Locus 2864

Sequence ID	2R_DroMel_CAF1
Location	9,888,839 – 9,888,985
Length	146
Max. P	0.857875

overview

Window 6

Location	9,888,839 – 9,888,945
Length	106
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	76.41
Mean single sequence MFE	-30.90
Consensus MFE	-19.60
Energy contribution	-19.30
Covariance contribution	-0.30
Combinations/Pair	1.50
Mean z-score	-1.63
Structure conservation index	0.63
SVM decision value	0.82
SVM RNA-class probability	0.857875
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9888839 106 - 20766785
AUACCAAUCUACUGAUGAAAGCUAUAAUGCAGCAUGCCAAACGUUUGGGCAUGAGCCUGGAUGAACUUGGUGAGCAAUCGUACU-----UUGGAUUUUGG--UGGUAAUGCAG
.((((((((((..(((((..((......)).((.((((((.((((..(((....)))..))))...)))))).))..)))).).-----.)))))..)))--))......... ( -32.30)
>DroSec_CAF1 12112 100 - 1
AUUCCAAUCUACUGAUGAAAGCUCUAAUGCAGCAUGCCAAUCGUUUGGGCAUGAGCCUGGAUGAACUUGGUGAGCAAUCGUAAU-----UUGGA--------UGGUAGUGCAG
..(((((..(((.(((....((......)).((.(((((((((((..(((....)))..)))))..)))))).)).))))))..-----)))))--------........... ( -32.40)
>DroSim_CAF1 11232 100 - 1
AUACCAAUUUACUGAUGAAAGCUCUAGUGCAGCAUGCGAAUCGUUUGGGCAUGAGCCUGGAUGAACUUGGUGAGCAAUAGUACU-----UUGGA--------UGGUAGUGCAG
...((((..(((((.((...(((..(((((.....))...(((((..(((....)))..)))))))).)))...)).)))))..-----)))).--------........... ( -29.50)
>DroEre_CAF1 16213 100 - 1
AUACCAAUCUGCUGAUGAAGGCUCUAAUGCAGCAUGCCAAACGAUUGGGCAUGAGUUUGGAGGAACUUGGUGAGCAGUCGGACU-----UCGCA--------UGGUAGUUCAG
.(((((..(((((.((.(((.((((((.....((((((.........))))))...))))))...))).)).))))).((....-----.))..--------)))))...... ( -31.30)
>DroYak_CAF1 12078 105 - 1
AUACCAAUCUGCUGAUGAAAGCUCUAAUGCAGCAUGCCAAUCGCUUGGGCAUGAGUUUGGAAGAACUUGGUGAGCAGUCGGACUCAAAGUAGCA--------UGGUAGUUCAG
.(((((..(((((..(((..((((........((((((.........))))))(((((....)))))....))))..))).......)))))..--------)))))...... ( -28.10)
>DroMoj_CAF1 14021 103 - 1
AUACACAGCUGCUGAUCUCAGCGCUCGUGCAGCAUGCUCAACGUCUGGGCAUGAGCCUGGACCAAUUGGGUGGGUAU--AAAGC-----UCUAU---UCGUAAAUCAUUUCAA
...((((((.((((....))))))).)))..((..((((((.(((..(((....)))..)))...))))))((((..--...))-----))...---..))............ ( -31.80)
>consensus
AUACCAAUCUACUGAUGAAAGCUCUAAUGCAGCAUGCCAAACGUUUGGGCAUGAGCCUGGAUGAACUUGGUGAGCAAUCGUACU_____UUGGA________UGGUAGUGCAG
........(((((.......((......)).((.((((((.((((..(((....)))..))))...)))))).))............................)))))..... (-19.60 = -19.30 +  -0.30)

alignment

secondary structure

dotplot

Window 7

Location	9,888,865 – 9,888,985
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	74.08
Mean single sequence MFE	-40.10
Consensus MFE	-17.83
Energy contribution	-16.17
Covariance contribution	-1.66
Combinations/Pair	1.64
Mean z-score	-1.80
Structure conservation index	0.44
SVM decision value	-0.02
SVM RNA-class probability	0.524614
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9888865 120 - 20766785
AUGGUGUCAUUCCAGGAUGUACAGCAUGAUGGAAUAGUGGAUACCAAUCUACUGAUGAAAGCUAUAAUGCAGCAUGCCAAACGUUUGGGCAUGAGCCUGGAUGAACUUGGUGAGCAAUCG
.(((((((((((((..(((.....)))..))))))....))))))).......(((....((......)).((.((((((.((((..(((....)))..))))...)))))).)).))). ( -40.10)
>DroVir_CAF1 9986 118 - 1
CUGAUCUCAUUCCAUGAUGUGGAACAAGAUGGCAUUGUCGACACACAGCUGCUGCUCGCAGCGCUCAUGCAACAUGCCCAACGUCUGGGCAUGAAUCUGGAGCAAUUGGGUAGGUAC--A
...((((...((((((.((((..((((.......))))...))))))(((((.....)))))((((......((((((((.....))))))))......))))...)))).))))..--. ( -39.70)
>DroEre_CAF1 16233 120 - 1
AUGGUGUCAUUCCAGGACGUGCAACAUGAUGGAUAUGUGGAUACCAAUCUGCUGAUGAAGGCUCUAAUGCAGCAUGCCAAACGAUUGGGCAUGAGUUUGGAGGAACUUGGUGAGCAGUCG
.(((((((..((((...((((...)))).))))......)))))))..(((((.((.(((.((((((.....((((((.........))))))...))))))...))).)).)))))... ( -41.80)
>DroYak_CAF1 12103 120 - 1
AUGGUGUCAUUCCAGGAUGUACAGCAUGACGGAAUUGUGGAUACCAAUCUGCUGAUGAAAGCUCUAAUGCAGCAUGCCAAUCGCUUGGGCAUGAGUUUGGAAGAACUUGGUGAGCAGUCG
.((((((((((((...(((.....)))...)))))....)))))))..(((((.((.((..((((((.....((((((.........))))))...)))).))...)).)).)))))... ( -34.80)
>DroMoj_CAF1 14046 118 - 1
UUGAUAUCCUUUCAGGAUGUGGAACAGGAUGGCGUUAUAGAUACACAGCUGCUGAUCUCAGCGCUCGUGCAGCAUGCUCAACGUCUGGGCAUGAGCCUGGACCAAUUGGGUGGGUAU--A
...((((((.(((((....(((..((((...............((((((.((((....))))))).)))...((((((((.....))))))))..))))..))).))))).))))))--. ( -42.70)
>DroPer_CAF1 13872 120 - 1
CUCGUCUCGUUUCAGAGCGUAGAGCGUGAUGGCAUUGUCGAUACUCAACUGCUGUUGAAGGCUCUCAUGCAGCACGCCCAACGCCUGGGCCUGAGCUUGGAUGAAUUGGGUGAGAGCAUU
((((.((((.((((..((((.(.(((((...((((.(((.....(((((....))))).)))....))))..))))).).))))(..(((....)))..).)))).))))))))...... ( -41.50)
>consensus
AUGGUGUCAUUCCAGGAUGUACAACAUGAUGGAAUUGUGGAUACCAAUCUGCUGAUGAAAGCUCUAAUGCAGCAUGCCAAACGUCUGGGCAUGAGCCUGGAGGAACUGGGUGAGCACUCG
(((.(((((((....)))).))).))).........((((........))))........((......)).((.((((((....(..(((....)))..)......)))))).))..... (-17.83 = -16.17 +  -1.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:28 2006