Locus 4536

Sequence ID	3R_DroMel_CAF1
Location	12,034,117 – 12,034,235
Length	118
Max. P	0.953300

overview

Window 4

Location	12,034,117 – 12,034,235
Length	118
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	95.25
Mean single sequence MFE	-38.22
Consensus MFE	-34.57
Energy contribution	-34.78
Covariance contribution	0.21
Combinations/Pair	1.03
Mean z-score	-1.56
Structure conservation index	0.90
SVM decision value	1.43
SVM RNA-class probability	0.953300
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12034117 118 + 27905053
UGGGGCAGAAGGUUGACGGUGGCUGGGCUGGUUGCUUGGCCAAGUGGAUGGGGGGCAGCAACGACGAAACGUCGAAAGAAAACAAGAAACUCCAGCAGCAGUGGCCCAAGGGGAUGGG
..((((.....((((((..((((..(((.....)))..)))).))...((((((....)..(((((...)))))...............))))).))))....))))........... ( -38.30)
>DroSec_CAF1 5505 118 + 1
UGGGGCAGAAGGUUGACGGUGGCUGGGCUGGUUGCUUGGCCAAGUGGAUGGGGGGCAGCAACGACGAAACGUCGAAAGAAAACAAGAAACUCCAGCAGCAGUGGCCCAAGGGGAUGGG
..((((.....((((((..((((..(((.....)))..)))).))...((((((....)..(((((...)))))...............))))).))))....))))........... ( -38.30)
>DroSim_CAF1 5525 118 + 1
UGGGGCAGAAGGCUGACGGUGGCUGGGCUGGUUGCUUGGCCAAGUGGAUGGGGGGCAGCAACGACGAAACGUCGAAAGAAAACAAGAAACUCCAGCAGCAGUGGCCCAAGGGGAUGGG
..((((.....((((((..((((..(((.....)))..)))).))...((((((....)..(((((...)))))...............))))).))))....))))........... ( -40.70)
>DroEre_CAF1 4714 110 + 1
UGGGGCAGAAGGUUGACGGUGGCUGGGCUGGCUGCUUG--------GAUGGGGGGCAGCAACGACGAAACGUCGAAAGAAAACAAGAAACUCCAGCAGCAGUGGCCCAAGAGGAUGGG
((((.((...(.....).((.(((((((((.((.((..--------...)).)).))))..(((((...))))).................))))).))..)).)))).......... ( -35.70)
>DroYak_CAF1 4941 118 + 1
UGGGGCAGAAGGUUGACGGUGGCUGGGCUGGCAGCUUGGCCAAGUGGAGGGGGGGCAGCAACGACGAAACGUCGAAAGAAAACAAGAAACUCCAGCAGCAGUGGCCCAAGAGGAUGGG
..((((.....((((.(..((((..(((.....)))..))))..(((((..(......)..(((((...)))))...............))))))))))....))))........... ( -38.10)
>consensus
UGGGGCAGAAGGUUGACGGUGGCUGGGCUGGUUGCUUGGCCAAGUGGAUGGGGGGCAGCAACGACGAAACGUCGAAAGAAAACAAGAAACUCCAGCAGCAGUGGCCCAAGGGGAUGGG
((((.((...(.....).((.(((((((((.((.((...((....))..)).)).))))..(((((...))))).................))))).))..)).)))).......... (-34.57 = -34.78 +   0.21)

alignment

secondary structure

dotplot

Window 5

Location	12,034,117 – 12,034,235
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	95.25
Mean single sequence MFE	-27.55
Consensus MFE	-24.30
Energy contribution	-24.86
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-1.17
Structure conservation index	0.88
SVM decision value	-0.05
SVM RNA-class probability	0.505882
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12034117 118 - 27905053
CCCAUCCCCUUGGGCCACUGCUGCUGGAGUUUCUUGUUUUCUUUCGACGUUUCGUCGUUGCUGCCCCCCAUCCACUUGGCCAAGCAACCAGCCCAGCCACCGUCAACCUUCUGCCCCA
((((......))))........(((((.(((..............((((...))))((((((.....(((......)))...)))))).))))))))..................... ( -27.70)
>DroSec_CAF1 5505 118 - 1
CCCAUCCCCUUGGGCCACUGCUGCUGGAGUUUCUUGUUUUCUUUCGACGUUUCGUCGUUGCUGCCCCCCAUCCACUUGGCCAAGCAACCAGCCCAGCCACCGUCAACCUUCUGCCCCA
((((......))))........(((((.(((..............((((...))))((((((.....(((......)))...)))))).))))))))..................... ( -27.70)
>DroSim_CAF1 5525 118 - 1
CCCAUCCCCUUGGGCCACUGCUGCUGGAGUUUCUUGUUUUCUUUCGACGUUUCGUCGUUGCUGCCCCCCAUCCACUUGGCCAAGCAACCAGCCCAGCCACCGUCAGCCUUCUGCCCCA
...........((((....((((((((.(((..............((((...))))((((((.....(((......)))...)))))).)))))))).......))).....)))).. ( -30.41)
>DroEre_CAF1 4714 110 - 1
CCCAUCCUCUUGGGCCACUGCUGCUGGAGUUUCUUGUUUUCUUUCGACGUUUCGUCGUUGCUGCCCCCCAUC--------CAAGCAGCCAGCCCAGCCACCGUCAACCUUCUGCCCCA
.........((((((....(((((((((.......((.......(((((...))))).....))......))--------).))))))..))))))...................... ( -27.22)
>DroYak_CAF1 4941 118 - 1
CCCAUCCUCUUGGGCCACUGCUGCUGGAGUUUCUUGUUUUCUUUCGACGUUUCGUCGUUGCUGCCCCCCCUCCACUUGGCCAAGCUGCCAGCCCAGCCACCGUCAACCUUCUGCCCCA
((((......)))).....(((((((((((((............(((((...))))).....(((............))).))))).)))))..)))..................... ( -24.70)
>consensus
CCCAUCCCCUUGGGCCACUGCUGCUGGAGUUUCUUGUUUUCUUUCGACGUUUCGUCGUUGCUGCCCCCCAUCCACUUGGCCAAGCAACCAGCCCAGCCACCGUCAACCUUCUGCCCCA
((((......))))........(((((.(((..............((((...))))(((((((((............)))..)))))).))))))))..................... (-24.30 = -24.86 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:41 2006