Locus 1891

Sequence ID	3L_DroMel_CAF1
Location	5,291,127 – 5,291,221
Length	94
Max. P	0.955630

overview

Window 5

Location	5,291,127 – 5,291,221
Length	94
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	79.41
Mean single sequence MFE	-26.61
Consensus MFE	-15.69
Energy contribution	-16.97
Covariance contribution	1.28
Combinations/Pair	1.13
Mean z-score	-1.82
Structure conservation index	0.59
SVM decision value	0.38
SVM RNA-class probability	0.713356
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5291127 94 + 23771897
UUGCAACUGUAAAAGGAACUACUGCCAUCGGCAGCAGCACAAG-----GAAUGACAGUAGUGGUAGUGCUACUAGCAACUGCAAUUGCAGCAAACCUAU
((((.(((((.....(..((.(((((...))))).))..)...-----.....)))))(((((.....))))).))))((((....))))......... ( -24.12)
>DroSec_CAF1 38546 94 + 1
UUGCAACUGUAAAAGGAACUACUGCCAUCGGCAGCAGCACAAG-----GAAUGACAGUAGUGGCAGUGCUACUAGCAACUGCAGUUGCACCAGACCUAU
.((((((((((.......((.(((((...))))).))......-----...((..((((((......))))))..))..)))))))))).......... ( -29.00)
>DroSim_CAF1 39373 94 + 1
UUGCAACUGUAAAAGGAACUACUGCCAUCGGCAGCAGCGCAAG-----GAAUGACAGUAGUGGUAGUGCUACUAGCAACUGCAGUUGCACCAGACCUAU
.((((((((((....(..((.(((((...))))).))..)...-----...((..((((((......))))))..))..)))))))))).......... ( -29.90)
>DroEre_CAF1 38106 81 + 1
UUGCAACUGUAAAAGGGACUACUGCCAUCGGCAGCAGCACCAG-----GAAUGACAGUAGUGGUAGUGCUACUAGCAACUGCACAU-------------
..((.(((((....((..((.(((((...))))).))..))..-----.....))))).)).(((((((.....)).)))))....------------- ( -24.30)
>DroYak_CAF1 39864 94 + 1
UUGCAACUGUAAGAGGGACUACUGCCAUCGGCAGCAGCACAAG-----GAAUGACAGUGGUGGUUGUACUACUAGCAACUGCAAUUGCAGAAGACCUAU
((((.(((((.....(..((.(((((...))))).))..)...-----.....)))))(((((.....))))).))))((((....))))......... ( -26.52)
>DroPer_CAF1 79141 88 + 1
UUGCAACUGUAAAAGGGGCUACUGCCAUCGGCAGCAAUACCAGCAGCAGAAUGGCUGUAGCAGCAACAAGAAUGG----GGCAAUUGUACUG-------
.(((((...........(((((.((((((.((.((.......)).)).).))))).))))).((..((....)).----.))..)))))...------- ( -25.80)
>consensus
UUGCAACUGUAAAAGGAACUACUGCCAUCGGCAGCAGCACAAG_____GAAUGACAGUAGUGGUAGUGCUACUAGCAACUGCAAUUGCACCAGACCUAU
.(((((.((((....(..((.(((((...))))).))..).................((((((.....)))))).....)))).))))).......... (-15.69 = -16.97 +   1.28)

alignment

secondary structure

dotplot

Window 6

Location	5,291,127 – 5,291,221
Length	94
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	79.41
Mean single sequence MFE	-28.62
Consensus MFE	-20.86
Energy contribution	-22.58
Covariance contribution	1.72
Combinations/Pair	1.12
Mean z-score	-2.42
Structure conservation index	0.73
SVM decision value	1.46
SVM RNA-class probability	0.955630
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5291127 94 - 23771897
AUAGGUUUGCUGCAAUUGCAGUUGCUAGUAGCACUACCACUACUGUCAUUC-----CUUGUGCUGCUGCCGAUGGCAGUAGUUCCUUUUACAGUUGCAA
...(((.((((((....((....))..))))))..)))...(((((.....-----.....(((((((((...))))))))).......)))))..... ( -29.43)
>DroSec_CAF1 38546 94 - 1
AUAGGUCUGGUGCAACUGCAGUUGCUAGUAGCACUGCCACUACUGUCAUUC-----CUUGUGCUGCUGCCGAUGGCAGUAGUUCCUUUUACAGUUGCAA
..........((((((((((((.((.....))))))).((((((((((((.-----...(.((....))))))))))))))).........))))))). ( -33.20)
>DroSim_CAF1 39373 94 - 1
AUAGGUCUGGUGCAACUGCAGUUGCUAGUAGCACUACCACUACUGUCAUUC-----CUUGCGCUGCUGCCGAUGGCAGUAGUUCCUUUUACAGUUGCAA
..........(((((((((((.((.((((((........)))))).))...-----.))))(((((((((...))))))))).........))))))). ( -31.40)
>DroEre_CAF1 38106 81 - 1
-------------AUGUGCAGUUGCUAGUAGCACUACCACUACUGUCAUUC-----CUGGUGCUGCUGCCGAUGGCAGUAGUCCCUUUUACAGUUGCAA
-------------...((((..((.((((((........))))))......-----..((..((((((((...))))))))..)).....))..)))). ( -28.20)
>DroYak_CAF1 39864 94 - 1
AUAGGUCUUCUGCAAUUGCAGUUGCUAGUAGUACAACCACCACUGUCAUUC-----CUUGUGCUGCUGCCGAUGGCAGUAGUCCCUCUUACAGUUGCAA
..........((((((((....((.((((.((......)).)))).))...-----...(..((((((((...))))))))..)......)))))))). ( -25.40)
>DroPer_CAF1 79141 88 - 1
-------CAGUACAAUUGCC----CCAUUCUUGUUGCUGCUACAGCCAUUCUGCUGCUGGUAUUGCUGCCGAUGGCAGUAGCCCCUUUUACAGUUGCAA
-------.....((((((..----........((((((((((((((......)))).(((((....))))).))))))))))........))))))... ( -24.07)
>consensus
AUAGGUCUGGUGCAAUUGCAGUUGCUAGUAGCACUACCACUACUGUCAUUC_____CUUGUGCUGCUGCCGAUGGCAGUAGUCCCUUUUACAGUUGCAA
..........((((((((....((.((((((........)))))).))...........(..((((((((...))))))))..)......)))))))). (-20.86 = -22.58 +   1.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:14 2006