Locus 1087

Sequence ID	2L_DroMel_CAF1
Location	2,993,832 – 2,993,992
Length	160
Max. P	0.896594

overview

Window 3

Location	2,993,832 – 2,993,952
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	96.67
Mean single sequence MFE	-49.57
Consensus MFE	-48.36
Energy contribution	-48.03
Covariance contribution	-0.33
Combinations/Pair	1.07
Mean z-score	-1.61
Structure conservation index	0.98
SVM decision value	0.32
SVM RNA-class probability	0.686925
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2993832 120 + 22407834
GCGCGCUUGCUACGACAGCUUCUGUAAGCACUGGCAGCAGGCCUUCGAGAUCAUCCAGCACAGUGCACCGCCCUCGCACGACGACGUGCUGGGCGUGGUCUCGCACUUGGACUACAUGGU
..(((((((((.(((..((((((((........)))).))))..))).(......))))).)))))(((((((..(((((....))))).))))(((((((.......)))))))..))) ( -47.60)
>DroSim_CAF1 5569 120 + 1
GCGCGCUUGCUACGACAGCUUCUGCAAGCACUGGCAGCAGGCCUUCGAGAUCAUCCAGCACAGUGCGCCGCCCUCGCACGACGACGUGCUGGGCGUGGUCUCGCACUUGGACUACAUGGU
(((((((((((.(((..((((((((........)))).))))..))).(......))))).))))))).((((..(((((....))))).))))(((((((.......)))))))..... ( -51.50)
>DroYak_CAF1 5603 120 + 1
GCGCGCCUGCUACGACAGCUUCUGCAAGCACUGGCAGCAGGCCUUCGAGAUCAUCCAGCACAGUGCGCCGCCCUCGCACGAUGACGUGCUGGGCGUAGUCUCCCACUUGGACUACAUGGU
((((((.((((.(((..((((((((........)))).))))..))).(......)))))..)))))).((((..(((((....))))).))))(((((((.......)))))))..... ( -49.60)
>consensus
GCGCGCUUGCUACGACAGCUUCUGCAAGCACUGGCAGCAGGCCUUCGAGAUCAUCCAGCACAGUGCGCCGCCCUCGCACGACGACGUGCUGGGCGUGGUCUCGCACUUGGACUACAUGGU
..(((((((((.(((..((((((((........)))).))))..))).(......))))).)))))(((((((..(((((....))))).))))(((((((.......)))))))..))) (-48.36 = -48.03 +  -0.33)

alignment

secondary structure

dotplot

Window 4

Location	2,993,872 – 2,993,992
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	96.11
Mean single sequence MFE	-46.67
Consensus MFE	-45.86
Energy contribution	-45.20
Covariance contribution	-0.66
Combinations/Pair	1.08
Mean z-score	-1.95
Structure conservation index	0.98
SVM decision value	0.99
SVM RNA-class probability	0.896594
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2993872 120 + 22407834
GCCUUCGAGAUCAUCCAGCACAGUGCACCGCCCUCGCACGACGACGUGCUGGGCGUGGUCUCGCACUUGGACUACAUGGUCACCCUGCUGCUCGUGGAGCUGCAUCACUGCAACAAAGUC
((((.((((......(((((..(((.(((((((..(((((....))))).))))(((((((.......)))))))..))))))..))))))))).)).))((((....))))........ ( -47.90)
>DroSim_CAF1 5609 120 + 1
GCCUUCGAGAUCAUCCAGCACAGUGCGCCGCCCUCGCACGACGACGUGCUGGGCGUGGUCUCGCACUUGGACUACAUGGUCACCCUGCUGCUCGUGGAGCUGCAUCACUGCAACAAAGUC
((((.((((......(((((..(((.(((((((..(((((....))))).))))(((((((.......)))))))..))))))..))))))))).)).))((((....))))........ ( -47.30)
>DroYak_CAF1 5643 120 + 1
GCCUUCGAGAUCAUCCAGCACAGUGCGCCGCCCUCGCACGAUGACGUGCUGGGCGUAGUCUCCCACUUGGACUACAUGGUUACCCUGCUGCUCGUGGAACUGCAUCACUGCAACAAGGUC
(((((((((......(((((..(((.(((((((..(((((....))))).))))(((((((.......)))))))..))))))..)))))))))......((((....))))..))))). ( -44.80)
>consensus
GCCUUCGAGAUCAUCCAGCACAGUGCGCCGCCCUCGCACGACGACGUGCUGGGCGUGGUCUCGCACUUGGACUACAUGGUCACCCUGCUGCUCGUGGAGCUGCAUCACUGCAACAAAGUC
.((..((((......(((((..(((.(((((((..(((((....))))).))))(((((((.......)))))))..))))))..))))))))).))...((((....))))........ (-45.86 = -45.20 +  -0.66)

alignment

secondary structure

dotplot

Window 5

Location	2,993,872 – 2,993,992
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	96.11
Mean single sequence MFE	-51.47
Consensus MFE	-49.04
Energy contribution	-48.93
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-1.84
Structure conservation index	0.95
SVM decision value	0.56
SVM RNA-class probability	0.781058
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2993872 120 - 22407834
GACUUUGUUGCAGUGAUGCAGCUCCACGAGCAGCAGGGUGACCAUGUAGUCCAAGUGCGAGACCACGCCCAGCACGUCGUCGUGCGAGGGCGGUGCACUGUGCUGGAUGAUCUCGAAGGC
..((((((((((....))))))....(((((((((.(((((((..((.((((......).))).))((((.(((((....)))))..))))))).)))).)))))......)))))))). ( -51.50)
>DroSim_CAF1 5609 120 - 1
GACUUUGUUGCAGUGAUGCAGCUCCACGAGCAGCAGGGUGACCAUGUAGUCCAAGUGCGAGACCACGCCCAGCACGUCGUCGUGCGAGGGCGGCGCACUGUGCUGGAUGAUCUCGAAGGC
..((((((((((....))))))....((((..(((((....)).))).(((((((((((......(((((.(((((....)))))..))))).))))))....)))))...)))))))). ( -52.50)
>DroYak_CAF1 5643 120 - 1
GACCUUGUUGCAGUGAUGCAGUUCCACGAGCAGCAGGGUAACCAUGUAGUCCAAGUGGGAGACUACGCCCAGCACGUCAUCGUGCGAGGGCGGCGCACUGUGCUGGAUGAUCUCGAAGGC
.((((((((((.(((.........)))..)))))))))).........((((..((((....))))((((.(((((....)))))..))))(((((...)))))))))............ ( -50.40)
>consensus
GACUUUGUUGCAGUGAUGCAGCUCCACGAGCAGCAGGGUGACCAUGUAGUCCAAGUGCGAGACCACGCCCAGCACGUCGUCGUGCGAGGGCGGCGCACUGUGCUGGAUGAUCUCGAAGGC
.((((((((((.(((.........)))..))))))))))...(((.(((..((.(((((......(((((.(((((....)))))..))))).)))))))..))).)))........... (-49.04 = -48.93 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:15 2006