Locus 248

Sequence ID	3L_DroMel_CAF1
Location	677,099 – 677,201
Length	102
Max. P	0.992541

overview

Window 1

Location	677,099 – 677,201
Length	102
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	75.79
Mean single sequence MFE	-43.95
Consensus MFE	-21.61
Energy contribution	-21.25
Covariance contribution	-0.36
Combinations/Pair	1.32
Mean z-score	-2.85
Structure conservation index	0.49
SVM decision value	2.34
SVM RNA-class probability	0.992541
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 677099 102 + 23771897
UCGAGCUGGUGCAGGUGAGUCCUUUCCCUUGGAAGAAAGGGCAGGCGUGGAUUUGCCACUUGUUCCGCC---UCCCUUGGGGGCGUUCUCCUUGCUGCUGGCACU
....((..(((((((.((((((((((........)))))))).((((......))))........((((---(((...)))))))...))))))).))..))... ( -42.90)
>DroPse_CAF1 39452 98 + 1
-------UGCGCCGGGGAGUUGUUGCCCUUGGUGGAGUUAGCUGGAGUGGAUUUUCCACUGAGGCCACCGUUUGUCUUAGGAGCAUUCUCCUUGCUACUGGCGCU
-------.(((((((((((....((((((((((((..((((.(((((......)))))))))..))))))........))).)))..))))......))))))). ( -42.20)
>DroSim_CAF1 32972 102 + 1
UCGAGCUGGUGCAGGUGAGUCCUUUCCCUUGGAGGAGAGGGCAGGCGUGGAUUUGCCACUUGCGCCGCC---UCCCUUGGGGGCGUUCUCCUUGCUGCUGGCACU
..((((.(((((((((..(((((((((......))))))))).((((......)))))))))))))(((---(((...))))))))))....(((.....))).. ( -51.10)
>DroYak_CAF1 34780 102 + 1
UCGUGCUGGUGCAGGUGAGUCCUUUCCCUUGGAGGAGAGGGCAGGCGUGGAUUUGCCACUAGCUCCGCC---UCCCUUGGGAGCGUUCUCCUUGCUGCUGGCACU
..((((..(((((((.(((..(.(((((..(((((.(.((((.((((......))))....))))).))---)))...))))).)..)))))))).))..)))). ( -51.50)
>DroAna_CAF1 34008 102 + 1
---ACCUGGCGCAGGAGAGUCCUUGCCCUUCAUUGAGGAUGCUGGAGUGGACUUCCCACUCAGUCCGCCAUUCCCCUUUGGAGCAUUCUCCUUACUACUGGCACU
---.((.((((.(((.....))))))).......(((((((((.((((((.....))))))......(((........)))))))))))).........)).... ( -33.80)
>DroPer_CAF1 43878 98 + 1
-------UGCGCCGGGGAGUUGUUGCCCUUGGUGGAGUUAGCUGGAGUGGAUUUUCCACUGAGGCCACCGUUUGUCUUAGGAGCAUUCUCCUUGCUACUGGCGCU
-------.(((((((((((....((((((((((((..((((.(((((......)))))))))..))))))........))).)))..))))......))))))). ( -42.20)
>consensus
___AGCUGGCGCAGGUGAGUCCUUGCCCUUGGAGGAGAGGGCAGGAGUGGAUUUGCCACUGAGGCCGCC___UCCCUUGGGAGCAUUCUCCUUGCUACUGGCACU
........((((.((...((((((.((......)).))))))....((((.....)))).....))...........(((.((((.......)))).))))))). (-21.61 = -21.25 +  -0.36)

alignment

secondary structure

dotplot

Window 2

Location	677,099 – 677,201
Length	102
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	75.79
Mean single sequence MFE	-35.37
Consensus MFE	-19.68
Energy contribution	-18.80
Covariance contribution	-0.88
Combinations/Pair	1.35
Mean z-score	-2.21
Structure conservation index	0.56
SVM decision value	1.52
SVM RNA-class probability	0.960729
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 677099 102 - 23771897
AGUGCCAGCAGCAAGGAGAACGCCCCCAAGGGA---GGCGGAACAAGUGGCAAAUCCACGCCUGCCCUUUCUUCCAAGGGAAAGGACUCACCUGCACCAGCUCGA
.((((..(((((........((((((....)).---))))......((((.....))))).))))(((((((......)))))))........))))........ ( -34.20)
>DroPse_CAF1 39452 98 - 1
AGCGCCAGUAGCAAGGAGAAUGCUCCUAAGACAAACGGUGGCCUCAGUGGAAAAUCCACUCCAGCUAACUCCACCAAGGGCAACAACUCCCCGGCGCA-------
.(((((.((....(((((....)))))...))....(((((....((((((........)))).))....)))))..(((.........)))))))).------- ( -34.00)
>DroSim_CAF1 32972 102 - 1
AGUGCCAGCAGCAAGGAGAACGCCCCCAAGGGA---GGCGGCGCAAGUGGCAAAUCCACGCCUGCCCUCUCCUCCAAGGGAAAGGACUCACCUGCACCAGCUCGA
.......(.(((.((((((..(((((....)).---)))((((...((((.....))))...)))).))))))....((...(((.....)))...)).)))).. ( -35.80)
>DroYak_CAF1 34780 102 - 1
AGUGCCAGCAGCAAGGAGAACGCUCCCAAGGGA---GGCGGAGCUAGUGGCAAAUCCACGCCUGCCCUCUCCUCCAAGGGAAAGGACUCACCUGCACCAGCACGA
.((((..((((....(((..(..((((...(((---((.((.((..((((.....))))....))))...)))))..))))..)..)))..))))....)))).. ( -40.10)
>DroAna_CAF1 34008 102 - 1
AGUGCCAGUAGUAAGGAGAAUGCUCCAAAGGGGAAUGGCGGACUGAGUGGGAAGUCCACUCCAGCAUCCUCAAUGAAGGGCAAGGACUCUCCUGCGCCAGGU---
...(((........((((....))))...(((((...((.....((((((.....))))))..)).))))).......(((.(((.....)))..))).)))--- ( -34.10)
>DroPer_CAF1 43878 98 - 1
AGCGCCAGUAGCAAGGAGAAUGCUCCUAAGACAAACGGUGGCCUCAGUGGAAAAUCCACUCCAGCUAACUCCACCAAGGGCAACAACUCCCCGGCGCA-------
.(((((.((....(((((....)))))...))....(((((....((((((........)))).))....)))))..(((.........)))))))).------- ( -34.00)
>consensus
AGUGCCAGCAGCAAGGAGAACGCUCCCAAGGGA___GGCGGACCAAGUGGCAAAUCCACGCCAGCCCUCUCCACCAAGGGAAAGGACUCACCUGCACCAGCU___
.((((.........((((....(((....)))....(((((.....((((.....)))).)).)))..)))).....(((......)))....))))........ (-19.68 = -18.80 +  -0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:26 2006