Locus 3190

Sequence ID	3R_DroMel_CAF1
Location	8,462,479 – 8,462,679
Length	200
Max. P	0.996092

overview

Window 0

Location	8,462,479 – 8,462,599
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.75
Mean single sequence MFE	-41.30
Consensus MFE	-36.24
Energy contribution	-36.60
Covariance contribution	0.36
Combinations/Pair	1.12
Mean z-score	-1.79
Structure conservation index	0.88
SVM decision value	1.87
SVM RNA-class probability	0.980574
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8462479 120 + 27905053
GCUACUCAGUGGAGACGCACACGGUUCGCACUGGAGAUGGAUACAUUCUGGAUAUGUUUCGGAUUCCCUCAUCACCCAACUGCAAGGAGGACGGUUUCAAGCCGUCUGUUCUUAUCCAGC
((.(((..(((....)))....)))..)).((((((((((......((((((.....)))))).....)))))..........((((((((((((.....))))))).))))).))))). ( -36.10)
>DroSec_CAF1 8338 120 + 1
GCUACCCGGUGGAGACGCACACGGUACGCACUGCAGAUGGAUACAUUCUAGAUAUGUUCCGGAUUCCCUCAUCACCCAACUGCAAGGAGGACGGUUUCAAGCCAUCUGUCCUCCUCCAGC
((((((..(((....)))....)))).))..(((((..(((.((((.......)))))))((....))...........)))))((((((((((...........))))))))))..... ( -40.70)
>DroSim_CAF1 8805 120 + 1
GCUACCCGGUGGAGACGCACACGGUUCGCACUGCAGAUGGAUACAUUCUAGAUAUGUUCCGGAUUCCCUCAUCACCCAACUGCAAGGAGGACGGUUUCAAGCCAUCUGUCCUCCUCCAGC
((.(((..(((....)))....)))..))..(((((..(((.((((.......)))))))((....))...........)))))((((((((((...........))))))))))..... ( -38.60)
>DroEre_CAF1 8342 120 + 1
GCUACCCGGUGGAGACGCACACGGUUCGCACUGGAGAUGGAUAUAUUCUGGAUAUGUUCCGGAUUCCCUCAUCACACAACUGCAAGGAGGACGGUAUCAAGCCGCCUGUCCUCCUCCAGC
((.(((..(((....)))....)))..)).((((((((((......((((((.....)))))).....)))))............((((((((((........))).)))))))))))). ( -45.00)
>DroYak_CAF1 6984 120 + 1
GCUACCCGGUGGAGACGCACACGGUUCGCACUGGAGAUGGAUAUAUUCUGGAUAUGUUCCGGAUUCCCUCAUCACACAACUGCAAGGAGGACGGAGUCAAGCCGCCUGUCCUCCUCCAGC
((.(((..(((....)))....)))..)).((((((((((......((((((.....)))))).....)))))............(((((((((.((......)))))))))))))))). ( -46.10)
>consensus
GCUACCCGGUGGAGACGCACACGGUUCGCACUGGAGAUGGAUACAUUCUGGAUAUGUUCCGGAUUCCCUCAUCACCCAACUGCAAGGAGGACGGUUUCAAGCCGUCUGUCCUCCUCCAGC
((.(((..(((....)))....)))..)).((((((((((......((((((.....)))))).....)))))............(((((((((...........)))))))))))))). (-36.24 = -36.60 +   0.36)

alignment

secondary structure

dotplot

Window 1

Location	8,462,519 – 8,462,639
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.08
Mean single sequence MFE	-41.61
Consensus MFE	-35.86
Energy contribution	-36.74
Covariance contribution	0.88
Combinations/Pair	1.12
Mean z-score	-2.25
Structure conservation index	0.86
SVM decision value	2.65
SVM RNA-class probability	0.996092
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8462519 120 + 27905053
AUACAUUCUGGAUAUGUUUCGGAUUCCCUCAUCACCCAACUGCAAGGAGGACGGUUUCAAGCCGUCUGUUCUUAUCCAGCACGGACUGAUCAGCCUGGCCGAUUCCUUCCUGGUGACGGG
......((((((.....))))))..((((((((..((........))((((.((..((..((((.(((.((...(((.....)))..)).)))..)))).))..)).))))))))).))) ( -35.30)
>DroSec_CAF1 8378 120 + 1
AUACAUUCUAGAUAUGUUCCGGAUUCCCUCAUCACCCAACUGCAAGGAGGACGGUUUCAAGCCAUCUGUCCUCCUCCAGCACGGCCUGAUCAGCCUGGCCGAUUCCUUCCUGAUGAUGGG
......((..((.....))..))..(((((((((......(((.((((((((((...........))))))))))...)))(((((.(......).))))).........)))))).))) ( -40.80)
>DroSim_CAF1 8845 120 + 1
AUACAUUCUAGAUAUGUUCCGGAUUCCCUCAUCACCCAACUGCAAGGAGGACGGUUUCAAGCCAUCUGUCCUCCUCCAGCACGGCCUGAUCAGCCUGGCCGAUUCCUUUCUGGUGACGGG
......((..((.....))..))..(((((((((......(((.((((((((((...........))))))))))...)))(((((.(......).))))).........)))))).))) ( -40.20)
>DroEre_CAF1 8382 120 + 1
AUAUAUUCUGGAUAUGUUCCGGAUUCCCUCAUCACACAACUGCAAGGAGGACGGUAUCAAGCCGCCUGUCCUCCUCCAGCACGGCCUGGUUGGCCUGGCAGACUCCUUCCUGAUGACGGG
......((((((.....))))))..(((((((((.....((((.(((((((((((........))).))))))))....((.((((.....)))))))))).........)))))).))) ( -46.74)
>DroYak_CAF1 7024 120 + 1
AUAUAUUCUGGAUAUGUUCCGGAUUCCCUCAUCACACAACUGCAAGGAGGACGGAGUCAAGCCGCCUGUCCUCCUCCAGCACGGCAUGAUCAGCGUGGCAGACUCCUUCCUGGUGACGGG
......((((((.....))))))..((((((((......((....))((((.((((((..((((((((((..((........))...)).))).))))).)))))).))))))))).))) ( -45.00)
>consensus
AUACAUUCUGGAUAUGUUCCGGAUUCCCUCAUCACCCAACUGCAAGGAGGACGGUUUCAAGCCGUCUGUCCUCCUCCAGCACGGCCUGAUCAGCCUGGCCGAUUCCUUCCUGGUGACGGG
......((((((.....))))))..(((((((((......(((.((((((((((...........))))))))))...)))(((((.(......).))))).........)))))).))) (-35.86 = -36.74 +   0.88)

alignment

secondary structure

dotplot

Window 2

Location	8,462,559 – 8,462,679
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.92
Mean single sequence MFE	-49.90
Consensus MFE	-41.40
Energy contribution	-43.24
Covariance contribution	1.84
Combinations/Pair	1.21
Mean z-score	-1.64
Structure conservation index	0.83
SVM decision value	0.69
SVM RNA-class probability	0.824485
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8462559 120 + 27905053
UGCAAGGAGGACGGUUUCAAGCCGUCUGUUCUUAUCCAGCACGGACUGAUCAGCCUGGCCGAUUCCUUCCUGGUGACGGGACCGAGGAGCGGACUUCCAUUCAUGCUGGCCGAUCGCUGC
.((((((((((((((.....))))))).)))))..((((((.((.((....))))((((((.((((((((((....)))))...))))))))....)))....))))))......))... ( -45.90)
>DroSec_CAF1 8418 120 + 1
UGCAAGGAGGACGGUUUCAAGCCAUCUGUCCUCCUCCAGCACGGCCUGAUCAGCCUGGCCGAUUCCUUCCUGAUGAUGGGACCGAGGAACGGACUUCCAUUCAUGCUGGCCGAUCGCUGC
.((.((((((((((...........))))))))))(((((((((((.(......).))))).(((((((((......))))...))))).((....)).....))))))......))... ( -46.30)
>DroSim_CAF1 8885 120 + 1
UGCAAGGAGGACGGUUUCAAGCCAUCUGUCCUCCUCCAGCACGGCCUGAUCAGCCUGGCCGAUUCCUUUCUGGUGACGGGACCGGGGACCGGACUUCCGUUCAUGCUGGCCGAUCGCUGC
.((.((((((((((...........))))))))))(((((((((((.(......).)))))...((((((((....)))))..)))((.(((....))).)).))))))......))... ( -50.90)
>DroEre_CAF1 8422 120 + 1
UGCAAGGAGGACGGUAUCAAGCCGCCUGUCCUCCUCCAGCACGGCCUGGUUGGCCUGGCAGACUCCUUCCUGAUGACGGGACCGAAGAGCGGACUGCCGUUUAUGCUGGCCGACCGCUGC
(((.(((((((((((........))).))))))))...)))((((..((((((((.(((((......(((((....)))))(((.....))).)))))((....)).)))))))))))). ( -55.50)
>DroYak_CAF1 7064 120 + 1
UGCAAGGAGGACGGAGUCAAGCCGCCUGUCCUCCUCCAGCACGGCAUGAUCAGCGUGGCAGACUCCUUCCUGGUGACGGGACCAAAGAACGGACUGCCGUUCAUGCUAGCCGACCGCUGC
....((((((((((.((......)))))))))))).((((.(((((((.....)))((((.......(((((....))))).....((((((....)))))).)))).))))...)))). ( -50.90)
>consensus
UGCAAGGAGGACGGUUUCAAGCCGUCUGUCCUCCUCCAGCACGGCCUGAUCAGCCUGGCCGAUUCCUUCCUGGUGACGGGACCGAGGAACGGACUUCCGUUCAUGCUGGCCGAUCGCUGC
(((.((((((((((...........))))))))))...)))((((..((((.(((.(((........(((((....))))).....((((((....))))))..)))))).)))))))). (-41.40 = -43.24 +   1.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:21 2006