Locus 5071

Sequence ID	2L_DroMel_CAF1
Location	14,502,509 – 14,502,619
Length	110
Max. P	0.965536

overview

Window 9

Location	14,502,509 – 14,502,609
Length	100
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	86.74
Mean single sequence MFE	-37.85
Consensus MFE	-31.51
Energy contribution	-31.52
Covariance contribution	0.00
Combinations/Pair	1.09
Mean z-score	-3.17
Structure conservation index	0.83
SVM decision value	1.58
SVM RNA-class probability	0.965536
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14502509 100 + 22407834
GU--------UGUGGGACAGAC------------GUCGAUGUUAUAAACACUACUGUCUUCCAGCUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUAAAAGCCGACUUGACAGCUGAA
..--------....(((.((((------------((.(.(((.....)))).)).)))))))(((((((((((((((......(((((....))))).....)))))))))))))))... ( -35.60)
>DroPse_CAF1 23226 120 + 1
GGUGUGGUGCUGCGGGGCAGACAGCGGCGGGGUUGUCGAUGUUAUAAACACUACUGUCUUCCAACUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUAAAAGCCAACUUGACAGCUGAA
...((((((......((((((((((......))))))..)))).....)))))).......((.(((((((((((((......(((((....))))).....))))))))))))).)).. ( -39.90)
>DroSim_CAF1 18558 100 + 1
GU--------UGUGGGACAGAC------------GUCGAUGUUAUAAACACUACUGUCUUCCAGCUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUAAAAGCCGACUUGACAGCUGAA
..--------....(((.((((------------((.(.(((.....)))).)).)))))))(((((((((((((((......(((((....))))).....)))))))))))))))... ( -35.60)
>DroEre_CAF1 27920 108 + 1
GCUGUGGGGCUGUGGGACAGAC------------GUCGAUGUUAUAAACACUACUGUCUUCCAACUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUAAAGGCCGACUUGACAGCUGAA
..((..((((.(((((((....------------)))..(((.....))))))).))))..)).(((((((((((((((....(((((....)))))...)))))))))))))))..... ( -39.30)
>DroYak_CAF1 23369 100 + 1
GU--------UGUGGGACAGAC------------GUCGAUGUUAUAAACACUACUGUCUUCCAACUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUAAAGGCCGACUUGACAGCUGAA
((--------((..((((((..------------...................))))))..))))((((((((((((((....(((((....)))))...))))))))))))))...... ( -35.60)
>DroPer_CAF1 22725 120 + 1
GGUGUGGUGCUGCGGGGCAGCCAGCGGCGGGGUUGUCGAUGUUAUAAACACUACUGUCUUCCAACUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUAAAAGCCAACUUGACAGCUGAA
...((((((..(((.(((((((........)))))))..)))......)))))).......((.(((((((((((((......(((((....))))).....))))))))))))).)).. ( -41.10)
>consensus
GU________UGUGGGACAGAC____________GUCGAUGUUAUAAACACUACUGUCUUCCAACUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUAAAAGCCGACUUGACAGCUGAA
..........((..(((((((((((......))))))..(((.....)))....)))))..)).((((((((((((.((....(((((....)))))....))))))))))))))..... (-31.51 = -31.52 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	14,502,509 – 14,502,609
Length	100
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	86.74
Mean single sequence MFE	-35.02
Consensus MFE	-26.89
Energy contribution	-27.33
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-3.92
Structure conservation index	0.77
SVM decision value	1.35
SVM RNA-class probability	0.945272
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14502509 100 - 22407834
UUCAGCUGUCAAGUCGGCUUUUAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGCUGGAAGACAGUAGUGUUUAUAACAUCGAC------------GUCUGUCCCACA--------AC
((((((((((((((.((((....(((((....)))))....)).)).)))))))))))))).(((((..((((.....))))....------------..))))).....--------.. ( -33.30)
>DroPse_CAF1 23226 120 - 1
UUCAGCUGUCAAGUUGGCUUUUAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGUUGGAAGACAGUAGUGUUUAUAACAUCGACAACCCCGCCGCUGUCUGCCCCGCAGCACCACACC
(((((((((((((((((((....(((((....)))))....)).)))))))))))))))))((((((..(((...................)))..))))))((......))........ ( -40.81)
>DroSim_CAF1 18558 100 - 1
UUCAGCUGUCAAGUCGGCUUUUAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGCUGGAAGACAGUAGUGUUUAUAACAUCGAC------------GUCUGUCCCACA--------AC
((((((((((((((.((((....(((((....)))))....)).)).)))))))))))))).(((((..((((.....))))....------------..))))).....--------.. ( -33.30)
>DroEre_CAF1 27920 108 - 1
UUCAGCUGUCAAGUCGGCCUUUAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGUUGGAAGACAGUAGUGUUUAUAACAUCGAC------------GUCUGUCCCACAGCCCCACAGC
((((((((((((((.((.((...(((((....)))))....)).)).)))))))))))))).(((((..((((.....))))....------------..)))))............... ( -30.50)
>DroYak_CAF1 23369 100 - 1
UUCAGCUGUCAAGUCGGCCUUUAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGUUGGAAGACAGUAGUGUUUAUAACAUCGAC------------GUCUGUCCCACA--------AC
((((((((((((((.((.((...(((((....)))))....)).)).)))))))))))))).(((((..((((.....))))....------------..))))).....--------.. ( -30.50)
>DroPer_CAF1 22725 120 - 1
UUCAGCUGUCAAGUUGGCUUUUAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGUUGGAAGACAGUAGUGUUUAUAACAUCGACAACCCCGCCGCUGGCUGCCCCGCAGCACCACACC
(((((((((((((((((((....(((((....)))))....)).)))))))))))))))))...(((..(((...................)))..)))(((((...)))))........ ( -41.71)
>consensus
UUCAGCUGUCAAGUCGGCUUUUAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGUUGGAAGACAGUAGUGUUUAUAACAUCGAC____________GUCUGUCCCACA________AC
((((((((((((((.((((....(((((....)))))....)).)).)))))))))))))).(((((..((((.....))))..................)))))............... (-26.89 = -27.33 +   0.44)

alignment

secondary structure

dotplot

Window 1

Location	14,502,529 – 14,502,619
Length	90
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.73
Mean single sequence MFE	-32.67
Consensus MFE	-26.54
Energy contribution	-26.10
Covariance contribution	-0.44
Combinations/Pair	1.08
Mean z-score	-3.58
Structure conservation index	0.81
SVM decision value	1.57
SVM RNA-class probability	0.964839
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14502529 90 + 22407834
GUUAUAAACACUACUGUCUUCCAGCUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUAAAAGCCGACUUGACAGCUGAACGGUCGACCA------------------------------
..........(.(((((....((((((((((((((((......(((((....))))).....)))))))))))))))).))))).)....------------------------------ ( -33.30)
>DroPse_CAF1 23266 120 + 1
GUUAUAAACACUACUGUCUUCCAACUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUAAAAGCCAACUUGACAGCUGAACGGUCUGUCUCCCUUCCGUCUGUUGGCGGCCAAACUGAUG
............(((((....((.(((((((((((((......(((((....))))).....))))))))))))).)).)))))..(((......(((((....))))).......))). ( -34.02)
>DroSim_CAF1 18578 90 + 1
GUUAUAAACACUACUGUCUUCCAGCUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUAAAAGCCGACUUGACAGCUGAACGGUCGACCA------------------------------
..........(.(((((....((((((((((((((((......(((((....))))).....)))))))))))))))).))))).)....------------------------------ ( -33.30)
>DroEre_CAF1 27948 90 + 1
GUUAUAAACACUACUGUCUUCCAACUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUAAAGGCCGACUUGACAGCUGAACGGUCGACCA------------------------------
..........(.(((((....((.(((((((((((((((....(((((....)))))...))))))))))))))).)).))))).)....------------------------------ ( -30.70)
>DroYak_CAF1 23389 90 + 1
GUUAUAAACACUACUGUCUUCCAACUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUAAAGGCCGACUUGACAGCUGAACGGUCGACCA------------------------------
..........(.(((((....((.(((((((((((((((....(((((....)))))...))))))))))))))).)).))))).)....------------------------------ ( -30.70)
>DroPer_CAF1 22765 120 + 1
GUUAUAAACACUACUGUCUUCCAACUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUAAAAGCCAACUUGACAGCUGAACGGUCUGUCUCCCUUCCGUCUGUUGGCGGCCAAACUGAUG
............(((((....((.(((((((((((((......(((((....))))).....))))))))))))).)).)))))..(((......(((((....))))).......))). ( -34.02)
>consensus
GUUAUAAACACUACUGUCUUCCAACUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUAAAAGCCGACUUGACAGCUGAACGGUCGACCA______________________________
............(((((....((.((((((((((((.((....(((((....)))))....)))))))))))))).)).))))).................................... (-26.54 = -26.10 +  -0.44)

alignment

secondary structure

dotplot

Window 2

Location	14,502,529 – 14,502,619
Length	90
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.73
Mean single sequence MFE	-32.90
Consensus MFE	-26.42
Energy contribution	-26.53
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-3.14
Structure conservation index	0.80
SVM decision value	1.45
SVM RNA-class probability	0.954954
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14502529 90 - 22407834
------------------------------UGGUCGACCGUUCAGCUGUCAAGUCGGCUUUUAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGCUGGAAGACAGUAGUGUUUAUAAC
------------------------------..(((.....((((((((((((((.((((....(((((....)))))....)).)).)))))))))))))).)))............... ( -30.90)
>DroPse_CAF1 23266 120 - 1
CAUCAGUUUGGCCGCCAACAGACGGAAGGGAGACAGACCGUUCAGCUGUCAAGUUGGCUUUUAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGUUGGAAGACAGUAGUGUUUAUAAC
.....(((((........)))))((...(....)...)).(((((((((((((((((((....(((((....)))))....)).)))))))))))))))))(((((....)))))..... ( -39.70)
>DroSim_CAF1 18578 90 - 1
------------------------------UGGUCGACCGUUCAGCUGUCAAGUCGGCUUUUAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGCUGGAAGACAGUAGUGUUUAUAAC
------------------------------..(((.....((((((((((((((.((((....(((((....)))))....)).)).)))))))))))))).)))............... ( -30.90)
>DroEre_CAF1 27948 90 - 1
------------------------------UGGUCGACCGUUCAGCUGUCAAGUCGGCCUUUAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGUUGGAAGACAGUAGUGUUUAUAAC
------------------------------..(((.....((((((((((((((.((.((...(((((....)))))....)).)).)))))))))))))).)))............... ( -28.10)
>DroYak_CAF1 23389 90 - 1
------------------------------UGGUCGACCGUUCAGCUGUCAAGUCGGCCUUUAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGUUGGAAGACAGUAGUGUUUAUAAC
------------------------------..(((.....((((((((((((((.((.((...(((((....)))))....)).)).)))))))))))))).)))............... ( -28.10)
>DroPer_CAF1 22765 120 - 1
CAUCAGUUUGGCCGCCAACAGACGGAAGGGAGACAGACCGUUCAGCUGUCAAGUUGGCUUUUAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGUUGGAAGACAGUAGUGUUUAUAAC
.....(((((........)))))((...(....)...)).(((((((((((((((((((....(((((....)))))....)).)))))))))))))))))(((((....)))))..... ( -39.70)
>consensus
______________________________UGGUCGACCGUUCAGCUGUCAAGUCGGCUUUUAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGUUGGAAGACAGUAGUGUUUAUAAC
........................................((((((((((((((.((((....(((((....)))))....)).)).))))))))))))))(((((....)))))..... (-26.42 = -26.53 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:14 2006