Locus 4018

Sequence ID	2R_DroMel_CAF1
Location	13,273,889 – 13,273,981
Length	92
Max. P	0.658510

overview

Window 1

Location	13,273,889 – 13,273,981
Length	92
Sequences	6
Columns	93
Reading direction	forward
Mean pairwise identity	83.15
Mean single sequence MFE	-32.33
Consensus MFE	-19.76
Energy contribution	-20.93
Covariance contribution	1.17
Combinations/Pair	1.17
Mean z-score	-2.63
Structure conservation index	0.61
SVM decision value	0.26
SVM RNA-class probability	0.658510
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13273889 92 + 20766785
AAGGAAUGUGGUGCAACAUCUGCUUGG-UGAUGCGGACGCGAUGCGGCGACAAGUAUUUCCACCUUUUCUAGAUGUGGAGGUGAACCACAAAC
......(((((((((.((((.....))-)).)))...(((......))).....(((((((((.((.....)).))))))))).))))))... ( -28.30)
>DroSec_CAF1 1459 90 + 1
AAGGAAUGUGGUGCAACAUCUGCUUGG-UGAUUCCGACGCGAUGCGGCGACAAGUAUUUCUACCUAUUCUAG--GUGGAGGUGAACCACAAAC
......((((((((..((((.((((((-.....)))).))))))..))......((((((((((((...)))--))))))))).))))))... ( -34.20)
>DroSim_CAF1 1513 90 + 1
AAGGAAUGUGGUGCAACAUCUGCUUGG-UGAUUCCGACGCGAUGCGGCGACAUGUAUUUCCACCUAUUCUAG--GUGGAGGUGAACCACAAAC
......((((((((..((((.((((((-.....)))).))))))..))......((((((((((((...)))--))))))))).))))))... ( -36.50)
>DroEre_CAF1 1634 90 + 1
AGCGAAUGUGGUGCAACAUCUGCUUGG-UGAUGGCGACGCGGUGUGGCGACAAGUAUUUCCACCUUUUCUAG--GUGGAGGUGGACCACAACC
......((((((((.(((.((((.(.(-(....)).).))))))).))......(((((((((((.....))--))))))))).))))))... ( -33.80)
>DroYak_CAF1 1307 90 + 1
AACGAAUGUGGUGCAACAUCUGCUUGG-UGAUGCCGACGCGAUGCGGCGACAAGUAUUUCCACCUUUUCUAG--GUGGAGAUGGACCACAACC
......((((((((..((((.((((((-.....)))).))))))..))......(((((((((((.....))--))))))))).))))))... ( -37.90)
>DroAna_CAF1 1066 86 + 1
CAUAUUUAUGUCGCAACAUCUGCUUGGGUGAAUC-----CGAUGCGGCGUCAUGUCUUUCCACCUUCAAAAG--AUGAAGGUGCAGUCCAUCC
......((((.(((..((((.....(((....))-----)))))..))).))))......((((((((....--.)))))))).......... ( -23.30)
>consensus
AAGGAAUGUGGUGCAACAUCUGCUUGG_UGAUGCCGACGCGAUGCGGCGACAAGUAUUUCCACCUUUUCUAG__GUGGAGGUGAACCACAAAC
......((((((((..((((.((((((......)))).))))))..))......(((((((((((.....))..))))))))).))))))... (-19.76 = -20.93 +   1.17)

alignment

secondary structure

dotplot

Window 2

Location	13,273,889 – 13,273,981
Length	92
Sequences	6
Columns	93
Reading direction	reverse
Mean pairwise identity	83.15
Mean single sequence MFE	-27.70
Consensus MFE	-18.67
Energy contribution	-19.11
Covariance contribution	0.45
Combinations/Pair	1.23
Mean z-score	-2.16
Structure conservation index	0.67
SVM decision value	0.24
SVM RNA-class probability	0.648168
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13273889 92 - 20766785
GUUUGUGGUUCACCUCCACAUCUAGAAAAGGUGGAAAUACUUGUCGCCGCAUCGCGUCCGCAUCA-CCAAGCAGAUGUUGCACCACAUUCCUU
(..((((((((((((.............))))))).............(((..(((((.((....-....)).)))))))).)))))..)... ( -23.72)
>DroSec_CAF1 1459 90 - 1
GUUUGUGGUUCACCUCCAC--CUAGAAUAGGUAGAAAUACUUGUCGCCGCAUCGCGUCGGAAUCA-CCAAGCAGAUGUUGCACCACAUUCCUU
(..((((((..........--...((.((((((....))))))))((.(((((((...((.....-))..)).))))).))))))))..)... ( -26.60)
>DroSim_CAF1 1513 90 - 1
GUUUGUGGUUCACCUCCAC--CUAGAAUAGGUGGAAAUACAUGUCGCCGCAUCGCGUCGGAAUCA-CCAAGCAGAUGUUGCACCACAUUCCUU
(..((((((.....(((((--(((...))))))))..........((.(((((((...((.....-))..)).))))).))))))))..)... ( -30.90)
>DroEre_CAF1 1634 90 - 1
GGUUGUGGUCCACCUCCAC--CUAGAAAAGGUGGAAAUACUUGUCGCCACACCGCGUCGCCAUCA-CCAAGCAGAUGUUGCACCACAUUCGCU
(((.(((((.....(((((--((.....))))))).......(.(((......))).)))))).)-)).(((..((((......))))..))) ( -30.30)
>DroYak_CAF1 1307 90 - 1
GGUUGUGGUCCAUCUCCAC--CUAGAAAAGGUGGAAAUACUUGUCGCCGCAUCGCGUCGGCAUCA-CCAAGCAGAUGUUGCACCACAUUCGUU
(..((((((.....(((((--((.....)))))))..........((.(((((((...((.....-))..)).))))).))))))))..)... ( -31.50)
>DroAna_CAF1 1066 86 - 1
GGAUGGACUGCACCUUCAU--CUUUUGAAGGUGGAAAGACAUGACGCCGCAUCG-----GAUUCACCCAAGCAGAUGUUGCGACAUAAAUAUG
..........((((((((.--....)))))))).......(((.(((.((((((-----(......)).....))))).))).)))....... ( -23.20)
>consensus
GGUUGUGGUUCACCUCCAC__CUAGAAAAGGUGGAAAUACUUGUCGCCGCAUCGCGUCGGAAUCA_CCAAGCAGAUGUUGCACCACAUUCCUU
(..((((((((((((.............)))))))..........((.(((((((...............)).))))).)).)))))..)... (-18.67 = -19.11 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:46 2006