Locus 4124

Sequence ID	2R_DroMel_CAF1
Location	13,539,516 – 13,539,655
Length	139
Max. P	0.763121

overview

Window 0

Location	13,539,516 – 13,539,616
Length	100
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	89.08
Mean single sequence MFE	-19.47
Consensus MFE	-16.65
Energy contribution	-16.09
Covariance contribution	-0.55
Combinations/Pair	1.21
Mean z-score	-1.83
Structure conservation index	0.86
SVM decision value	0.51
SVM RNA-class probability	0.763121
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13539516 100 - 20766785
GCA-UAUGCAGAUUCUAAAAAUGAAAUUAAAAUAAAUGGCA------------ACGCAAGCGGCAAACGAAGAAAAACUAUUUAUUUAUUUGUGUUUUUGGAAAA--UUGUGGCA
((.-...((((.(((((((((((((((..((((((((((..------------.(....)((.....))........)))))))))))))).)))))))))))..--)))).)). ( -18.70)
>DroSec_CAF1 87190 100 - 1
GCA-UAUGCAGAUUCUAAAAAUGAAAUUAAAAUAAAUGGCA------------ACGCAAGCGGCAAACGAAGAAAAACUAUUUAUUUAUUUGUGUUUUUAGAAAA--UUGUGGCA
((.-...((((.(((((((((((((((..((((((((((..------------.(....)((.....))........)))))))))))))).)))))))))))..--)))).)). ( -19.00)
>DroSim_CAF1 91123 100 - 1
GCA-UAUGCAGAUUCUAAAAAUGAAAUUAAAAUAAAUGGCA------------ACGCAAGCGGCAAACGAAGAAAAACUAUUUAUUUAUUUGUGUUUUUGGAAAA--UUGUGGCA
((.-...((((.(((((((((((((((..((((((((((..------------.(....)((.....))........)))))))))))))).)))))))))))..--)))).)). ( -18.70)
>DroEre_CAF1 88345 100 - 1
GCA-UAUGCAGAUUCUAAAAAUGAAAUUAAAAUAAAUGGAA------------ACGCAAGCGGCAAAUGAAGAAAAACUAUUUAUUUAUUUGUGUUUUUGGAAUA--UUGCGGCA
((.-...(((((((((((((((...............(...------------.).......(((((((((.(((.....))).)))))))))))))))))))).--)))).)). ( -22.40)
>DroYak_CAF1 92029 102 - 1
GCAAUAUACAGAUUCUAGAAAUGAAAUUAAAAUAAAUGGAA------------ACGCA-GCGGCAAAUGAAGAAAAACUAUUUAUUUAUUUGUGUUUUUGGAAAAUUUUGUGGCA
((....((((((((((((((((...............(...------------.)...-...(((((((((.(((.....))).)))))))))))))))))))...)))))))). ( -18.90)
>DroAna_CAF1 89228 108 - 1
GCA-UAUGCAGAUUCUAAAAAUGAAAUUAAAAUGAAUGGCAAACGCAACGCAAACGCAAGCGGCAAA---AGAAAAAGUAUUUAUUUGUUUGUGUUUUCAGAAAA---UGUAGCU
((.-..((((..((((.((((((......(((((((((((....))...((...(....)..))...---........))))))))).....)))))).))))..---)))))). ( -19.10)
>consensus
GCA_UAUGCAGAUUCUAAAAAUGAAAUUAAAAUAAAUGGCA____________ACGCAAGCGGCAAACGAAGAAAAACUAUUUAUUUAUUUGUGUUUUUGGAAAA__UUGUGGCA
((....(((((.(((((((((((((((..((((((((((...............((....))...............)))))))))))))).)))))))))))....))))))). (-16.65 = -16.09 +  -0.55)

alignment

secondary structure

dotplot

Window 1

Location	13,539,554 – 13,539,655
Length	101
Sequences	3
Columns	103
Reading direction	reverse
Mean pairwise identity	92.83
Mean single sequence MFE	-19.10
Consensus MFE	-18.19
Energy contribution	-17.97
Covariance contribution	-0.22
Combinations/Pair	1.06
Mean z-score	-1.51
Structure conservation index	0.95
SVM decision value	0.19
SVM RNA-class probability	0.626201
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13539554 101 - 20766785
-GUGCACUCGUUCCCGCAAAACCACGCACCACAGCGAAAUGCA-UAUGCAGAUUCUAAAAAUGAAAUUAAAAUAAAUGGCAACGCAAGCGGCAAACGAAGAAA
-......(((((.((((.......(((......))).......-..(((...(((.......)))............(....)))).))))..)))))..... ( -19.70)
>DroSim_CAF1 91161 101 - 1
-GUGCACUCGUCCCCGCAAAACCACGCACCGCAGCGAAAUGCA-UAUGCAGAUUCUAAAAAUGAAAUUAAAAUAAAUGGCAACGCAAGCGGCAAACGAAGAAA
-......((((..((((.......(((......))).......-..(((...(((.......)))............(....)))).))))...))))..... ( -18.80)
>DroYak_CAF1 92069 102 - 1
CGUCCACUCGUUCCCGCAAAACCACGCACCACAGCGAACUGCAAUAUACAGAUUCUAGAAAUGAAAUUAAAAUAAAUGGAAACGCA-GCGGCAAAUGAAGAAA
.......(((((.((((.......(((......)))...(((........((((.((....)).)))).........(....))))-))))..)))))..... ( -18.80)
>consensus
_GUGCACUCGUUCCCGCAAAACCACGCACCACAGCGAAAUGCA_UAUGCAGAUUCUAAAAAUGAAAUUAAAAUAAAUGGCAACGCAAGCGGCAAACGAAGAAA
.......((((..((((.......(((......)))...(((..........(((.......)))............(....)))).))))...))))..... (-18.19 = -17.97 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:23 2006