Locus 4982

Sequence ID	3L_DroMel_CAF1
Location	13,743,085 – 13,743,325
Length	240
Max. P	0.948485

overview

Window 6

Location	13,743,085 – 13,743,205
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.33
Mean single sequence MFE	-32.42
Consensus MFE	-29.32
Energy contribution	-29.60
Covariance contribution	0.28
Combinations/Pair	1.05
Mean z-score	-1.66
Structure conservation index	0.90
SVM decision value	1.38
SVM RNA-class probability	0.948485
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13743085 120 - 23771897
GCAAUUUAGUUGACUGCGAAAGAAAACUGAGGCAUGAACCUGACUCAAGUGAAAGGCCGCUUGGGGCUCUUAGGUACAGCAAAACACAAGUAAGACCGCUGAUGUUUAGCGGAUUAACAA
....(((((((.....(....)..)))))))((.((.((((((((((((((......))))))))....)))))).)))).........((.((.(((((((...))))))).)).)).. ( -34.20)
>DroSec_CAF1 149815 120 - 1
GCAAUUUAGUUGACUGCGAAAGAAAACUGAGGCAUGAACCUGACUCAAGUGAAAGGCCGCUUGGGGCUCUUAGGUACAGCAAAACACAAGUAAGACUGCUGAUGUUUAGUGGAUUAACAA
........((((((..(..............((.((.((((((((((((((......))))))))....)))))).)))).(((((..((((....))))..))))).)..).))))).. ( -31.90)
>DroSim_CAF1 160958 120 - 1
GCAAUUUAGUUGACUGCAAAAGAAAACUGAGGCAUGAACCUGACUCAAGUGAAAGGCCGCUUGGGGCUCUUAGGUACAGCAAAACACAAGUAAGACCGCUGAUGUUUAGUGGAUUAACAA
....(((((((..((.....))..)))))))((.((.((((((((((((((......))))))))....)))))).)))).........((.((.(((((((...))))))).)).)).. ( -31.70)
>DroEre_CAF1 156489 120 - 1
GCAAUUUAGCCGACUGAGAAAGAAAACUGAGGCAUGAACCUGACUCAAGUGAAAGGCCGCUUGGGGCUCUUAGGUACAGCAAAACACAAGUAAGACCGCUGAUGUUUAGUGGAUUAACAA
((......(((...................))).((.((((((((((((((......))))))))....)))))).)))).........((.((.(((((((...))))))).)).)).. ( -29.41)
>DroYak_CAF1 160791 120 - 1
GCAAUUUAGUCGACUGAGAAAGAAAACUGAGGCAUGAACCUGACUCAAGUGAAAGGCCGCUUGGGGCUCUUAGGUACAGCCAAACACAAGUAAGACCGCUGAUGUUUAGUGGAUUAACAA
.....((((((.(((((.............(((.((.((((((((((((((......))))))))....)))))).)))))..(((..(((......)))..)))))))).))))))... ( -34.90)
>consensus
GCAAUUUAGUUGACUGCGAAAGAAAACUGAGGCAUGAACCUGACUCAAGUGAAAGGCCGCUUGGGGCUCUUAGGUACAGCAAAACACAAGUAAGACCGCUGAUGUUUAGUGGAUUAACAA
....(((((((..((.....))..)))))))((.((.((((((((((((((......))))))))....)))))).)))).........((.((.(((((((...))))))).)).)).. (-29.32 = -29.60 +   0.28)

alignment

secondary structure

dotplot

Window 7

Location	13,743,205 – 13,743,325
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.82
Mean single sequence MFE	-29.14
Consensus MFE	-28.28
Energy contribution	-28.32
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.22
Structure conservation index	0.97
SVM decision value	0.41
SVM RNA-class probability	0.725446
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13743205 120 + 23771897
UCCCAGUUAAAAAGCACUUAAGAGGGGUACUUACUCUAGUAUUCCACUUUACGCUAAAAAAAAAGACAUUUCAUCGUCGGCAGGCACGUUUAACAGCUUGUCCCACGGACAGUCGUUGUG
..((.(((....(((....(((.((((((((......)))))))).)))...))).........(((........)))))).))........(((((((((((...))))))..))))). ( -27.30)
>DroSec_CAF1 149935 119 + 1
UCCCAGUUAAAAAGCACUUAAGAGGGGUACUUACUCUAGUAUUCCACUUUACGCUAAAA-AAAAGACAUUUCAUCGUCGGCAGGCACGUUUAACAGCUUGUCCCGCGGACAGUCGUCCUG
............(((....(((.((((((((......)))))))).)))...)))....-....(((........)))(((((((..........)))))))....((((....)))).. ( -29.60)
>DroSim_CAF1 161078 119 + 1
UCCCAGUUAAAAAGCACUUAAGAGGGGUACUUACUCUAGUAUUCCACUUUACGCUAAAA-AAAAGACAUUUCAUCGUCGGCAGGCACGUUUAACAGCUUGUCCCGCGGACAGUCGUCCUG
............(((....(((.((((((((......)))))))).)))...)))....-....(((........)))(((((((..........)))))))....((((....)))).. ( -29.60)
>DroEre_CAF1 156609 119 + 1
UCCCAGUUAAAAAGCACUUAAGAGGGGUACUUACUCUAGUAUUCCACUUUACGCUAAAA-AAAAGACAUUUCAUCGUCGGCAGGCACGUUUAACAGCUUGUCCCACGGACAGUCGUCCUC
............(((....(((.((((((((......)))))))).)))...)))....-....(((........)))(((((((..........)))))))....((((....)))).. ( -29.60)
>DroYak_CAF1 160911 119 + 1
UCCCAGUUAAAAAGCACUUAAGAGGGGUACUUACUCUAGUAUUCCACUUUACGCUAAAA-AAAAGACAUUUCAUCGUCGGCAGGCACGUUUAACAGCUUGUCCCACGGACAUUCGUCCUG
............(((....(((.((((((((......)))))))).)))...)))....-....(((........)))(((((((..........)))))))....((((....)))).. ( -29.60)
>consensus
UCCCAGUUAAAAAGCACUUAAGAGGGGUACUUACUCUAGUAUUCCACUUUACGCUAAAA_AAAAGACAUUUCAUCGUCGGCAGGCACGUUUAACAGCUUGUCCCACGGACAGUCGUCCUG
............(((....(((.((((((((......)))))))).)))...))).........(((........)))(((((((..........)))))))....((((....)))).. (-28.28 = -28.32 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:36 2006