Locus 6540

Sequence ID	3R_DroMel_CAF1
Location	17,246,750 – 17,246,974
Length	224
Max. P	0.792461

overview

Window 4

Location	17,246,750 – 17,246,863
Length	113
Sequences	3
Columns	113
Reading direction	forward
Mean pairwise identity	88.20
Mean single sequence MFE	-26.21
Consensus MFE	-21.27
Energy contribution	-21.17
Covariance contribution	-0.10
Combinations/Pair	1.15
Mean z-score	-2.09
Structure conservation index	0.81
SVM decision value	0.32
SVM RNA-class probability	0.686980
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17246750 113 + 27905053
UGCGAGAAGUUGGAAAAAUGCCACUUGGCUACCAGCUGAGAGGCAGAAAAAGACAUUUGACUCAAAUAGAGUUGGCAUAAAAAGAUAAUCUUAUUUAAAUUUAUUAAAUUCAA
...((((.(((.......((((.((..((.....))..)).))))......)))..(..((((.....))))..).............))))..................... ( -24.42)
>DroEre_CAF1 43888 113 + 1
CGCGAGAAGGUGGAAAAAUGCCACUUGGCUACCAGCUGAGAGGCACCAAAACCCAUUUGACUCAAAUAGCGUUGGCAUAAAAAGAUAGACCUAUGUAAAUGUAUCUACUUCAA
...(((.((((((.....((((.((..((.....))..)).)))).......))))))..))).....(((((.(((((............))))).)))))........... ( -27.50)
>DroYak_CAF1 65942 113 + 1
CUCGGGAAGGUGGAAAAAUGCCACUUGGCUACCAGCUGAGAGGCACCAAAAGCCAUUUGACUCAAAUAGAGUCGGCAUAAAAAGAUGAACUUAUUUAAAAUUAUUAAAUUCAA
....((....(((.....((((.((..((.....))..)).)))))))....))..(((((((.....)))))))..........((((.(((...........))).)))). ( -26.70)
>consensus
CGCGAGAAGGUGGAAAAAUGCCACUUGGCUACCAGCUGAGAGGCACCAAAAGCCAUUUGACUCAAAUAGAGUUGGCAUAAAAAGAUAAACUUAUUUAAAUUUAUUAAAUUCAA
...(((.((((((.....((((.((..((.....))..)).)))).......))))))..)))((((((..(((.(.......).)))..))))))................. (-21.27 = -21.17 +  -0.10)

alignment

secondary structure

dotplot

Window 5

Location	17,246,863 – 17,246,974
Length	111
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	75.49
Mean single sequence MFE	-22.41
Consensus MFE	-1.60
Energy contribution	-2.28
Covariance contribution	0.68
Combinations/Pair	1.11
Mean z-score	-1.61
Structure conservation index	0.07
SVM decision value	0.59
SVM RNA-class probability	0.792461
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17246863 111 - 27905053
GAUUUGAAACUUAAAACUUUACAAUUUAAUACAUGCUUAUGUUGCAA-----CAAUCAUAAGUAAAAUUGAAGGAAACGUCAAGUAUUAUCUGAGAGUUUUGUGUUGCGAUACCUA
...(((.(((.(((((((((.((...((((((.(((((((((((...-----))).))))))))...((((.(....).))))))))))..))))))))))).))).)))...... ( -27.60)
>DroSec_CAF1 43249 110 - 1
GAUUUGGAACUUA-AACUUUACAAUUGAAUACAGGUUUACGUUGCAA-----CAACGAGAUUGUAGAUUGAAGGAAACAUCAAGUAUUAUCUGAGAAUUUUGUGUUGCGAUACCUA
.....((....((-(((((.............))))))).(((((((-----((.(((((((.((((((((.(....).)))......)))))..)))))))))))))))).)).. ( -25.42)
>DroSim_CAF1 43933 111 - 1
AAUUUGCAACUUAAAACUUUACAAUUUAUUACAGGUUUAAGUUGCAA-----UAACGAGAUGGUAGAUUAAAGGAAACAUCCAGUAUUAUCUGAGAAUUUUGUGUUGCGAUACCUA
...((((((((((((.((.((........)).)).))))))))))))-----..(((((((..(((((((..(((....)))..))..)))))...)))))))............. ( -23.80)
>DroEre_CAF1 44001 116 - 1
GACUUGCAACUUAAAACUUUAGAGUGUAAUACAUCUUUAUGUAUUAAAUUAUUAAACAUGCAUAAGAUUGAAGGAAACACCAAGUAUUGUCUGAGAAUUUAGUGCUGCGAUACCUA
...(((((.((((((..((((((...((((((.((((.((((((.............))))))))))(((..(....)..)))))))))))))))..))))).).)))))...... ( -20.42)
>DroYak_CAF1 66055 99 - 1
GAUUUGCAACUUAAAACUUUAG------------CUUUAUGUUGCAA-----CAACCAUAACUUAGAUUGAAGAAAACACCAAGUAUUGUCAGAGAAACUCGGCCUACGAUACCAC
...(((((((.((((.(....)------------.)))).)))))))-----...............................(((((((..(((...))).....)))))))... ( -14.80)
>consensus
GAUUUGCAACUUAAAACUUUACAAUUUAAUACAGGUUUAUGUUGCAA_____CAACCAUAAGUUAGAUUGAAGGAAACAUCAAGUAUUAUCUGAGAAUUUUGUGUUGCGAUACCUA
........................................((((((..........................(....)....((......)).............))))))..... ( -1.60 =  -2.28 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:58 2006