Locus 5824

Sequence ID	X_DroMel_CAF1
Location	15,070,971 – 15,071,069
Length	98
Max. P	0.808912

overview

Window 0

Location	15,070,971 – 15,071,069
Length	98
Sequences	4
Columns	109
Reading direction	forward
Mean pairwise identity	87.38
Mean single sequence MFE	-32.58
Consensus MFE	-25.15
Energy contribution	-25.40
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.86
Structure conservation index	0.77
SVM decision value	0.63
SVM RNA-class probability	0.805182
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15070971 98 + 22224390
AAGGAAGCAGG----------GAGGAAG-CAGACUGUCAAUUACCAGUCGGGGCUAUAAAUUGCAUGUCAGUUGCUCAGAGCCCAACUUCCAUAGCAUCCCAUCCCAGC
......((.((----------(((((.(-(.(((((........))))).(((((.......(((.......)))....)))))..........)).)))..)))).)) ( -31.10)
>DroSec_CAF1 32044 97 + 1
AAGGAAGCAGG----------GAGG-GG-CCGACUGUCAAUUACCAGUCGGGGCUAUAAAUUGCAUGUCAGUUGCUCAGAGCCCAACUUCCAUAGCAUCCCAUCCCAAC
..(((.((..(----------((((-..-.((((((........))))))(((((.......(((.......)))....)))))..)))))...)).)))......... ( -33.10)
>DroSim_CAF1 18359 97 + 1
AAGGAAGCGGG----------GAGG-GG-CCGACUGUCAAUUACCAGUCGGGGCUAUAAAUUGCAUGUCAGUUGCUCAGAGCCCAACUUCCAUAGCAUCCCAUCCCAGC
..(((.((..(----------((((-..-.((((((........))))))(((((.......(((.......)))....)))))..)))))...)).)))......... ( -34.20)
>DroYak_CAF1 25451 102 + 1
AAGGAAGCAGGAGUGCGCGGGAAAG-GGA-CGACUGUCAAUUACCAGUCGGGGCUAUAAAUUGCAUGUCAGUUGCUCAGAGCCCAACUUCCAUGGCAUC-----CAAGC
.........(((.(((.((((((..-...-((((((........))))))(((((.......(((.......)))....)))))...)))).)))))))-----).... ( -31.90)
>consensus
AAGGAAGCAGG__________GAGG_GG_CCGACUGUCAAUUACCAGUCGGGGCUAUAAAUUGCAUGUCAGUUGCUCAGAGCCCAACUUCCAUAGCAUCCCAUCCCAGC
..(((((.......................((((((........))))))(((((.......(((.......)))....)))))..))))).................. (-25.15 = -25.40 +   0.25)

alignment

secondary structure

dotplot

Window 1

Location	15,070,971 – 15,071,069
Length	98
Sequences	4
Columns	109
Reading direction	reverse
Mean pairwise identity	87.38
Mean single sequence MFE	-34.70
Consensus MFE	-25.23
Energy contribution	-25.47
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.01
Structure conservation index	0.73
SVM decision value	0.64
SVM RNA-class probability	0.808912
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15070971 98 - 22224390
GCUGGGAUGGGAUGCUAUGGAAGUUGGGCUCUGAGCAACUGACAUGCAAUUUAUAGCCCCGACUGGUAAUUGACAGUCUG-CUUCCUC----------CCUGCUUCCUU
((.((((.((((.((..........(((((.((((((.......)))...))).))))).(((((........))))).)-)))))))----------)).))...... ( -32.70)
>DroSec_CAF1 32044 97 - 1
GUUGGGAUGGGAUGCUAUGGAAGUUGGGCUCUGAGCAACUGACAUGCAAUUUAUAGCCCCGACUGGUAAUUGACAGUCGG-CC-CCUC----------CCUGCUUCCUU
((.((((.(((.(((.(((..(((((.........)))))..))))))..........(((((((........)))))))-))-).))----------)).))...... ( -36.60)
>DroSim_CAF1 18359 97 - 1
GCUGGGAUGGGAUGCUAUGGAAGUUGGGCUCUGAGCAACUGACAUGCAAUUUAUAGCCCCGACUGGUAAUUGACAGUCGG-CC-CCUC----------CCCGCUUCCUU
((.((((.(((.(((.(((..(((((.........)))))..))))))..........(((((((........)))))))-))-).))----------)).))...... ( -38.20)
>DroYak_CAF1 25451 102 - 1
GCUUG-----GAUGCCAUGGAAGUUGGGCUCUGAGCAACUGACAUGCAAUUUAUAGCCCCGACUGGUAAUUGACAGUCG-UCC-CUUUCCCGCGCACUCCUGCUUCCUU
((..(-----(((((...(((((..(((((.((((((.......)))...))).)))))((((((........))))))-...-.)))))...))).))).))...... ( -31.30)
>consensus
GCUGGGAUGGGAUGCUAUGGAAGUUGGGCUCUGAGCAACUGACAUGCAAUUUAUAGCCCCGACUGGUAAUUGACAGUCGG_CC_CCUC__________CCUGCUUCCUU
..................((((((.(((((.((((((.......)))...))).)))))((((((........))))))......................)))))).. (-25.23 = -25.47 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:15 2006