Locus 1095

Sequence ID	3R_DroMel_CAF1
Location	3,310,649 – 3,310,803
Length	154
Max. P	0.952073

overview

Window 9

Location	3,310,649 – 3,310,764
Length	115
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.68
Mean single sequence MFE	-36.05
Consensus MFE	-27.62
Energy contribution	-28.38
Covariance contribution	0.75
Combinations/Pair	1.11
Mean z-score	-2.96
Structure conservation index	0.77
SVM decision value	1.42
SVM RNA-class probability	0.952073
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3310649 115 + 27905053
GAGUGACUGCGAUGAGCAACAAGCAAAAGGGUACAAAAAGCUCCCCACGACAAGUGGCAACACGGCGGAUGAAUUUGGCUUAUGCAGCCAAACAC--ACGGCCACGCAGCA---ACACAU
..(((.(((((.((.((.....))....(((..(.....)..))).....)).(((....)))(((.(.((..(((((((.....)))))))..)--)).))).)))))..---.))).. ( -35.70)
>DroSec_CAF1 14822 119 + 1
GAGUGACUGCGAUAAGCAACAAGCGAAGUGGUA-AAAAAACCGCCCACGACAAGUGGCAACACGGCGGAUGAAUUUGGCUUAUGCAGCCAAACACACACUGCCACGCACCACCUACACAU
..(((..(((.....)))....(((..(((((.-.....))))).........(((....)))(((((.((..(((((((.....)))))))..))..))))).)))........))).. ( -37.70)
>DroSim_CAF1 19065 120 + 1
GAGUGACUGCGAUAAGCAACAAGCGAAGGGGUAUAAAAAACCCCCCACGACAAGUGGCAACACGGCGGAUGAAUUUGGCUUAUGCAGCCAAACACACACUGCCACGCACCACCUACACAU
..(((..(((.....)))....(((..(((((.......))))).........(((....)))(((((.((..(((((((.....)))))))..))..))))).)))........))).. ( -39.90)
>DroYak_CAF1 25084 113 + 1
GAGUGACUGCGAUAAGCAACAAGCAAAAGAGUGCAAAAAG-CCCCCACGACAAGUGGCAACACGGCGGAUGAAUUUGGCUUAUGCAGGCAAACA---ACUGCCACGCAC---CUACACAU
..(((..(((.....))).........((.((((......-............(((....)))(((((.((..((((.((.....)).))))))---.)))))..))))---)).))).. ( -30.90)
>consensus
GAGUGACUGCGAUAAGCAACAAGCAAAAGGGUACAAAAAACCCCCCACGACAAGUGGCAACACGGCGGAUGAAUUUGGCUUAUGCAGCCAAACAC__ACUGCCACGCACCA_CUACACAU
..(((..(((.....)))....((...(((((.......))))).........(((....)))(((((.....(((((((.....)))))))......)))))..))........))).. (-27.62 = -28.38 +   0.75)

alignment

secondary structure

dotplot

Window 0

Location	3,310,689 – 3,310,803
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.53
Mean single sequence MFE	-31.87
Consensus MFE	-22.58
Energy contribution	-23.82
Covariance contribution	1.25
Combinations/Pair	1.00
Mean z-score	-2.44
Structure conservation index	0.71
SVM decision value	0.62
SVM RNA-class probability	0.800744
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3310689 114 + 27905053
CUCCCCACGACAAGUGGCAACACGGCGGAUGAAUUUGGCUUAUGCAGCCAAACAC--ACGGCCACGCAGCA---ACACAUUGACAUGUUCGAGCAUUAAGCUAAAAAAAAC-AUUUUUUA
.......(((((.(((....)))(((.(.((..(((((((.....)))))))..)--)).)))........---...........)).)))(((.....))).........-........ ( -26.30)
>DroSec_CAF1 14861 120 + 1
CCGCCCACGACAAGUGGCAACACGGCGGAUGAAUUUGGCUUAUGCAGCCAAACACACACUGCCACGCACCACCUACACAUUGACAGGUUGGGGCAUUAAGCUAAAAAAAAUGAUUUUUUA
..((((.((((..(((....)))(((((.((..(((((((.....)))))))..))..))))).......................)))))))).......(((((((.....))))))) ( -35.80)
>DroSim_CAF1 19105 120 + 1
CCCCCCACGACAAGUGGCAACACGGCGGAUGAAUUUGGCUUAUGCAGCCAAACACACACUGCCACGCACCACCUACACAUUGACAUGUUGGGGCAUUAAGCUAAAAAAAAUGAUUUUUUA
...(((.(((((.(((....)))(((((.((..(((((((.....)))))))..))..)))))......................))))))))........(((((((.....))))))) ( -32.10)
>DroYak_CAF1 25124 110 + 1
-CCCCCACGACAAGUGGCAACACGGCGGAUGAAUUUGGCUUAUGCAGGCAAACA---ACUGCCACGCAC---CUACACAUUGACAUGUGGGGGCAUUAAACUAAAAAAAC--A-UUUUUA
-((((((((....(((....)))(((((.((..((((.((.....)).))))))---.)))))......---.............)))))))).................--.-...... ( -33.30)
>consensus
CCCCCCACGACAAGUGGCAACACGGCGGAUGAAUUUGGCUUAUGCAGCCAAACAC__ACUGCCACGCACCA_CUACACAUUGACAUGUUGGGGCAUUAAGCUAAAAAAAAU_AUUUUUUA
...(((.((((..(((....)))(((((.....(((((((.....)))))))......))))).......................)))))))........................... (-22.58 = -23.82 +   1.25)

alignment

secondary structure

dotplot

Window 1

Location	3,310,689 – 3,310,803
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	89.53
Mean single sequence MFE	-37.50
Consensus MFE	-25.17
Energy contribution	-26.55
Covariance contribution	1.38
Combinations/Pair	1.03
Mean z-score	-1.83
Structure conservation index	0.67
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3310689 114 - 27905053
UAAAAAAU-GUUUUUUUUAGCUUAAUGCUCGAACAUGUCAAUGUGU---UGCUGCGUGGCCGU--GUGUUUGGCUGCAUAAGCCAAAUUCAUCCGCCGUGUUGCCACUUGUCGUGGGGAG
(((((((.-...)))))))........(((...((((.(((.(((.---.((.(((((((.((--(.((((((((.....)))))))).)))..))))))).)))))))).))))..))) ( -35.50)
>DroSec_CAF1 14861 120 - 1
UAAAAAAUCAUUUUUUUUAGCUUAAUGCCCCAACCUGUCAAUGUGUAGGUGGUGCGUGGCAGUGUGUGUUUGGCUGCAUAAGCCAAAUUCAUCCGCCGUGUUGCCACUUGUCGUGGGCGG
(((((((.....)))))))(((((..((.(((.((((.(.....)))))))).))(((((((..((.((((((((.....))))))))........))..)))))))......))))).. ( -39.30)
>DroSim_CAF1 19105 120 - 1
UAAAAAAUCAUUUUUUUUAGCUUAAUGCCCCAACAUGUCAAUGUGUAGGUGGUGCGUGGCAGUGUGUGUUUGGCUGCAUAAGCCAAAUUCAUCCGCCGUGUUGCCACUUGUCGUGGGGGG
(((((((.....)))))))........(((((((((....))))((((((((((((((((.(..((.((((((((.....)))))))).))..))))))).))))))))).).))))).. ( -43.50)
>DroYak_CAF1 25124 110 - 1
UAAAAA-U--GUUUUUUUAGUUUAAUGCCCCCACAUGUCAAUGUGUAG---GUGCGUGGCAGU---UGUUUGCCUGCAUAAGCCAAAUUCAUCCGCCGUGUUGCCACUUGUCGUGGGGG-
((((((-.--...))))))........((((((((((....((.((..---(((((.(((((.---...))))))))))..))))....))).....(((....))).....)))))))- ( -31.70)
>consensus
UAAAAAAU_AUUUUUUUUAGCUUAAUGCCCCAACAUGUCAAUGUGUAG_UGGUGCGUGGCAGU__GUGUUUGGCUGCAUAAGCCAAAUUCAUCCGCCGUGUUGCCACUUGUCGUGGGGGG
(((((((.....)))))))........((((..((((.(((.(((........(((((((.(.....((((((((.....))))))))....).)))))))...)))))).)))))))). (-25.17 = -26.55 +   1.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:44 2006