Locus 4084

Sequence ID	2L_DroMel_CAF1
Location	11,773,777 – 11,773,962
Length	185
Max. P	0.974451

overview

Window 3

Location	11,773,777 – 11,773,885
Length	108
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	80.74
Mean single sequence MFE	-21.32
Consensus MFE	-15.42
Energy contribution	-15.62
Covariance contribution	0.20
Combinations/Pair	1.20
Mean z-score	-2.39
Structure conservation index	0.72
SVM decision value	1.73
SVM RNA-class probability	0.974451
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11773777 108 - 22407834
GCUAAAUUGACAGGCAAAAAUUAAAGACGAAAGUCGACUAGCGUAAUAAUCUUCAACAAAGAAAAUAUUAGGUUAAGCAUGAGCUA-ACAUAAAUAUAUAUGAUUAGGU
.((((.......(((..........(((....)))(..((((.(((((.((((.....))))...))))).))))..)....))).-.((((......)))).)))).. ( -19.50)
>DroSec_CAF1 31808 108 - 1
GCUAAAUUGACAGGCAAAAAUUAAAGACGGAAGUCGACUAGCGUAAUAAUCUUUACCAGAGAAAAUAUUAGGCUAAGCAUGAGCUA-ACAUAAAUAUAUAUGAAUAGGU
.(((........(((..........(((....)))(..((((.(((((.((((.....))))...))))).))))..)....))).-.((((......))))..))).. ( -21.80)
>DroSim_CAF1 30936 108 - 1
GCAAAAUUGACAGGCAAAAAUUAAAGACGGAAGUCGACUAGCGUAAUAAUCUUUACCAGAGAAAAUAUUAGGCUAAGCAUGAGCUA-ACAUAAAUAUAUAUGAAUAGGU
............(((..........(((....)))(..((((.(((((.((((.....))))...))))).))))..)....))).-.((((......))))....... ( -20.90)
>DroEre_CAF1 42208 95 - 1
GCCAAAUUGACAGGCAAAAAUUACAGACGGAAGUCGACCUGC-UGAUAAUCUUUAACAGAGAAAAUAUCAGGCUAGUCACGAGCUAAUCACUAAUA-------------
.......(((..(((..........(((....)))(((..((-(((((.((((.....))))...))))).))..)))....)))..)))......------------- ( -22.70)
>DroYak_CAF1 33262 99 - 1
GCUAAAUUGACAGGCGGGAAUAGAAGACGGAAGUCGACCUGC-UAAUAAUCUUUAGCUAAGAAAAUAUAAAGCUAAUUGUGAGCUA-UCAUAAAUAUACAU--------
((((((......((((((.......(((....)))..)))))-).......))))))...................((((((....-))))))........-------- ( -21.72)
>consensus
GCUAAAUUGACAGGCAAAAAUUAAAGACGGAAGUCGACUAGCGUAAUAAUCUUUAACAGAGAAAAUAUUAGGCUAAGCAUGAGCUA_ACAUAAAUAUAUAUGA_UAGGU
............(((..........(((....)))(..((((.(((((.((((.....))))...))))).))))..)....)))........................ (-15.42 = -15.62 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	11,773,805 – 11,773,924
Length	119
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	89.57
Mean single sequence MFE	-25.08
Consensus MFE	-20.66
Energy contribution	-20.70
Covariance contribution	0.04
Combinations/Pair	1.27
Mean z-score	-1.65
Structure conservation index	0.82
SVM decision value	0.72
SVM RNA-class probability	0.831898
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11773805 119 - 22407834
UUGCCACAACAUAUUACUAAUACAUGGCCAAGUCACGGGGCUAAAUUGACAGGCAAAAAUUAAAGACGAAAGUCGACUAGCGUAAUAAUCUUCAACAAAGAAAAUAUUAGGUUAAGCAU
(((((......(((.....)))..(((((.........)))))........)))))........(((....)))(..((((.(((((.((((.....))))...))))).))))..).. ( -23.50)
>DroSec_CAF1 31836 119 - 1
UUGCCACAACAUAUUACUAAUACAUGGCCAAGUCACGGAGCUAAAUUGACAGGCAAAAAUUAAAGACGGAAGUCGACUAGCGUAAUAAUCUUUACCAGAGAAAAUAUUAGGCUAAGCAU
(((((....(((...........))).....((((...........)))).)))))........(((....)))(..((((.(((((.((((.....))))...))))).))))..).. ( -24.80)
>DroSim_CAF1 30964 119 - 1
UUGCCACAACAUAUUACUAAUACAUGGCCAAGUCACGGGGCAAAAUUGACAGGCAAAAAUUAAAGACGGAAGUCGACUAGCGUAAUAAUCUUUACCAGAGAAAAUAUUAGGCUAAGCAU
(((((....(((...........)))(((.........)))..........)))))........(((....)))(..((((.(((((.((((.....))))...))))).))))..).. ( -26.00)
>DroEre_CAF1 42224 118 - 1
UUGCCACAACAUAUUACUAAUACAUGGCUAAGUCACGGGGCCAAAUUGACAGGCAAAAAUUACAGACGGAAGUCGACCUGC-UGAUAAUCUUUAACAGAGAAAAUAUCAGGCUAGUCAC
(((((......(((.....)))..(((((..(...)..)))))........)))))........(((....)))(((..((-(((((.((((.....))))...))))).))..))).. ( -28.20)
>DroYak_CAF1 33282 118 - 1
UUGCCACAACAUAUUACUAAUACAUGGCCAAGUCACGGGGCUAAAUUGACAGGCGGGAAUAGAAGACGGAAGUCGACCUGC-UAAUAAUCUUUAGCUAAGAAAAUAUAAAGCUAAUUGU
.....((((..((((.........(((((.........)))))........((((((.......(((....)))..)))))-)))))....((((((............)))))))))) ( -22.90)
>consensus
UUGCCACAACAUAUUACUAAUACAUGGCCAAGUCACGGGGCUAAAUUGACAGGCAAAAAUUAAAGACGGAAGUCGACUAGCGUAAUAAUCUUUAACAGAGAAAAUAUUAGGCUAAGCAU
(((((......(((.....)))..(((((.........)))))........)))))........(((....)))(..((((.(((((.((((.....))))...))))).))))..).. (-20.66 = -20.70 +   0.04)

alignment

secondary structure

dotplot

Window 5

Location	11,773,845 – 11,773,962
Length	117
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	94.46
Mean single sequence MFE	-25.39
Consensus MFE	-23.80
Energy contribution	-23.64
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.16
Structure conservation index	0.94
SVM decision value	0.40
SVM RNA-class probability	0.719535
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11773845 117 - 22407834
GCUAAACAAUGGCCAA-AACUUUCGAUGGUUUCGAACUUUUGCCACAACAUAUUACUAAUACAUGGCCAAGUCACGGGGCUAAAUUGACAGGCAAAAAUUAAAGACGAAAGUCGACUA
(((...(((((((.((-((..(((((.....))))).)))))))...................(((((.........))))).))))...)))..........(((....)))..... ( -25.30)
>DroSec_CAF1 31876 117 - 1
GCUAAACAAUGGCCAA-AACUUUCGAUGGUUUCGAACUUUUGCCACAACAUAUUACUAAUACAUGGCCAAGUCACGGAGCUAAAUUGACAGGCAAAAAUUAAAGACGGAAGUCGACUA
.........((((((.-....(((((.....)))))....((......)).............))))))((((.....(((.........)))..........(((....))))))). ( -24.90)
>DroSim_CAF1 31004 117 - 1
GCUAAACAAUGGCCAA-AACUUUCGAUGGUUUCGAACUUUUGCCACAACAUAUUACUAAUACAUGGCCAAGUCACGGGGCAAAAUUGACAGGCAAAAAUUAAAGACGGAAGUCGACUA
((((.....))))...-..((.(((((.((..((.((((..((((..................)))).))))..))..))...))))).))............(((....)))..... ( -24.77)
>DroEre_CAF1 42263 117 - 1
GCUAAACAAUGGCCAA-AACUUUCGAUUGUUUCGAACUUUUGCCACAACAUAUUACUAAUACAUGGCUAAGUCACGGGGCCAAAUUGACAGGCAAAAAUUACAGACGGAAGUCGACCU
(((...((((((((..-.....((((.....))))((((..((((..................)))).)))).....)))))..)))...)))..........(((....)))..... ( -27.07)
>DroYak_CAF1 33321 118 - 1
GCUAAACAAUGGCCAAAAACUUUCGAUUGUUUCGAACUUUUGCCACAACAUAUUACUAAUACAUGGCCAAGUCACGGGGCUAAAUUGACAGGCGGGAAUAGAAGACGGAAGUCGACCU
(((...(((((((.((((...(((((.....))))).)))))))...................(((((.........))))).))))...)))..........(((....)))..... ( -24.90)
>consensus
GCUAAACAAUGGCCAA_AACUUUCGAUGGUUUCGAACUUUUGCCACAACAUAUUACUAAUACAUGGCCAAGUCACGGGGCUAAAUUGACAGGCAAAAAUUAAAGACGGAAGUCGACUA
(((......((((((......(((((.....)))))....((......)).............)))))).((((...........)))).)))..........(((....)))..... (-23.80 = -23.64 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:55 2006