Locus 7508

Sequence ID	3R_DroMel_CAF1
Location	20,066,006 – 20,066,148
Length	142
Max. P	0.963371

overview

Window 6

Location	20,066,006 – 20,066,117
Length	111
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	76.40
Mean single sequence MFE	-43.32
Consensus MFE	-22.48
Energy contribution	-23.87
Covariance contribution	1.39
Combinations/Pair	1.46
Mean z-score	-2.21
Structure conservation index	0.52
SVM decision value	1.20
SVM RNA-class probability	0.929054
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20066006 111 + 27905053
CCUCGGGCCGAGAUGAAGAACUUGGCCACGCUCUGCUCGGCCGCAGCAGCAGCUGCUGCUGUGGCAGCGGUUAACAAGGAUCAGGUUGAGAUUAGUUCGGAUCUUGAGAGC
.....(((((((........)))))))..((((.(((..(((((((((((....))))))))))))))((((......))))...(..(((((......)))))..))))) ( -49.40)
>DroVir_CAF1 12982 111 + 1
ACCCGGGCCGAAAUGAAGAAUCUGGCCACGCUCUGCUCUGCAGCCGCCAUGGCGGCUCAGGUGACAGCGGCAAAUAAGGAAAUCGAUGAAAUUGCUACCGAUAUCGAGAGU
..((.(((((............)))))..(((((((((((.((((((....)))))))))).).))).)))......))...(((((...((((....))))))))).... ( -36.00)
>DroGri_CAF1 14247 111 + 1
ACGCGUGCAGAGAUGAAGAAUUUGGCCACGCUGUGCUCGGCAGCAGCCAUGGCGGCUGCCGUAACAGCAGCUAAUAAGGAGUCCGAAGAAGUUGCAACUGAUAACGAAAGU
..((((((..((((.....)))).).)))))(((...(((((((.((....)).)))))))..)))((((((.....((...)).....))))))........((....)) ( -38.60)
>DroSec_CAF1 8171 111 + 1
CCUCCUGCCGAGAUGAAGAACUUGGCCACGCUGUGCUCGGCCGCAGCAGCAGCUGCUGCUGUGGCAGCGGUUAACAAGGAUCAGGUUGAGAUUAGUUCGGAUCUUGAGAGC
..((((((((((........))))))...(((((.....(((((((((((....))))))))))).))))).....)))).....(..(((((......)))))..).... ( -45.10)
>DroEre_CAF1 10869 111 + 1
CCUAGGGCCGAGAUGAAAAAUUUGGCCACGCUCUGCUCGGCCGCAGCAGCAGCUGCUGCUGUGGCUGCGGUUAACAAGGAUCAGGAUGAGAUUAGUUCGGAACUUGAGAGC
.....(((((((.(....).)))))))..(((((((((((((((((((((....))))))))))))).)))...((((..((.((((.......)))).)).))))))))) ( -50.50)
>DroAna_CAF1 11710 111 + 1
CCUCGAUCCGAGAUGAAGAACCUGGCCACGCUCUGUUCAGCAGCAGCCGCAGCAGCGGCUGUGGCAGCCGCCAACAAGGAGCAGGACGAGAUCAGCACUGAUAUCGAAAGC
.((((...))))........((((((((((((((....)).)))((((((....)))))))))))..((........))..)))).(((.((((....)))).)))..... ( -40.30)
>consensus
CCUCGGGCCGAGAUGAAGAACUUGGCCACGCUCUGCUCGGCAGCAGCAGCAGCUGCUGCUGUGGCAGCGGCUAACAAGGAUCAGGAUGAGAUUAGUACGGAUAUCGAGAGC
.(((((((((((........))))))...((((((((((((.(((((....))))).)))).))))).)))................................)))))... (-22.48 = -23.87 +   1.39)

alignment

secondary structure

dotplot

Window 7

Location	20,066,037 – 20,066,148
Length	111
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	74.06
Mean single sequence MFE	-37.17
Consensus MFE	-22.00
Energy contribution	-21.20
Covariance contribution	-0.80
Combinations/Pair	1.32
Mean z-score	-1.60
Structure conservation index	0.59
SVM decision value	0.70
SVM RNA-class probability	0.825968
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20066037 111 + 27905053
UCUGCUCGGCCGCAGCAGCAGCUGCUGCUGUGGCAGCGGUUAACAAGGAUCAGGUUGAGAUUAGUUCGGAUCUUGAGAGCGA---AUGCGAGGAUGAUGCAGAAGGUGGUGCUG
(((((((((((((((((((....))))))))))).((((((......))))...(..(((((......)))))..)..))..---.........))).)))))........... ( -41.60)
>DroPse_CAF1 9795 96 + 1
UUUGUUCAGCAGCAGCAGCGGCCGCUGCUGUGGCAGCAGGCCACAGGGAUGAAGAUGAAAUCAGUACAGAUAUAUACACUGA------UGAGGAC------------GAUGCUA
.((((((((((((.((....)).))))))(((((.....)))))...............((((((............)))))------)..))))------------))..... ( -29.80)
>DroSec_CAF1 8202 105 + 1
UGUGCUCGGCCGCAGCAGCAGCUGCUGCUGUGGCAGCGGUUAACAAGGAUCAGGUUGAGAUUAGUUCGGAUCUUGAGAGCGA---AUGCGAGGAUGAC------GGUGGUGCUG
.((.(((((((((((((((....))))))))))).((((((......))))...(..(((((......)))))..)..))..---...)))).))..(------((.....))) ( -40.40)
>DroSim_CAF1 10156 105 + 1
UCUGCUCGGCCGCAGCAGCAGCUGCUGCUGUGGCAGCGGUUAACAAGGAUCAGGUUGAGAUUAGUUCGGAUCUUGAGAGCGA---AUGCGAGGAUGAC------GGUGGUGCUG
(((.(((((((((((((((....))))))))))).((((((......))))...(..(((((......)))))..)..))..---...)))).).))(------((.....))) ( -39.30)
>DroAna_CAF1 11741 108 + 1
UCUGUUCAGCAGCAGCCGCAGCAGCGGCUGUGGCAGCCGCCAACAAGGAGCAGGACGAGAUCAGCACUGAUAUCGAAAGCGACGGAGGCGAGGGCG------AAGGUGAUGCUG
......(((((((.((((((((....)))))))).))((((.....(..((....(((.((((....)))).)))...))..)...))))...((.------...))..))))) ( -39.30)
>DroPer_CAF1 16388 96 + 1
UUUGUUCAGCAGCAGCAGCGGCCGCUGCUGUGGCAGCAGGCCACAAGGAUGAAGAUGACCUCAGUACAGAUCAAUACAGUGA------UGAGGAC------------GAUGCUA
((..(((((((((.((....)).))))))(((((.....)))))..)))..)).....(((((.(((...........))).------)))))..------------....... ( -32.60)
>consensus
UCUGCUCAGCAGCAGCAGCAGCUGCUGCUGUGGCAGCGGUCAACAAGGAUCAGGAUGAGAUCAGUACGGAUCUUGAGAGCGA___AUGCGAGGACG________GGUGAUGCUG
..(.((((((.((((((((....)))))))).)).............((((.......))))..........................)))).).................... (-22.00 = -21.20 +  -0.80)

alignment

secondary structure

dotplot

Window 8

Location	20,066,037 – 20,066,148
Length	111
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	74.06
Mean single sequence MFE	-31.59
Consensus MFE	-14.89
Energy contribution	-14.70
Covariance contribution	-0.19
Combinations/Pair	1.14
Mean z-score	-2.30
Structure conservation index	0.47
SVM decision value	1.55
SVM RNA-class probability	0.963371
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20066037 111 - 27905053
CAGCACCACCUUCUGCAUCAUCCUCGCAU---UCGCUCUCAAGAUCCGAACUAAUCUCAACCUGAUCCUUGUUAACCGCUGCCACAGCAGCAGCUGCUGCUGCGGCCGAGCAGA
...........(((((.((......((.(---(((.((....))..))))...(((.......)))...........)).(((.(((((((....))))))).))).))))))) ( -30.70)
>DroPse_CAF1 9795 96 - 1
UAGCAUC------------GUCCUCA------UCAGUGUAUAUAUCUGUACUGAUUUCAUCUUCAUCCCUGUGGCCUGCUGCCACAGCAGCGGCCGCUGCUGCUGCUGAACAAA
(((((.(------------......(------((((((((......)))))))))...............((((((.(((((....)))))))))))....).)))))...... ( -30.40)
>DroSec_CAF1 8202 105 - 1
CAGCACCACC------GUCAUCCUCGCAU---UCGCUCUCAAGAUCCGAACUAAUCUCAACCUGAUCCUUGUUAACCGCUGCCACAGCAGCAGCUGCUGCUGCGGCCGAGCACA
..........------.............---..((((.(((((((.(.............).))).)))).........(((.(((((((....))))))).))).))))... ( -28.32)
>DroSim_CAF1 10156 105 - 1
CAGCACCACC------GUCAUCCUCGCAU---UCGCUCUCAAGAUCCGAACUAAUCUCAACCUGAUCCUUGUUAACCGCUGCCACAGCAGCAGCUGCUGCUGCGGCCGAGCAGA
..........------.............---..((((.(((((((.(.............).))).)))).........(((.(((((((....))))))).))).))))... ( -28.32)
>DroAna_CAF1 11741 108 - 1
CAGCAUCACCUU------CGCCCUCGCCUCCGUCGCUUUCGAUAUCAGUGCUGAUCUCGUCCUGCUCCUUGUUGGCGGCUGCCACAGCCGCUGCUGCGGCUGCUGCUGAACAGA
(((((.......------.((..(((((..((..((...(((.((((....)))).)))....))....))..)))))..))..(((((((....))))))).)))))...... ( -38.40)
>DroPer_CAF1 16388 96 - 1
UAGCAUC------------GUCCUCA------UCACUGUAUUGAUCUGUACUGAGGUCAUCUUCAUCCUUGUGGCCUGCUGCCACAGCAGCGGCCGCUGCUGCUGCUGAACAAA
(((((.(------------(.(((((------.....((((......))))))))).)............((((((.(((((....)))))))))))....).)))))...... ( -33.40)
>consensus
CAGCACCACC________CAUCCUCGCAU___UCGCUCUCAAGAUCCGAACUAAUCUCAACCUGAUCCUUGUUAACCGCUGCCACAGCAGCAGCUGCUGCUGCGGCCGAACAGA
.....................................................................((((....((.((...((((((....)))))))).))..)))).. (-14.89 = -14.70 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:47:40 2006