUGCAAACGCACAUAAACCAUUUAAGCCGAAAAGAAAUCGGCGCGCUGGCAACUCUAACGAGAUA--AACAACUCGGAGCCACUUUGAAUGGUAUUUUAUUUUG
(((((((......)))..((....))))))..((((((((((((((.......)))))....((((..(((....)))...--..(.....)..))))..)))))))))........... ( -27.70)
>DroYak_CAF1 8649 118 - 1
AUGUCCAUAAAACUGGUUGCAAACGCACAUAAACCAUUUAAGCCGAAAAGAAAUCGGCGCGCUGGCAACUCUAACGAGAUA--AACAACUCGGAGCCACUUUGAAUGGUAUUUUAUUUUG
(((((((......)))..((....))))))..((((((((((((((.......)))))....((((..(((....)))...--..(.....)..))))..)))))))))........... ( -27.70)
>consensus
AUGUCCAUAAAACUGGUUGCAAACGCACAUAAACCAUUUAAGCCGAAAAGAAAUCGGCGCGCUGGCAACUCUAACGAGAUAAAAACAACUCGCAGCCACUUUGAAUGGUAUUUUAUUUUG
.((((((......)))..)))...........((((((((((((((.......)))))....((((..(((....))).......(.....)..))))..)))))))))........... (-26.24 = -25.92 +  -0.32)

alignment

secondary structure

dotplot

Window 8

Location	15,979,362 – 15,979,478
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.80
Mean single sequence MFE	-34.02
Consensus MFE	-33.72
Energy contribution	-33.32
Covariance contribution	-0.40
Combinations/Pair	1.08
Mean z-score	-1.75
Structure conservation index	0.99
SVM decision value	2.66
SVM RNA-class probability	0.996177
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15979362 116 - 23771897
UAU----AUAAUCAGGCCGCUCCGCCAGGCUGCGGAGGCGAUGUCCAUAAAACUGGUUGCAAACGCACAUAAACCAUUUAAGUCGAAAAGAAAUCGGCGCGCUGGCAACUCUAACGAGAU
...----........(((.((((((......))))))(((.............(((((((....))).....)))).....(((((.......))))).))).)))..(((....))).. ( -32.90)
>DroSec_CAF1 8564 120 - 1
UAUACAUAUAAUCAGGCCGCUCCGCCAGGCUGCGGAGGCGAUGUCCAUAAAACUGGUUACAAACGCACAUAAACCAUUUAAGCCGAAAAGAAAUCGGCGCGCUGGCAACUCUAACGAGAU
...............(((.((((((......))))))(((.............(((((.............))))).....(((((.......))))).))).)))..(((....))).. ( -33.82)
>DroSim_CAF1 9246 120 - 1
UAUACAUAUAAUCAGGCCGCUCCGCCAGGCUGCGGAGGCGAUGUCCAUAAAACUGGUUGCAAACGCACAUAAACCAUUUAAGCCGAAAAGAAAUCGGCGCGCUGGCAACUCUAACGAGAU
...............(((.((((((......))))))(((.............(((((((....))).....)))).....(((((.......))))).))).)))..(((....))).. ( -35.60)
>DroEre_CAF1 8749 116 - 1
UAU----AUAAUCAGGCCGCUCCGUCAGGCUGCGGAGGCGAUGUCCAUAAAACUGGUUGCAAACGCACAUAAACCAUUUAAGCCGAAAAGAAAUCGGCGCGCUGGCAACUCUAACGAGAU
...----........(((.((((((......))))))(((.............(((((((....))).....)))).....(((((.......))))).))).)))..(((....))).. ( -33.90)
>DroYak_CAF1 8687 116 - 1
UAU----AUAAUCAGGCCGCUCCGUCAGGCUGCGGAGGCGAUGUCCAUAAAACUGGUUGCAAACGCACAUAAACCAUUUAAGCCGAAAAGAAAUCGGCGCGCUGGCAACUCUAACGAGAU
...----........(((.((((((......))))))(((.............(((((((....))).....)))).....(((((.......))))).))).)))..(((....))).. ( -33.90)
>consensus
UAU____AUAAUCAGGCCGCUCCGCCAGGCUGCGGAGGCGAUGUCCAUAAAACUGGUUGCAAACGCACAUAAACCAUUUAAGCCGAAAAGAAAUCGGCGCGCUGGCAACUCUAACGAGAU
...............(((.((((((......))))))(((.............(((((.............))))).....(((((.......))))).))).)))..(((....))).. (-33.72 = -33.32 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:20 2006