Locus 2168

Sequence ID	3R_DroMel_CAF1
Location	6,224,513 – 6,224,655
Length	142
Max. P	0.883695

overview

Window 8

Location	6,224,513 – 6,224,615
Length	102
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	79.26
Mean single sequence MFE	-42.80
Consensus MFE	-26.47
Energy contribution	-27.03
Covariance contribution	0.56
Combinations/Pair	1.28
Mean z-score	-2.08
Structure conservation index	0.62
SVM decision value	0.93
SVM RNA-class probability	0.883695
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6224513 102 - 27905053
AGUUUGGCCAGCAGUGGGCUGGAGUUGGAGUUACCGUUGUGCAGCUCCGCCUUGAUGUCCUUGAUGUCGCUGAAGUUGAAC---GAGGGCGAGGGCUUGU---CC---------AGC
.(((..((((((...((((.(((((((.(..........).))))))))))).((((((...))))))))))..))..)))---..((((((....))))---))---------... ( -38.30)
>DroPse_CAF1 47671 111 - 1
AGCUUGGCCAGCAGCGGACUGGAGUUGGAGUUGCUGUUGUGCAGCUCCGACUUGAUGUCCUUGAUGUCGCUGAAGUUGAAC---GAGGGCGAGGGCUUGCUGUCC---UCGCGCAGC
.(.(..((...(((((((((.(((((((((((((......))))))))))))).).))))..(....)))))..))..).)---..(.((((((((.....))))---)))).)... ( -55.20)
>DroGri_CAF1 44960 105 - 1
AGCUUUGCGAGCAGUGGACUGGAGUUGGAGCUGCUGUUGUGCAAUUCCGAUUUGAUGUCCUUGAUGUCACUGAAGUUGAAC---GAGG------GCUUGU---UGUCUUCGCGCCCC
(((((((.((.(((.(((((.(((((((((.(((......))).))))))))).).)))))))...)).).))))))...(---((((------((....---.)))))))...... ( -34.80)
>DroWil_CAF1 57337 114 - 1
AGUUUGGCCAACAGUGGACUGGAAUUGGAGUUGCUGUUGUGCAGCUCCGAUUUAAUAUCCUUGAUGUCGCUGAAAUUGAACGUCGACGGCGAGGGCUUAU---CCUCGUUGCGUACC
..((..((..(((..(((...(((((((((((((......)))))))))))))....)))....))).))..)).......((((.(((((((((....)---)))))))))).)). ( -43.90)
>DroMoj_CAF1 44327 102 - 1
AGCUUGGCCAGCAGCGGACUAGAAUUGGAAUUGGUAUUGUGCAGCUCCGACUUGAUGUCCUUGAUAUCACUGAAGCUGAAG---GAGG------GCUUGU---CG---UCACGCCCC
.......((..((((((((..((.(((((.(((........))).))))).))...)))).((....)).....))))..)---).((------((.((.---..---.)).)))). ( -28.80)
>DroPer_CAF1 47992 111 - 1
AGCUUGGCCAGCAGCGGACUGGAGUUGGAGUUGCUGUUGUGCAGCUCCGACUUGAUGUCCUUGAUGUCGCUGAAGUUGAAC---GAGGGCGAGGACUUGGUGUCC---UCGCGCAGC
.(.(..((...(((((((((.(((((((((((((......))))))))))))).).))))..(....)))))..))..).)---..(.((((((((.....))))---)))).)... ( -55.80)
>consensus
AGCUUGGCCAGCAGCGGACUGGAGUUGGAGUUGCUGUUGUGCAGCUCCGACUUGAUGUCCUUGAUGUCGCUGAAGUUGAAC___GAGGGCGAGGGCUUGU___CC___UCGCGCACC
...(..((...((((((((..(((((((((((((......)))))))))))))...))))..(....)))))..))..)...................................... (-26.47 = -27.03 +   0.56)

alignment

secondary structure

dotplot

Window 9

Location	6,224,535 – 6,224,655
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.41
Mean single sequence MFE	-42.02
Consensus MFE	-26.50
Energy contribution	-27.95
Covariance contribution	1.45
Combinations/Pair	1.37
Mean z-score	-1.66
Structure conservation index	0.63
SVM decision value	0.85
SVM RNA-class probability	0.865759
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6224535 120 - 27905053
CGGAGUGCUCAACUGGCCACCGGCAGCAGCCACCGCACUCAGUUUGGCCAGCAGUGGGCUGGAGUUGGAGUUACCGUUGUGCAGCUCCGCCUUGAUGUCCUUGAUGUCGCUGAAGUUGAA
..((((((......((...))(((....)))...))))))..((..((((((...((((.(((((((.(..........).))))))))))).((((((...))))))))))..))..)) ( -41.10)
>DroVir_CAF1 41605 111 - 1
GGGUGUGCUUAACUGUGCGCCUG---CA------GCGCUCAGCUUAGCCAGUAGCGGACCGGAGUUGGAGUUGCUAUUGUGUAGCUCCGCUUUGAUGUCCUUAAUAUCACUGAAGCUAAA
(((((..(......)..))))).---.(------((..((((....((.....))((((((((((.((((((((......))))))))))))))..)))).........)))).)))... ( -42.20)
>DroGri_CAF1 44985 111 - 1
GGGUGUGCUCAGCUGGGCGCCAG---CA------GCACUCAGCUUUGCGAGCAGUGGACUGGAGUUGGAGCUGCUGUUGUGCAAUUCCGAUUUGAUGUCCUUGAUGUCACUGAAGUUGAA
....(((((..(((((...))))---))------))))(((((((((.((.(((.(((((.(((((((((.(((......))).))))))))).).)))))))...)).).)))))))). ( -43.60)
>DroWil_CAF1 57371 105 - 1
CGGUGUGCUCAACUGGGC---------------GGCACUCAGUUUGGCCAACAGUGGACUGGAAUUGGAGUUGCUGUUGUGCAGCUCCGAUUUAAUAUCCUUGAUGUCGCUGAAAUUGAA
..((((((((....))))---------------.))))((((((((((..(((..(((...(((((((((((((......)))))))))))))....)))....))).))).))))))). ( -41.30)
>DroMoj_CAF1 44349 114 - 1
CGGCGUGCUCAACUGGGCGCCAGCAGCA------GCGCUGAGCUUGGCCAGCAGCGGACUAGAAUUGGAAUUGGUAUUGUGCAGCUCCGACUUGAUGUCCUUGAUAUCACUGAAGCUGAA
.(((((.(......).)))))..((((.------((((((.((...)))))).))((((..((.(((((.(((........))).))))).))...))))..............)))).. ( -39.10)
>DroAna_CAF1 46920 108 - 1
CGGCGUGCUCAGCUGGGCUCCGGCAGC------------CAACUUGGCCAUGAGGGGACUCGAGUUGGAGUUUCCGUUGUGUAUCUCCGACUUGAUGUCCUUGAGGUCGCUGAAGUUGAA
(((((..(((.(((((...))))).((------------(.....))).....(((((((((((((((((...(......)...))))))))))).)))))))))..)))))........ ( -44.80)
>consensus
CGGUGUGCUCAACUGGGCGCCAG___CA______GCACUCAGCUUGGCCAGCAGUGGACUGGAGUUGGAGUUGCUGUUGUGCAGCUCCGACUUGAUGUCCUUGAUGUCACUGAAGUUGAA
....((((((....))))))..................(((((((((....(((.((((..(((((((((((((......)))))))))))))...)))))))......)).))))))). (-26.50 = -27.95 +   1.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:58 2006