Locus 2800

Sequence ID	3L_DroMel_CAF1
Location	7,962,711 – 7,962,871
Length	160
Max. P	0.999948

overview

Window 2

Location	7,962,711 – 7,962,831
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.00
Mean single sequence MFE	-35.94
Consensus MFE	-32.32
Energy contribution	-32.92
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.79
Structure conservation index	0.90
SVM decision value	2.09
SVM RNA-class probability	0.987713
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7962711 120 - 23771897
UUUUCGUUUUGGUGGCACUUGGUUGACUAUUAUUUUUCAUUUGGGGCGCUCGCAGCUCGCAGGCGGUCCAAGUGAAAAUUAUUUCAAGAUACUGGUAAAACGCAAAGGCACACGCAUAGA
(((((((((((.(((..(((((........((.((((((((((((.(((..((.....))..))).)))))))))))).))..)))))...))).))))))).))))((....))..... ( -35.90)
>DroSec_CAF1 5832 120 - 1
UUUUCGUUUUGGUGGCACUUAGUUGACUAUUAUUUUUCAUUUGGGGCGCUCGCAGCUCGCAGGCGGUCCAAGUGAAAAUUAUUUCAAGAUACUGGUAAAACGCAAAGGCACACGCAUAGA
(((((((((((.(((.......((((....((.((((((((((((.(((..((.....))..))).)))))))))))).))..))))....))).))))))).))))((....))..... ( -34.00)
>DroSim_CAF1 5845 120 - 1
UUUUCGUUUUGGUGGCACUUGGUUGACUAUUAUUUUUCAUUUGGGGCGCUCGCAGCUCGCAGGCGGUCCAAGUGAAAAUUAUUUCAAGAUACUGGUAAAACGCAAAGGCACACGCAUAGA
(((((((((((.(((..(((((........((.((((((((((((.(((..((.....))..))).)))))))))))).))..)))))...))).))))))).))))((....))..... ( -35.90)
>DroEre_CAF1 5995 119 - 1
-UUACGUUUUGGUGGCACUUGGUUGACUAUUAUUUUUCAUUUGGGGCGCUCGCAGCUCGCAGGCGGUCCAAGUGAAAAUUAUUUCAAGAUACUGGUAAAACGCACAGGCACACGCACAGC
-....(((.(((((((.(((((........((.((((((((((((.(((..((.....))..))).)))))))))))).))..)))))...(((((.....)).))))).))).)).))) ( -37.30)
>DroYak_CAF1 6369 112 - 1
-UUACGUUUUGGUGGCACUUGGUUGACUAUUAUUUUUCAUUUGGGCCGCU-------CGCAGGCGGUCCAAGUGAAAAUUAUUUCAAGAUACUGGUAAAACGCAAAGGCACACGCAUAGA
-...(((((((.(((..(((((........((.(((((((((((((((((-------....))))))))))))))))).))..)))))...))).))))))).....((....))..... ( -36.60)
>consensus
UUUUCGUUUUGGUGGCACUUGGUUGACUAUUAUUUUUCAUUUGGGGCGCUCGCAGCUCGCAGGCGGUCCAAGUGAAAAUUAUUUCAAGAUACUGGUAAAACGCAAAGGCACACGCAUAGA
....(((((((.(((..(((((........((.((((((((((((.((((.((.....)).)))).)))))))))))).))..)))))...))).))))))).....((....))..... (-32.32 = -32.92 +   0.60)

alignment

secondary structure

dotplot

Window 3

Location	7,962,751 – 7,962,871
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.66
Mean single sequence MFE	-39.93
Consensus MFE	-35.86
Energy contribution	-36.50
Covariance contribution	0.64
Combinations/Pair	1.05
Mean z-score	-3.37
Structure conservation index	0.90
SVM decision value	4.77
SVM RNA-class probability	0.999948
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7962751 120 - 23771897
CUCAGUUCACCAAUUCCAACAUAGAACCCAUGGAAGAUUUUUUUCGUUUUGGUGGCACUUGGUUGACUAUUAUUUUUCAUUUGGGGCGCUCGCAGCUCGCAGGCGGUCCAAGUGAAAAUU
...((((.(((((..(((...((((((....(((((....))))))))))).)))...))))).)))).....((((((((((((.(((..((.....))..))).)))))))))))).. ( -39.30)
>DroSec_CAF1 5872 120 - 1
CUCAGUCCACCAAUCCCAACAUAGAACCCAUGGAAGCUUUUUUUCGUUUUGGUGGCACUUAGUUGACUAUUAUUUUUCAUUUGGGGCGCUCGCAGCUCGCAGGCGGUCCAAGUGAAAAUU
((.((((((((((..(...(((.......)))((((.....)))))..))))))).))).))...........((((((((((((.(((..((.....))..))).)))))))))))).. ( -38.60)
>DroSim_CAF1 5885 120 - 1
CUCAGUCCACCAAUCCCAACAUAGAACCCAUGGAAGCUUUUUUUCGUUUUGGUGGCACUUGGUUGACUAUUAUUUUUCAUUUGGGGCGCUCGCAGCUCGCAGGCGGUCCAAGUGAAAAUU
...((((.(((((((........))..((((.(((((........))))).))))...))))).)))).....((((((((((((.(((..((.....))..))).)))))))))))).. ( -42.10)
>DroEre_CAF1 6035 119 - 1
CCCAGUUCACCAAUCCCAACAUAGAAUCCAUGGAAGCUUU-UUACGUUUUGGUGGCACUUGGUUGACUAUUAUUUUUCAUUUGGGGCGCUCGCAGCUCGCAGGCGGUCCAAGUGAAAAUU
...((((.(((((((........))..((((.(((((...-....))))).))))...))))).)))).....((((((((((((.(((..((.....))..))).)))))))))))).. ( -39.90)
>DroYak_CAF1 6409 112 - 1
CCCAGUUCACCAAUCCCAACAUACAACCCAUGGAAGCUUU-UUACGUUUUGGUGGCACUUGGUUGACUAUUAUUUUUCAUUUGGGCCGCU-------CGCAGGCGGUCCAAGUGAAAAUU
...((((.(((((..............((((.(((((...-....))))).))))...))))).)))).....(((((((((((((((((-------....))))))))))))))))).. ( -39.73)
>consensus
CUCAGUUCACCAAUCCCAACAUAGAACCCAUGGAAGCUUUUUUUCGUUUUGGUGGCACUUGGUUGACUAUUAUUUUUCAUUUGGGGCGCUCGCAGCUCGCAGGCGGUCCAAGUGAAAAUU
...((((.(((((((........))..((((.(((((........))))).))))...))))).)))).....((((((((((((.((((.((.....)).)))).)))))))))))).. (-35.86 = -36.50 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:01 2006