Locus 565

Sequence ID	3L_DroMel_CAF1
Location	1,624,113 – 1,624,212
Length	99
Max. P	0.634514

overview

Window 3

Location	1,624,113 – 1,624,212
Length	99
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	81.26
Mean single sequence MFE	-45.68
Consensus MFE	-35.45
Energy contribution	-35.23
Covariance contribution	-0.22
Combinations/Pair	1.31
Mean z-score	-1.14
Structure conservation index	0.78
SVM decision value	-0.04
SVM RNA-class probability	0.514251
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1624113 99 + 23771897
ACGGGGCGUGGCCUCCGGAGGCAUUGGCGUUGGCGCCAGCAUGUGGCGUCGUUAGUUGGACCUGUGGACGGCUCCUGGGCCGUCCCAUCCGCAGCUGCC
.((((((...))).)))..((((...((...(((((((.....))))))).......(((..((.((((((((....)))))))))))))))...)))) ( -48.10)
>DroVir_CAF1 8115 95 + 1
ACGUGGCGUCGCCUCCGGCGGCAUUGGCGUCGGCGCCAGCAUGUGGCGACGUUAGUUGGACUUUUGGACGGCAACGACGCCGUCCCAGCACCAGC----
...((((((((((..((...((..(((((....))))))).)).))))))))))(((((......(((((((......))))))).....)))))---- ( -45.70)
>DroPse_CAF1 8959 97 + 1
CAGGGGCGUCGCCUCCGGCGGCAUUGGUGUGGGCGCCAGCAUGUGGCGACGUUAGUUGGACCUGUGGACGGCGCCAGCGCCGUCCCUCCAACA-CGAC-
....(((((((((..((...((..(((((....))))))).)).))))))))).((((((...(.((((((((....))))))))))))))).-....- ( -49.00)
>DroSec_CAF1 8757 99 + 1
AAGAGGCGUGGCCUCCGGAGGCAUUGGCGUCGGCGCCAGCAUGUGGCGUCGUUAGUUGGACCUGUGGGCGGCUCCUGGGCCGUCCCAUCCGCAGCUGCC
..(((((...)))))....((((...((..((((((((.....))))))))......(((..((.((((((((....)))))))))))))))...)))) ( -47.40)
>DroWil_CAF1 8405 92 + 1
ACGGGGUGUCGCUUCUGGCGGAAUUGGUGUAGGAGCCAGUAUGUGGCGACGUUAGUUAGACCUUUGGACGGCAACUGUGCCGUCCCAGUCGC-------
(((...((((((..(((((...............)))))...)))))).)))......(((....((((((((....))))))))..)))..------- ( -34.86)
>DroPer_CAF1 8844 97 + 1
CAGGGGCGUCGCCUCCGGCGGCAUUGGUGUGGGCGCCAGCAUGUGGCGACGUUAGUUGGACCUGUGGACGGCGCCAGCGCCGUCCCUCCAACA-CGAC-
....(((((((((..((...((..(((((....))))))).)).))))))))).((((((...(.((((((((....))))))))))))))).-....- ( -49.00)
>consensus
AAGGGGCGUCGCCUCCGGCGGCAUUGGCGUCGGCGCCAGCAUGUGGCGACGUUAGUUGGACCUGUGGACGGCACCUGCGCCGUCCCACCAGCA_C__C_
....(((((((((..((...((..(((((....))))))).)).)))))))))............((((((((....)))))))).............. (-35.45 = -35.23 +  -0.22)

alignment

secondary structure

dotplot

Window 4

Location	1,624,113 – 1,624,212
Length	99
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	81.26
Mean single sequence MFE	-42.11
Consensus MFE	-27.50
Energy contribution	-29.17
Covariance contribution	1.67
Combinations/Pair	1.14
Mean z-score	-1.65
Structure conservation index	0.65
SVM decision value	0.21
SVM RNA-class probability	0.634514
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1624113 99 - 23771897
GGCAGCUGCGGAUGGGACGGCCCAGGAGCCGUCCACAGGUCCAACUAACGACGCCACAUGCUGGCGCCAACGCCAAUGCCUCCGGAGGCCACGCCCCGU
((((...((((((.(((((((......)))))))....)))).......(.(((((.....))))).)...))...))))..(((.(((...)))))). ( -42.50)
>DroVir_CAF1 8115 95 - 1
----GCUGGUGCUGGGACGGCGUCGUUGCCGUCCAAAAGUCCAACUAACGUCGCCACAUGCUGGCGCCGACGCCAAUGCCGCCGGAGGCGACGCCACGU
----..(((.(((.((((((((....))))))))...)))))).....(((((((.....((((((.((.......)).)))))).)))))))...... ( -42.40)
>DroPse_CAF1 8959 97 - 1
-GUCG-UGUUGGAGGGACGGCGCUGGCGCCGUCCACAGGUCCAACUAACGUCGCCACAUGCUGGCGCCCACACCAAUGCCGCCGGAGGCGACGCCCCUG
-....-.((((((.((((((((....)))))))).....))))))...(((((((.....((((((..((......)).)))))).)))))))...... ( -45.70)
>DroSec_CAF1 8757 99 - 1
GGCAGCUGCGGAUGGGACGGCCCAGGAGCCGCCCACAGGUCCAACUAACGACGCCACAUGCUGGCGCCGACGCCAAUGCCUCCGGAGGCCACGCCUCUU
((((...(((((((((.((((......))))))))....)))......((.(((((.....))))).))..))...))))...((((((...)))))). ( -42.20)
>DroWil_CAF1 8405 92 - 1
-------GCGACUGGGACGGCACAGUUGCCGUCCAAAGGUCUAACUAACGUCGCCACAUACUGGCUCCUACACCAAUUCCGCCAGAAGCGACACCCCGU
-------..((((.((((((((....))))))))...))))........(((((......(((((...............)))))..)))))....... ( -34.16)
>DroPer_CAF1 8844 97 - 1
-GUCG-UGUUGGAGGGACGGCGCUGGCGCCGUCCACAGGUCCAACUAACGUCGCCACAUGCUGGCGCCCACACCAAUGCCGCCGGAGGCGACGCCCCUG
-....-.((((((.((((((((....)))))))).....))))))...(((((((.....((((((..((......)).)))))).)))))))...... ( -45.70)
>consensus
_G__G_UGCGGAUGGGACGGCGCAGGAGCCGUCCACAGGUCCAACUAACGUCGCCACAUGCUGGCGCCCACACCAAUGCCGCCGGAGGCGACGCCCCGU
..............((((((((....))))))))..............(((((((.....((((((.............)))))).)))))))...... (-27.50 = -29.17 +   1.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:27 2006