Locus 1225

Sequence ID	X_DroMel_CAF1
Location	3,657,664 – 3,657,794
Length	130
Max. P	0.883189

overview

Window 9

Location	3,657,664 – 3,657,764
Length	100
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	87.64
Mean single sequence MFE	-35.34
Consensus MFE	-22.68
Energy contribution	-22.48
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-2.70
Structure conservation index	0.64
SVM decision value	0.37
SVM RNA-class probability	0.710677
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3657664 100 + 22224390
GCUG--------AUCCGCCUGGGAAGUGAUUUUCUACGGUUUGCCAGGGAAAAGAG---AAUCCCCAAGGAAAGAA------AAUGACUUCUAGACAGGCGUCAUUUGACCGGUGAU
((((--------....(((((((((((.(((((((..((....)).((((......---..)))).......))))------))).))))))...)))))(((....)))))))... ( -35.00)
>DroSec_CAF1 9581 100 + 1
GCUG--------AUCCGCCUGGGAAGUGAUUUUCUACGGUUCGCCAGGGAAAAGAG---AAUCCCCAAGGAAAGAA------AAUGACUUCUAGAGAGGCGUCAUUUGACCGGUGAU
((((--------....((((.((((((.(((((((..((....)).((((......---..)))).......))))------))).))))))....))))(((....)))))))... ( -33.00)
>DroSim_CAF1 5413 100 + 1
GCUG--------AUCCGCCUGGGAAGUGAUUUUCUACGGUUUGCCGGGGAAAAGAG---AAUCCCCAAGGAAAGAA------AAUGACUUCUAGAGAGGCGUCAUUUGACCGGUGAU
((((--------....((((.((((((.(((((((..((....))(((((......---..)))))......))))------))).))))))....))))(((....)))))))... ( -37.30)
>DroEre_CAF1 10546 114 + 1
GCUGAUCCGCUGAUCCGCCUGGGAAGUGAUUUUCUACGGUUUGCCAGGGAAAACAG---AACCCCGAAGGGAAGAAAAUGAAAAUGACUUCUGGAGAGGCGUCAUUUGAUAGGUGAU
(((..(((((......))...((((((.((((((.....(((.((.(((.......---...)))...)).))).....)))))).)))))))))..)))((((((.....)))))) ( -33.90)
>DroYak_CAF1 10599 102 + 1
GCUG--------AUCCGCCUGGGAAGUGAUUUUCUACGGUUUGCCAGGGAAA-CAGGGAAACCCCAAAGGAAAGAA------AAUGACUUCUGGAGAGGCGUCAUUGGACGGAUGAU
....--------((((((((.((((((.(((((((..(((((.((..(....-).)).)))))((...))..))))------))).))))))....))))(((....)))))))... ( -37.50)
>consensus
GCUG________AUCCGCCUGGGAAGUGAUUUUCUACGGUUUGCCAGGGAAAAGAG___AAUCCCCAAGGAAAGAA______AAUGACUUCUAGAGAGGCGUCAUUUGACCGGUGAU
...............(((((.((((((.(((((((..((....))..))))).........(((....)))............)).))))))....)))))(((((.....))))). (-22.68 = -22.48 +  -0.20)

alignment

secondary structure

dotplot

Window 0

Location	3,657,664 – 3,657,764
Length	100
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	87.64
Mean single sequence MFE	-29.92
Consensus MFE	-19.56
Energy contribution	-19.24
Covariance contribution	-0.32
Combinations/Pair	1.16
Mean z-score	-2.83
Structure conservation index	0.65
SVM decision value	0.63
SVM RNA-class probability	0.804046
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3657664 100 - 22224390
AUCACCGGUCAAAUGACGCCUGUCUAGAAGUCAUU------UUCUUUCCUUGGGGAUU---CUCUUUUCCCUGGCAAACCGUAGAAAAUCACUUCCCAGGCGGAU--------CAGC
....((.(((....)))(((((....(((((.(((------((((......(((((..---......)))))((....))..))))))).))))).)))))))..--------.... ( -31.30)
>DroSec_CAF1 9581 100 - 1
AUCACCGGUCAAAUGACGCCUCUCUAGAAGUCAUU------UUCUUUCCUUGGGGAUU---CUCUUUUCCCUGGCGAACCGUAGAAAAUCACUUCCCAGGCGGAU--------CAGC
....((.(((....)))((((.....(((((.(((------(((((((.(..((((..---......))))..).)))....))))))).)))))..))))))..--------.... ( -31.00)
>DroSim_CAF1 5413 100 - 1
AUCACCGGUCAAAUGACGCCUCUCUAGAAGUCAUU------UUCUUUCCUUGGGGAUU---CUCUUUUCCCCGGCAAACCGUAGAAAAUCACUUCCCAGGCGGAU--------CAGC
....((.(((....)))((((.....(((((.(((------((((......(((((..---......)))))((....))..))))))).)))))..))))))..--------.... ( -30.90)
>DroEre_CAF1 10546 114 - 1
AUCACCUAUCAAAUGACGCCUCUCCAGAAGUCAUUUUCAUUUUCUUCCCUUCGGGGUU---CUGUUUUCCCUGGCAAACCGUAGAAAAUCACUUCCCAGGCGGAUCAGCGGAUCAGC
................(((((.....(((((.((((((........(((....)))..---..((((.(....).))))....)))))).)))))..)))))((((....))))... ( -28.90)
>DroYak_CAF1 10599 102 - 1
AUCAUCCGUCCAAUGACGCCUCUCCAGAAGUCAUU------UUCUUUCCUUUGGGGUUUCCCUG-UUUCCCUGGCAAACCGUAGAAAAUCACUUCCCAGGCGGAU--------CAGC
...(((((((....)))((((.....(((((.(((------((((..((...))(((((.((..-.......)).)))))..))))))).)))))..))))))))--------.... ( -27.50)
>consensus
AUCACCGGUCAAAUGACGCCUCUCUAGAAGUCAUU______UUCUUUCCUUGGGGAUU___CUCUUUUCCCUGGCAAACCGUAGAAAAUCACUUCCCAGGCGGAU________CAGC
....((.(((....)))((((.....(((((...............(((....)))........(((((..(((....)))..)))))..)))))..)))))).............. (-19.56 = -19.24 +  -0.32)

alignment

secondary structure

dotplot

Window 1

Location	3,657,693 – 3,657,794
Length	101
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.94
Mean single sequence MFE	-30.52
Consensus MFE	-18.82
Energy contribution	-18.70
Covariance contribution	-0.12
Combinations/Pair	1.09
Mean z-score	-2.07
Structure conservation index	0.62
SVM decision value	0.25
SVM RNA-class probability	0.652003
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3657693 101 + 22224390
GGUUUGCCAGGGAAAAGAG---AAUCCCCAAGGAAAGAA------AAUGACUUCUAGACAGGCGUCAUUUGACCGGUGAUCAGGGUUU--------CCCGUCAAAGGUGAAACAAAUU--
((.(..((.((((......---..))))...((.....(------((((((.(((....))).)))))))..))))..)))...((((--------(((......)).))))).....-- ( -26.50)
>DroSec_CAF1 9610 103 + 1
GGUUCGCCAGGGAAAAGAG---AAUCCCCAAGGAAAGAA------AAUGACUUCUAGAGAGGCGUCAUUUGACCGGUGAUCAGGGUUU--------CCCGUCAAAGGUGAAACAAAUUUU
(((.((((.((((......---..))))...((.....(------((((((.(((....))).)))))))..)))))))))...((((--------(((......)).)))))....... ( -29.20)
>DroSim_CAF1 5442 103 + 1
GGUUUGCCGGGGAAAAGAG---AAUCCCCAAGGAAAGAA------AAUGACUUCUAGAGAGGCGUCAUUUGACCGGUGAUCAGGGUUU--------CCCGUCAAAGGUGAAACAAAUUUU
((.(..(((((((......---..)))))..((.....(------((((((.(((....))).)))))))..))))..)))...((((--------(((......)).)))))....... ( -31.10)
>DroEre_CAF1 10583 109 + 1
GGUUUGCCAGGGAAAACAG---AACCCCGAAGGGAAGAAAAUGAAAAUGACUUCUGGAGAGGCGUCAUUUGAUAGGUGAUCAGGGUUU--------CCCGUCAAAGGUGAAACAAAUUUU
.(((((((.(((.......---...)))((.((((((....((((((((((.(((....))).))))))).........)))...)))--------))).))...))).))))....... ( -27.30)
>DroYak_CAF1 10628 103 + 1
GGUUUGCCAGGGAAA-CAGGGAAACCCCAAAGGAAAGAA------AAUGACUUCUGGAGAGGCGUCAUUGGACGGAUGAUCAGGGUUUCCCGGUUUCCCGUCAAAGGUGA----------
((....)).((((((-(.(((((((((............------.....((((....))))((((....))))........))))))))).)))))))...........---------- ( -38.50)
>consensus
GGUUUGCCAGGGAAAAGAG___AAUCCCCAAGGAAAGAA______AAUGACUUCUAGAGAGGCGUCAUUUGACCGGUGAUCAGGGUUU________CCCGUCAAAGGUGAAACAAAUUUU
..((((((.(((.............)))...................((((.....((..(.((((....))).).)..)).(((...........)))))))..))))))......... (-18.82 = -18.70 +  -0.12)

alignment

secondary structure

dotplot

Window 2

Location	3,657,693 – 3,657,794
Length	101
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.94
Mean single sequence MFE	-28.57
Consensus MFE	-15.34
Energy contribution	-14.66
Covariance contribution	-0.68
Combinations/Pair	1.22
Mean z-score	-3.02
Structure conservation index	0.54
SVM decision value	0.93
SVM RNA-class probability	0.883189
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3657693 101 - 22224390
--AAUUUGUUUCACCUUUGACGGG--------AAACCCUGAUCACCGGUCAAAUGACGCCUGUCUAGAAGUCAUU------UUCUUUCCUUGGGGAUU---CUCUUUUCCCUGGCAAACC
--...(..(((.(((..(((((((--------....)))).)))..))).)))..).(((.....(((((....)------))))......(((((..---......))))))))..... ( -25.70)
>DroSec_CAF1 9610 103 - 1
AAAAUUUGUUUCACCUUUGACGGG--------AAACCCUGAUCACCGGUCAAAUGACGCCUCUCUAGAAGUCAUU------UUCUUUCCUUGGGGAUU---CUCUUUUCCCUGGCGAACC
.....(..(((.(((..(((((((--------....)))).)))..))).)))..)((((.....(((((....)------))))......(((((..---......))))))))).... ( -27.70)
>DroSim_CAF1 5442 103 - 1
AAAAUUUGUUUCACCUUUGACGGG--------AAACCCUGAUCACCGGUCAAAUGACGCCUCUCUAGAAGUCAUU------UUCUUUCCUUGGGGAUU---CUCUUUUCCCCGGCAAACC
.....(..(((.(((..(((((((--------....)))).)))..))).)))..).(((.....(((((....)------))))......(((((..---......))))))))..... ( -28.50)
>DroEre_CAF1 10583 109 - 1
AAAAUUUGUUUCACCUUUGACGGG--------AAACCCUGAUCACCUAUCAAAUGACGCCUCUCCAGAAGUCAUUUUCAUUUUCUUCCCUUCGGGGUU---CUGUUUUCCCUGGCAAACC
....((((((........((((((--------..(((((((.........(((((((...((....)).)))))))..............))))))))---)))))......)))))).. ( -21.94)
>DroYak_CAF1 10628 103 - 1
----------UCACCUUUGACGGGAAACCGGGAAACCCUGAUCAUCCGUCCAAUGACGCCUCUCCAGAAGUCAUU------UUCUUUCCUUUGGGGUUUCCCUG-UUUCCCUGGCAAACC
----------.....((((..(((((((.(((((((((..(..........((((((...((....)).))))))------.........)..))))))))).)-))))))...)))).. ( -39.01)
>consensus
AAAAUUUGUUUCACCUUUGACGGG________AAACCCUGAUCACCGGUCAAAUGACGCCUCUCUAGAAGUCAUU______UUCUUUCCUUGGGGAUU___CUCUUUUCCCUGGCAAACC
...............((((.((((..............((((.....))))((((((..((....))..))))))...........(((....))).............)))).)))).. (-15.34 = -14.66 +  -0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:24 2006