Locus 5668

Sequence ID	2R_DroMel_CAF1
Location	17,981,582 – 17,981,682
Length	100
Max. P	0.952526

overview

Window 0

Location	17,981,582 – 17,981,682
Length	100
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	79.65
Mean single sequence MFE	-23.75
Consensus MFE	-16.86
Energy contribution	-17.78
Covariance contribution	0.92
Combinations/Pair	1.22
Mean z-score	-1.90
Structure conservation index	0.71
SVM decision value	0.98
SVM RNA-class probability	0.893237
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17981582 100 + 20766785
AGUAGGUCAUAAAAACAGCUGCAGCUUCGAUGGUUCCCACAAGGAUGUGGGACACAAAGAAAAGUCUA----CAGGAUACGUUUUGGAA---AAACAUCGAA---UAAAG
.((((.(.........).))))...(((((((..(((((((....)))))))..(((((....(((..----...)))...)))))...---...)))))))---..... ( -24.50)
>DroVir_CAF1 3104 105 + 1
AAUAGGUGAUUACCACGGCGCUGGCUUCAAUGAUGCCCACUUGUACGUAGGCCACAAAAAUCAGGCUAAGUGUAUGAGCCGUGUUAAAAUAAAAACAUGA-----CAAAA
.........(((.((((((...(((.........)))...(..((((..((((..........))))...))))..))))))).))).............-----..... ( -23.40)
>DroSec_CAF1 2954 103 + 1
AGUAGGUCAUAAAAACAGCUGCAGCUUCGAUGGUUCCCACAAGGAUGUGGGACACAAAGAAAAGUCUA----CAGGAUACGUUUUGGAA---AAACAUCGAAUAAUAAAG
.((((.(.........).))))...(((((((..(((((((....)))))))..(((((....(((..----...)))...)))))...---...)))))))........ ( -24.50)
>DroSim_CAF1 4118 96 + 1
AGUAGGUCAUAAAAACAGCUGCAGCUUCGAAGGUUCCCACAA-GAUGUGGGAAACAAA-AAAAGUCUA----CAGGAUACGUUUUG-AA---AAACAUCGA----UAUAA
.((((.(.........).))))....((((.(.(((((((..-...))))))).((((-(...(((..----...)))...)))))-..---...).))))----..... ( -20.80)
>DroEre_CAF1 2932 93 + 1
AGUAGGUCAUAAAAACAGCUGCAGCUUCGAUGGUUCCCACAAGGAUGUGGGACACAAGGAAAAGCCUA----CAGGAUACGUUUUGGAA----AACAUCGA---------
.((((.(.........).))))....((((((..(((((((....)))))))..(((((.....((..----..)).....)))))...----..))))))--------- ( -24.10)
>DroYak_CAF1 3033 104 + 1
AGUAGGUCAUAAAAACAGCUGCAGCUUCGAUGGUUCCCACAAGGAUGUGGGACACAAAGAAAAGUCUA----CAGGAUACGUUUUGGAAA--AAACAUCGAACAAUGAAG
......((((......(((....)))((((((..(((((((....)))))))..(((((....(((..----...)))...)))))....--...))))))...)))).. ( -25.20)
>consensus
AGUAGGUCAUAAAAACAGCUGCAGCUUCGAUGGUUCCCACAAGGAUGUGGGACACAAAGAAAAGUCUA____CAGGAUACGUUUUGGAA___AAACAUCGA____UAAAG
................(((....)))((((((..((((((......))))))..(((((.....(((......))).....))))).........))))))......... (-16.86 = -17.78 +   0.92)

alignment

secondary structure

dotplot

Window 1

Location	17,981,582 – 17,981,682
Length	100
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	79.65
Mean single sequence MFE	-25.10
Consensus MFE	-15.79
Energy contribution	-15.85
Covariance contribution	0.06
Combinations/Pair	1.24
Mean z-score	-2.64
Structure conservation index	0.63
SVM decision value	1.42
SVM RNA-class probability	0.952526
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17981582 100 - 20766785
CUUUA---UUCGAUGUUU---UUCCAAAACGUAUCCUG----UAGACUUUUCUUUGUGUCCCACAUCCUUGUGGGAACCAUCGAAGCUGCAGCUGUUUUUAUGACCUACU
.....---....((((((---.....))))))...(((----(((.((((....((..(((((((....)))))))..))..)))))))))).................. ( -25.10)
>DroVir_CAF1 3104 105 - 1
UUUUG-----UCAUGUUUUUAUUUUAACACGGCUCAUACACUUAGCCUGAUUUUUGUGGCCUACGUACAAGUGGGCAUCAUUGAAGCCAGCGCCGUGGUAAUCACCUAUU
....(-----((.((((........)))).))).....(((...(((((..(((.(((((((((......))))))..))).)))..))).)).)))............. ( -24.60)
>DroSec_CAF1 2954 103 - 1
CUUUAUUAUUCGAUGUUU---UUCCAAAACGUAUCCUG----UAGACUUUUCUUUGUGUCCCACAUCCUUGUGGGAACCAUCGAAGCUGCAGCUGUUUUUAUGACCUACU
............((((((---.....))))))...(((----(((.((((....((..(((((((....)))))))..))..)))))))))).................. ( -25.10)
>DroSim_CAF1 4118 96 - 1
UUAUA----UCGAUGUUU---UU-CAAAACGUAUCCUG----UAGACUUUU-UUUGUUUCCCACAUC-UUGUGGGAACCUUCGAAGCUGCAGCUGUUUUUAUGACCUACU
(((((----...((((((---..-..))))))...(((----(((.((((.-...(.(((((((...-..))))))).)...)))))))))).......)))))...... ( -23.50)
>DroEre_CAF1 2932 93 - 1
---------UCGAUGUU----UUCCAAAACGUAUCCUG----UAGGCUUUUCCUUGUGUCCCACAUCCUUGUGGGAACCAUCGAAGCUGCAGCUGUUUUUAUGACCUACU
---------.....(((----....((((((....(((----(((.((((....((..(((((((....)))))))..))..)))))))))).))))))...)))..... ( -25.50)
>DroYak_CAF1 3033 104 - 1
CUUCAUUGUUCGAUGUUU--UUUCCAAAACGUAUCCUG----UAGACUUUUCUUUGUGUCCCACAUCCUUGUGGGAACCAUCGAAGCUGCAGCUGUUUUUAUGACCUACU
..((((......((((((--(....)))))))...(((----(((.((((....((..(((((((....)))))))..))..))))))))))........))))...... ( -26.80)
>consensus
CUUUA____UCGAUGUUU___UUCCAAAACGUAUCCUG____UAGACUUUUCUUUGUGUCCCACAUCCUUGUGGGAACCAUCGAAGCUGCAGCUGUUUUUAUGACCUACU
.........((((((..............................((........)).(((((((....)))))))..))))))(((....)))(((.....)))..... (-15.79 = -15.85 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:24 2006