Locus 3491

Sequence ID	3R_DroMel_CAF1
Location	9,429,461 – 9,429,554
Length	93
Max. P	0.850759

overview

Window 0

Location	9,429,461 – 9,429,554
Length	93
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	79.17
Mean single sequence MFE	-30.47
Consensus MFE	-19.62
Energy contribution	-21.52
Covariance contribution	1.89
Combinations/Pair	1.22
Mean z-score	-1.86
Structure conservation index	0.64
SVM decision value	0.79
SVM RNA-class probability	0.850759
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9429461 93 + 27905053
--CAGGAUCACGGGACCGAGUCCAGCACAGUCCAGCUCACACUUCAUUGUUCCCAACUUGAUGCGAAGGGGAACAAUAAAACUGAAGUGGCUGCA
--..((((....((((...))))......)))).((...(((((((((((((((..(((......)))))))))))......)))))))...)). ( -30.20)
>DroSec_CAF1 59091 90 + 1
--CAGGAUCACGGUGCCGAG---GGCACAGUCCAGCUCACACUUCAUUGUUCGCAACUUGAUGCGGAGGGGAACAAUAUAACUGAAGUGGCUGCA
--..((((....(((((...---))))).)))).((...(((((((...((((((......)))))).(....)........)))))))...)). ( -30.00)
>DroEre_CAF1 65228 92 + 1
GGCAGGAUCAUGGGGCCGAG---GGCACAGUCCAGCUCACACUUCAUUGUUCCCAACUUGAUGCGGAGGGGAACAAUAAAACUGAAGUGGCUGCC
(((((.......((((...(---(((...)))).)))).(((((((((((((((..((......))..))))))))......))))))).))))) ( -35.50)
>DroYak_CAF1 61319 90 + 1
--CAGGACCACGGGGCCGAG---GGCGCAGUCCAGCUCACACUUCAUUGUUCCCAACUUGAUGCGGAGGGGAACAAUAAAACUGAAGUGGCUGCA
--..((((....(.(((...---))).).)))).((...(((((((((((((((..((......))..))))))))......)))))))...)). ( -33.70)
>DroAna_CAF1 55865 75 + 1
-----------------GAG---GGCACUGGCGAGCUCACACUUCAUUGUUCCCAGCUGGACGAGAAGGGAAACAAUAAAACUGAAGUGGCUGCA
-----------------..(---(((........)))).(((((((((((((((..((.....))..))).)))))......)))))))...... ( -21.10)
>DroPer_CAF1 58614 86 + 1
----GAGCCACGGAGCCAGG---GGU-CCUUUCGGCUCACACUUCAUUGUUCCCGGCCAUA-GCGGAGGGGCACAAUAAAACUGAAGUGGCUGUG
----.((((((.((((((((---...-.)))..))))).......(((((.(((..((...-..))..))).))))).........))))))... ( -32.30)
>consensus
__CAGGAUCACGGGGCCGAG___GGCACAGUCCAGCUCACACUUCAUUGUUCCCAACUUGAUGCGGAGGGGAACAAUAAAACUGAAGUGGCUGCA
....((((....(.(((......))).).)))).((...(((((((((((((((..((......))..))))))))......)))))))...)). (-19.62 = -21.52 +   1.89)

alignment

secondary structure

dotplot

Window 1

Location	9,429,461 – 9,429,554
Length	93
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	79.17
Mean single sequence MFE	-28.58
Consensus MFE	-19.21
Energy contribution	-19.68
Covariance contribution	0.47
Combinations/Pair	1.10
Mean z-score	-1.45
Structure conservation index	0.67
SVM decision value	0.38
SVM RNA-class probability	0.713473
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9429461 93 - 27905053
UGCAGCCACUUCAGUUUUAUUGUUCCCCUUCGCAUCAAGUUGGGAACAAUGAAGUGUGAGCUGGACUGUGCUGGACUCGGUCCCGUGAUCCUG--
.((((((((((((.((((((((((((((((......)))..))))))))))))))).))).))).))))...((((.((....)).).)))..-- ( -31.50)
>DroSec_CAF1 59091 90 - 1
UGCAGCCACUUCAGUUAUAUUGUUCCCCUCCGCAUCAAGUUGCGAACAAUGAAGUGUGAGCUGGACUGUGCC---CUCGGCACCGUGAUCCUG--
..(((((((((((......((((((......(((......))))))))))))))))...)))).((.(((((---...))))).)).......-- ( -25.30)
>DroEre_CAF1 65228 92 - 1
GGCAGCCACUUCAGUUUUAUUGUUCCCCUCCGCAUCAAGUUGGGAACAAUGAAGUGUGAGCUGGACUGUGCC---CUCGGCCCCAUGAUCCUGCC
(((((((((((((.(((((((((((((..(........)..))))))))))))))).))).))).....(((---...))).........))))) ( -29.90)
>DroYak_CAF1 61319 90 - 1
UGCAGCCACUUCAGUUUUAUUGUUCCCCUCCGCAUCAAGUUGGGAACAAUGAAGUGUGAGCUGGACUGCGCC---CUCGGCCCCGUGGUCCUG--
.((((((((((((.(((((((((((((..(........)..))))))))))))))).))).))).))))..(---(.((....)).)).....-- ( -32.90)
>DroAna_CAF1 55865 75 - 1
UGCAGCCACUUCAGUUUUAUUGUUUCCCUUCUCGUCCAGCUGGGAACAAUGAAGUGUGAGCUCGCCAGUGCC---CUC-----------------
.((((((((.....((((((((((.(((..((.....))..))))))))))))).))).))).)).......---...----------------- ( -20.30)
>DroPer_CAF1 58614 86 - 1
CACAGCCACUUCAGUUUUAUUGUGCCCCUCCGC-UAUGGCCGGGAACAAUGAAGUGUGAGCCGAAAGG-ACC---CCUGGCUCCGUGGCUC----
...((((((.....(((((((((.(((..((..-...))..))).))))))))).(.(((((...(((-...---))))))))))))))).---- ( -31.60)
>consensus
UGCAGCCACUUCAGUUUUAUUGUUCCCCUCCGCAUCAAGUUGGGAACAAUGAAGUGUGAGCUGGACUGUGCC___CUCGGCCCCGUGAUCCUG__
..(((((((.....(((((((((((((..(........)..))))))))))))).))).))))................................ (-19.21 = -19.68 +   0.47)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:27 2006