Locus 5985

Sequence ID	X_DroMel_CAF1
Location	15,384,775 – 15,384,932
Length	157
Max. P	0.995913

overview

Window 2

Location	15,384,775 – 15,384,892
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.92
Mean single sequence MFE	-23.66
Consensus MFE	-16.29
Energy contribution	-16.10
Covariance contribution	-0.19
Combinations/Pair	1.05
Mean z-score	-1.58
Structure conservation index	0.69
SVM decision value	0.09
SVM RNA-class probability	0.581003
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15384775 117 - 22224390
GAAA-GUGC--AGAUGCUCAUCUGGUAUUAUCCAGAUCCAGAUGAAAUCAAAUAUUUUUUUAUUGAUUUUUUAACAAGCAAAUAGAAUCCGAGCGCGAAGCUGUUUUAAAAUGCCAAGCA
....-((((--.(((..((((((((.(((.....))))))))))).)))...(((((.(((.((((....)))).))).)))))........))))...(((..............))). ( -24.74)
>DroSec_CAF1 26735 115 - 1
--AA-GUGC--AGAUGCUCAUCUGGUAUUAUACAGAUCCAGAUGAAAUCAAAUAUUUUCUUAUUGAUUUAUUAACAAACAAAUAGAAUUCGAGCGUGAAGCUGUUUUAAAAUUCCAAGCA
--..-.(((--.(((..((((((((.(((.....))))))))))).)))(((((.((((...((((((((((........))))))..))))....)))).)))))...........))) ( -23.30)
>DroEre_CAF1 24247 109 - 1
CAAA-GUGC--AGAUGCUCAUCUGGUAUUAU------CCAGAUGAAGUCAAAUAUUU--UUAUUGAUUUAUUAACAAACAAAUAGAAUCCGAGCGCAAAGCUGUUUUGAAAUGCCUAGCA
....-((((--.(((..((((((((......------)))))))).)))......((--(((((..(((......)))..))))))).....))))...((((............)))). ( -25.30)
>DroYak_CAF1 16238 112 - 1
GAUAUGUACAUAGAUGCUCAUCUGGUAUUAU------CCAGAUGAUGUGAAAUAUUU--UUAUUGAUUUAUUAACAAACAAAUAGAAUCCGAGCACAGAGCUGUUUUAAAAUGCCUAGCA
..........((((.((((((((((......------))))))..((((......((--(((((..(((......)))..)))))))......))))))))...))))............ ( -21.30)
>consensus
GAAA_GUGC__AGAUGCUCAUCUGGUAUUAU______CCAGAUGAAAUCAAAUAUUU__UUAUUGAUUUAUUAACAAACAAAUAGAAUCCGAGCGCAAAGCUGUUUUAAAAUGCCAAGCA
..............(((((((((((............)))))))).....................................((((((...(((.....))))))))).........))) (-16.29 = -16.10 +  -0.19)

alignment

secondary structure

dotplot

Window 3

Location	15,384,815 – 15,384,932
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.08
Mean single sequence MFE	-22.70
Consensus MFE	-15.70
Energy contribution	-16.32
Covariance contribution	0.63
Combinations/Pair	1.00
Mean z-score	-1.85
Structure conservation index	0.69
SVM decision value	0.58
SVM RNA-class probability	0.788324
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15384815 117 + 22224390
UGCUUGUUAAAAAAUCAAUAAAAAAAUAUUUGAUUUCAUCUGGAUCUGGAUAAUACCAGAUGAGCAUCU--GCAC-UUUCAAUGCUAACAUUGAAUUUUGUCUAUUGGACUAGCACUUGA
((((.(((....(((..((((((........((((((((((((............))))))))).))).--....-.(((((((....)))))))))))))..))).))).))))..... ( -26.60)
>DroSec_CAF1 26775 98 + 1
UGUUUGUUAAUAAAUCAAUAAGAAAAUAUUUGAUUUCAUCUGGAUCUGUAUAAUACCAGAUGAGCAUCU--GCAC-UU-------------------UUGUCUAUUCGACUAGCACUUGA
((((.(((((((...(((.(((.............((((((((............))))))))((....--)).)-))-------------------)))..)))).))).))))..... ( -17.80)
>DroEre_CAF1 24287 109 + 1
UGUUUGUUAAUAAAUCAAUAA--AAAUAUUUGACUUCAUCUGG------AUAAUACCAGAUGAGCAUCU--GCAC-UUUGAAUGCCAACAUUGAAUUUUGUCUAUUGGACUAGCACUUGA
....(((((.....(((((..--...((((..(..((((((((------......))))))))((....--))..-.)..)))).....))))).....(((.....))))))))..... ( -22.40)
>DroYak_CAF1 16278 112 + 1
UGUUUGUUAAUAAAUCAAUAA--AAAUAUUUCACAUCAUCUGG------AUAAUACCAGAUGAGCAUCUAUGUACAUAUCAAUGCCAGCAUUGAACUUUGUCUAUUGGACUAGCACUUGA
((((.(((....(((..((((--(.((((......((((((((------......))))))))......)))).....((((((....))))))..)))))..))).))).))))..... ( -24.00)
>consensus
UGUUUGUUAAUAAAUCAAUAA__AAAUAUUUGACUUCAUCUGG______AUAAUACCAGAUGAGCAUCU__GCAC_UUUCAAUGCCAACAUUGAAUUUUGUCUAUUGGACUAGCACUUGA
..............((((.................((((((((............))))))))((.............((((((....)))))).....(((.....)))..))..)))) (-15.70 = -16.32 +   0.63)

alignment

secondary structure

dotplot

Window 4

Location	15,384,815 – 15,384,932
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	81.08
Mean single sequence MFE	-25.92
Consensus MFE	-18.36
Energy contribution	-18.80
Covariance contribution	0.44
Combinations/Pair	1.07
Mean z-score	-2.88
Structure conservation index	0.71
SVM decision value	2.63
SVM RNA-class probability	0.995913
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15384815 117 - 22224390
UCAAGUGCUAGUCCAAUAGACAAAAUUCAAUGUUAGCAUUGAAA-GUGC--AGAUGCUCAUCUGGUAUUAUCCAGAUCCAGAUGAAAUCAAAUAUUUUUUUAUUGAUUUUUUAACAAGCA
(((((..((.(((.....)))....(((((((....))))))))-)..)--.(((..((((((((.(((.....))))))))))).))).............)))).............. ( -29.60)
>DroSec_CAF1 26775 98 - 1
UCAAGUGCUAGUCGAAUAGACAA-------------------AA-GUGC--AGAUGCUCAUCUGGUAUUAUACAGAUCCAGAUGAAAUCAAAUAUUUUCUUAUUGAUUUAUUAACAAACA
(((((..((.(((.....)))..-------------------.)-)..)--.(((..((((((((.(((.....))))))))))).))).............)))).............. ( -22.90)
>DroEre_CAF1 24287 109 - 1
UCAAGUGCUAGUCCAAUAGACAAAAUUCAAUGUUGGCAUUCAAA-GUGC--AGAUGCUCAUCUGGUAUUAU------CCAGAUGAAGUCAAAUAUUU--UUAUUGAUUUAUUAACAAACA
(((((..(((((((((((............)))))).)))...)-)..)--.(((..((((((((......------)))))))).)))........--...)))).............. ( -25.10)
>DroYak_CAF1 16278 112 - 1
UCAAGUGCUAGUCCAAUAGACAAAGUUCAAUGCUGGCAUUGAUAUGUACAUAGAUGCUCAUCUGGUAUUAU------CCAGAUGAUGUGAAAUAUUU--UUAUUGAUUUAUUAACAAACA
((((((((..(((.....))).....((((((....))))))...))))......((((((((((......------)))))))).)).........--...)))).............. ( -26.10)
>consensus
UCAAGUGCUAGUCCAAUAGACAAAAUUCAAUGUUGGCAUUGAAA_GUGC__AGAUGCUCAUCUGGUAUUAU______CCAGAUGAAAUCAAAUAUUU__UUAUUGAUUUAUUAACAAACA
((((((((..(((.....))).....((((((....))))))...))))...(((..((((((((............)))))))).))).............)))).............. (-18.36 = -18.80 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:01:27 2006