Locus 1507

Sequence ID	2L_DroMel_CAF1
Location	4,086,898 – 4,087,054
Length	156
Max. P	0.998233

overview

Window 6

Location	4,086,898 – 4,086,995
Length	97
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	77.42
Mean single sequence MFE	-24.18
Consensus MFE	-16.32
Energy contribution	-16.56
Covariance contribution	0.24
Combinations/Pair	1.05
Mean z-score	-2.84
Structure conservation index	0.67
SVM decision value	3.04
SVM RNA-class probability	0.998233
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4086898 97 + 22407834
CUUUUGCCACUUUCAACAGACCUCACUUCCUCCCUCC---CAUCUCGUUUUCGAGA-----GGAGAAUGCAAUGCAAUUUGCGCAAUGUGUGCAAAUUUGCACAA
...((((.....((....)).............((((---..(((((....)))))-----))))...))))((((((((((((.....))))))).)))))... ( -26.00)
>DroSec_CAF1 216355 100 + 1
CUUUUGCCACUUUCAACCGUCCUCACUCACUUCCUCCUCAAAUCUCGUUUUCGAGA-----GGAGAAUGCAAUGCAAUUUGCGCAAUGUGUGCAAAUUUGCACAA
...((((...........((....))..........(((...(((((....)))))-----.)))...))))((((((((((((.....))))))).)))))... ( -24.50)
>DroSim_CAF1 219239 89 + 1
CUUUUGCCACUUUUAACCGACCUCACUCAC-----------AUCUCGUUUUCCAGA-----GGAGAAUGCAAUGCAAUUUGCGCAAUGUGUGCAAAUUUGCACAA
...((((...........((......))..-----------.((((.((.....))-----.))))..))))((((((((((((.....))))))).)))))... ( -20.40)
>DroEre_CAF1 224735 96 + 1
CUUUUCCCACUUUCCACCAACCUCUUUUCCA-UCUCC---CAUCUCGUUUUCGAGC-----GGAGAAUGCAAUGCAAUUUGCGCAAUGUGUGCAAAUUUGCACAA
...............................-(((((---...((((....)))).-----)))))......((((((((((((.....))))))).)))))... ( -24.40)
>DroAna_CAF1 260610 86 + 1
CUUGUGUCACUCUAGCCCUAUAU-------------------CCUUGGCUUCCAGAGAGCUGGAGAAUGCCAUGCAAUUUGCGCAAUGUGUGCAAAUUUGCAGAA
......((...............-------------------...((((((((((....))))))...))))((((((((((((.....))))))).))))))). ( -25.60)
>consensus
CUUUUGCCACUUUCAACCGACCUCACUCAC___CUCC____AUCUCGUUUUCGAGA_____GGAGAAUGCAAUGCAAUUUGCGCAAUGUGUGCAAAUUUGCACAA
.............................................(((((((..........)))))))...((((((((((((.....))))))).)))))... (-16.32 = -16.56 +   0.24)

alignment

secondary structure

dotplot

Window 7

Location	4,086,959 – 4,087,054
Length	95
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	73.60
Mean single sequence MFE	-29.43
Consensus MFE	-8.77
Energy contribution	-8.46
Covariance contribution	-0.31
Combinations/Pair	1.19
Mean z-score	-2.88
Structure conservation index	0.30
SVM decision value	1.71
SVM RNA-class probability	0.973451
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4086959 95 - 22407834
UGCGUUGGCAAAAGUCAAAU-UUGGCAC----GAAAAUUUUGUAAAUA----AAA--UUUUUG----GUGCGGC--UUGUGCAAAUUU-GCACACAUUGCG-CAAAUUGCAUUG
.......((((..((((...-.)))).(----((((((((((....))----)))--))))))----((((((.--.((((((....)-)))))..)))))-)...)))).... ( -28.40)
>DroVir_CAF1 319904 89 - 1
UGU-------CGAGUCAAAU-GUGGCAG----CAAAUUUCUGUAAAUA----AGGA-AUUUUU----GUGCGGC--UUGCGCAAAUUU-GUGCAGAUUGCA-CAAAUUGCAUUG
...-------...((((...-.)))).(----(((((((((.......----))))-)).(((----((((((.--(((((((....)-)))))).)))))-)))))))).... ( -28.20)
>DroPse_CAF1 340021 108 - 1
UGGGGGCGAAAAAGUCAAAUUUUGGCACUCCAAAAAUUUUUGUAAAUACGAAAAA--UGUGUGCAAUGUGCGGC--UUGUGCAAAUUU-GCACACAUUGCG-CAAAUUGCAUUG
(((((((.((((.......)))).)).)))))....(((((((....))))))).--...(((((((((((((.--.((((((....)-)))))..)))))-))..)))))).. ( -35.00)
>DroGri_CAF1 313067 96 - 1
UGCG----CCCGACUCUAAU-GUGGCAG----CAAAGUUUUGUAAAUA----AAAAUUUGUGU----GUGCGGCUCUUGUGCCAAUUUGGUGCAGUUUGCG-CAGAUUGCAUUG
((((----(..(((......-((.((((----(((((((((.......----))))))).)))----.))).))...((..((.....))..))))).)))-)).......... ( -25.70)
>DroMoj_CAF1 363056 91 - 1
UGC-------GAAGUCAAAU-GUGGCUG----AAAAUUUUUGUAAAUA----AGGAAAUUUUU----GUGCGGC--UUGUGCAAAUUU-GUGCAGAUUGCGCCAAAUUGCAUUG
(((-------(((((((...-.)))))(----(((((((((.......----.))))))))))----((((((.--(((..((....)-)..))).))))))....)))))... ( -24.30)
>DroPer_CAF1 340818 108 - 1
UGGGGGCGAAAAAGUCAAAUUUUGGCACUCCAAAAAUUUUUGUAAAUACGAAAAA--UGUGUGCAAUGUGCGGC--UUGUGCAAAUUU-GCACACAUUGCG-CAAAUUGCAUUG
(((((((.((((.......)))).)).)))))....(((((((....))))))).--...(((((((((((((.--.((((((....)-)))))..)))))-))..)))))).. ( -35.00)
>consensus
UGCG_____AAAAGUCAAAU_GUGGCAC____AAAAUUUUUGUAAAUA____AAA__UUUUUG____GUGCGGC__UUGUGCAAAUUU_GCACACAUUGCG_CAAAUUGCAUUG
.............((((.....)))).........................................(((((((...(((((.......)))))....)).......))))).. ( -8.77 =  -8.46 +  -0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:20 2006