Locus 1931

Sequence ID	2R_DroMel_CAF1
Location	7,282,440 – 7,282,539
Length	99
Max. P	0.799603

overview

Window 1

Location	7,282,440 – 7,282,539
Length	99
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	79.40
Mean single sequence MFE	-25.66
Consensus MFE	-14.92
Energy contribution	-15.20
Covariance contribution	0.28
Combinations/Pair	1.09
Mean z-score	-2.02
Structure conservation index	0.58
SVM decision value	0.61
SVM RNA-class probability	0.799603
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7282440 99 + 20766785
UGGCGGUGGCAAAUUGAAAACAAUUUUAGCUAUUUGCAUAUAAAUGCAACUUGAGACGCUGCCAACCAGCAGCCG-----CAACAAAAGCAGCAACAACUGCUG
..((((((((((((((....))))))..)))))((((((....))))))........(((((......)))))))-----)......(((((......))))). ( -28.40)
>DroPse_CAF1 66332 99 + 1
GGACAGUGGCAAAUUGAAAACAAUUUUAGUUAUUUGCAUAUAAAUGCAACUUGAGACGGCGGCGGCAGGCGGCAC-----GGGGUGGAGGAGGCUCUAAGGGAU
....((((((((((((....))))))..))))))(((((....))))).(((....((((.((.....)).)).)-----)...(((((....))))))))... ( -20.30)
>DroSec_CAF1 78340 99 + 1
UGGCGGUGGCAAAUUGAAAACAAUUUUAGCUAUUUGCAUAUAAAUGCAACCUGAGACGCUGCCAACCAGCAGCCG-----CAACAAAAGCAGCAACAACUGCGG
((((((((((((((((....))))))..))...((((((....)))))).......)))))))).((.((....)-----).......((((......)))))) ( -28.70)
>DroSim_CAF1 81815 99 + 1
UGGCGGUGGCAAAUUGAAAACAAUUUUAGCUAUUUGCAUAUAAAUGCAACCUGAGACGCUGCCAACCAGCAGCCG-----CAACAAAAGCAACAACAACUGCGG
((((((((((((((((....))))))..))...((((((....)))))).......))))))))........(((-----((.................))))) ( -25.93)
>DroEre_CAF1 78156 104 + 1
UGGCGGUGGCAAAUUGAAAACAAUUUUAGCUAUUUGCAUAUAAAUGCAACCUGAGACGCUGCCAACCAGCAGCAGCCGACCAACAAAAGCUGCCACAACUGCGG
.((..(((((((((((....)))))).((((..((((((....))))))........(((((......)))))..............)))))))))..)).... ( -29.80)
>DroAna_CAF1 73645 80 + 1
UGGCGGUGGCAAAUUGAAAACAAUUUUAGAUAUUUGCAUAUAAAUGAAACCUGAGAAGCUGCCAACCGGCAGCUG-----CAAUA-------------------
..(((((.(((((((((((....)))))...))))))...........))).....(((((((....))))))))-----)....------------------- ( -20.80)
>consensus
UGGCGGUGGCAAAUUGAAAACAAUUUUAGCUAUUUGCAUAUAAAUGCAACCUGAGACGCUGCCAACCAGCAGCCG_____CAACAAAAGCAGCAACAACUGCGG
.....(((((((((((....))))))..)))))((((((....))))))........(((((......)))))............................... (-14.92 = -15.20 +   0.28)

alignment

secondary structure

dotplot

Window 2

Location	7,282,440 – 7,282,539
Length	99
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	79.40
Mean single sequence MFE	-26.70
Consensus MFE	-15.60
Energy contribution	-15.55
Covariance contribution	-0.05
Combinations/Pair	1.15
Mean z-score	-1.91
Structure conservation index	0.58
SVM decision value	0.48
SVM RNA-class probability	0.751874
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7282440 99 - 20766785
CAGCAGUUGUUGCUGCUUUUGUUG-----CGGCUGCUGGUUGGCAGCGUCUCAAGUUGCAUUUAUAUGCAAAUAGCUAAAAUUGUUUUCAAUUUGCCACCGCCA
.(((((((((.((.......)).)-----))))))))((((((((((........((((((....))))))...))).((((((....))))))))))..))). ( -33.10)
>DroPse_CAF1 66332 99 - 1
AUCCCUUAGAGCCUCCUCCACCCC-----GUGCCGCCUGCCGCCGCCGUCUCAAGUUGCAUUUAUAUGCAAAUAACUAAAAUUGUUUUCAAUUUGCCACUGUCC
......(((..............(-----(.((.((.....)).)))).......((((((....))))))....)))((((((....)))))).......... ( -13.00)
>DroSec_CAF1 78340 99 - 1
CCGCAGUUGUUGCUGCUUUUGUUG-----CGGCUGCUGGUUGGCAGCGUCUCAGGUUGCAUUUAUAUGCAAAUAGCUAAAAUUGUUUUCAAUUUGCCACCGCCA
..((((((((.((.......)).)-----))))))).((((((((((........((((((....))))))...))).((((((....))))))))))..))). ( -32.00)
>DroSim_CAF1 81815 99 - 1
CCGCAGUUGUUGUUGCUUUUGUUG-----CGGCUGCUGGUUGGCAGCGUCUCAGGUUGCAUUUAUAUGCAAAUAGCUAAAAUUGUUUUCAAUUUGCCACCGCCA
..((((((((....((....)).)-----))))))).((((((((((........((((((....))))))...))).((((((....))))))))))..))). ( -30.70)
>DroEre_CAF1 78156 104 - 1
CCGCAGUUGUGGCAGCUUUUGUUGGUCGGCUGCUGCUGGUUGGCAGCGUCUCAGGUUGCAUUUAUAUGCAAAUAGCUAAAAUUGUUUUCAAUUUGCCACCGCCA
..(((((((.(.((((....)))).)))))))).((.(((.((((((........((((((....))))))...))).((((((....)))))))))))))).. ( -33.70)
>DroAna_CAF1 73645 80 - 1
-------------------UAUUG-----CAGCUGCCGGUUGGCAGCUUCUCAGGUUUCAUUUAUAUGCAAAUAUCUAAAAUUGUUUUCAAUUUGCCACCGCCA
-------------------....(-----((((((((....))))))).....(((.......((((....))))...((((((....)))))))))...)).. ( -17.70)
>consensus
CCGCAGUUGUUGCUGCUUUUGUUG_____CGGCUGCUGGUUGGCAGCGUCUCAGGUUGCAUUUAUAUGCAAAUAGCUAAAAUUGUUUUCAAUUUGCCACCGCCA
...............................((((((....))))))......((((((((....)))))........((((((....))))))...))).... (-15.60 = -15.55 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:38 2006