Locus 2400

Sequence ID	3R_DroMel_CAF1
Location	6,750,236 – 6,750,494
Length	258
Max. P	0.828196

overview

Window 8

Location	6,750,236 – 6,750,349
Length	113
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.13
Mean single sequence MFE	-28.77
Consensus MFE	-22.01
Energy contribution	-21.82
Covariance contribution	-0.19
Combinations/Pair	1.03
Mean z-score	-2.02
Structure conservation index	0.76
SVM decision value	-0.02
SVM RNA-class probability	0.522313
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6750236 113 + 27905053
ACACAUUCUGAAUGUUUUAUUAGAUUUGGGUGGAGUGAAAGUUUACCAGACAAAUUCACCUCCGAAAGAGGAUAU----AUGCGCAAAUGUGUAUCCCUAUCAGG---ACCAACCAAGUU
......................(((((((.(((.(((((.(((.....)))...))))).(((((.((.((((((----((........)))))))))).)).))---)))).))))))) ( -28.10)
>DroSec_CAF1 14472 113 + 1
ACACAUUCUGAAUGUUUUAUUAGAUUUGGGUGGAGUGAAAGUUUAGCAGACAAAUUCACCUCCGAAAGAGGAUAU----AUGUGCAAAUGUGUAUUCCUAUCAGG---ACCAACCAAGUU
......................(((((((.(((.(((((.(((.....)))...))))).(((((.((.((((((----((((....)))))))))))).)).))---)))).))))))) ( -27.00)
>DroSim_CAF1 18803 113 + 1
ACACAUUCUGAAUGUUUUAUUAGAUUUGGGUGGAGUGAAAGUUUAGCAGACAAAUUCACCUCCGAAAGAGGAUAU----AUGUGCAAAUGUGUAUCCCUAUCAGG---ACCAACCAAGUU
......................(((((((.(((.(((((.(((.....)))...))))).(((((.((.((((((----((((....)))))))))))).)).))---)))).))))))) ( -29.90)
>DroYak_CAF1 10657 120 + 1
ACACAUUCUGAAUGUUUUAUUAGAUUUGGGUGGAGUGAAAGUUUACCAGACAAAUUCACCUCCGAAAGUGGAUAUACAUAUGCACAAAUGUGUAUCCCUAUCAGACCAACCAACCAAGUU
......................(((((((..((((((((.(((.....)))...)))).))))((.((.((((((((((........)))))))))))).))...........))))))) ( -30.10)
>consensus
ACACAUUCUGAAUGUUUUAUUAGAUUUGGGUGGAGUGAAAGUUUACCAGACAAAUUCACCUCCGAAAGAGGAUAU____AUGCGCAAAUGUGUAUCCCUAUCAGG___ACCAACCAAGUU
......................(((((((..((((((((.(((.....)))...)))).))))((.((.((((((....((......))..)))))))).))...........))))))) (-22.01 = -21.82 +  -0.19)

alignment

secondary structure

dotplot

Window 9

Location	6,750,349 – 6,750,454
Length	105
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.44
Mean single sequence MFE	-41.45
Consensus MFE	-27.27
Energy contribution	-27.53
Covariance contribution	0.25
Combinations/Pair	1.09
Mean z-score	-4.98
Structure conservation index	0.66
SVM decision value	0.56
SVM RNA-class probability	0.780564
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6750349 105 - 27905053
ACUGGCUUUAGCUCACCAAUGAGAA-------GGUGUUGGUUACCAUUCGGUAGC--------CAAUAUCUCUCUGGACAAAAUAACAAAAGUUGGCAAAUAAGCUAAAGUUGGCCACAG
.(..(((((((((..(((..((((.-------(((((((((((((....))))))--------))))))))))))))......((((....)))).......)))))))))..)...... ( -41.90)
>DroSec_CAF1 14585 105 - 1
ACUGGCUUUAGCCCACCAACGAGAA-------GGUGUUGGUUGCCAUUCGGUAGC--------CAAUAUCUCUCUGGACAAAAUAACAAAAGUUGGCAAAUAAGCUGAAGUUGGCCACAG
.(..((((((((...(((((((((.-------(((((((((((((....))))))--------)))))))))))((..........))...))))).......))))))))..)...... ( -41.50)
>DroSim_CAF1 18916 105 - 1
ACUGGCUUUAGCCCACCAACGAGAA-------GGUGUUGGUUACCAUUCGGUAGC--------CAAUAUCUCUCUGGACAAAAUAACAAAAGUUGGCAAAUAAGCUAAAGUUGGCCACAG
.(..((((((((...(((((((((.-------(((((((((((((....))))))--------)))))))))))((..........))...))))).......))))))))..)...... ( -41.40)
>DroYak_CAF1 10777 120 - 1
GCUGGCUUCGGCCCACAUACGAGAAGGUGGAAGGUGUUGGUUACCAUUGGGUAGCCGGGUAACCAAUAUCUCUCUGGACCAAAUAACAAAAGUUGGCAAAUAAGCUAAAGUUGGCCACAG
((..((((..((.............((((((((((((((((((((...((....)).)))))))))))))).)))..)))...((((....))))........))..))))..))..... ( -41.00)
>consensus
ACUGGCUUUAGCCCACCAACGAGAA_______GGUGUUGGUUACCAUUCGGUAGC________CAAUAUCUCUCUGGACAAAAUAACAAAAGUUGGCAAAUAAGCUAAAGUUGGCCACAG
.(..((((((((...(((..((((........(((((((((((((....))))))........))))))))))))))......((((....))))........))))))))..)...... (-27.27 = -27.53 +   0.25)

alignment

secondary structure

dotplot

Window 0

Location	6,750,389 – 6,750,494
Length	105
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.67
Mean single sequence MFE	-37.31
Consensus MFE	-23.11
Energy contribution	-22.93
Covariance contribution	-0.19
Combinations/Pair	1.15
Mean z-score	-3.01
Structure conservation index	0.62
SVM decision value	0.71
SVM RNA-class probability	0.828196
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6750389 105 - 27905053
UUUGUUGGCAAAUGAAUUCCAAUUGCUGCACCGUGAAGUAACUGGCUUUAGCUCACCAAUGAGAA-------GGUGUUGGUUACCAUUCGGUAGC--------CAAUAUCUCUCUGGACA
..(((.(((((.((.....)).))))))))...((((((.....)))))).....(((..((((.-------(((((((((((((....))))))--------))))))))))))))... ( -35.10)
>DroSec_CAF1 14625 105 - 1
UUUGUUGGCAAAUGAAUUCCAAUUGCUGCACCUCGAAGUAACUGGCUUUAGCCCACCAACGAGAA-------GGUGUUGGUUGCCAUUCGGUAGC--------CAAUAUCUCUCUGGACA
...(((((......((..(((.(((((.........))))).)))..))......)))))((((.-------(((((((((((((....))))))--------)))))))))))...... ( -37.30)
>DroSim_CAF1 18956 105 - 1
UUUGUUGGCAAAUGAAUUCCAAUUGCUGCACCUCGAAGUAACUGGCUUUAGCCCACCAACGAGAA-------GGUGUUGGUUACCAUUCGGUAGC--------CAAUAUCUCUCUGGACA
...(((((......((..(((.(((((.........))))).)))..))......)))))((((.-------(((((((((((((....))))))--------)))))))))))...... ( -37.30)
>DroYak_CAF1 10817 120 - 1
UUUGUUGGCAAAUGAAUUCCAAUUGCUGCAUUUCGAAGGAGCUGGCUUCGGCCCACAUACGAGAAGGUGGAAGGUGUUGGUUACCAUUGGGUAGCCGGGUAACCAAUAUCUCUCUGGACC
..(((.(((((.((.....)).))))))))(((((........(((....)))......))))).((((((((((((((((((((...((....)).)))))))))))))).)))..))) ( -39.54)
>consensus
UUUGUUGGCAAAUGAAUUCCAAUUGCUGCACCUCGAAGUAACUGGCUUUAGCCCACCAACGAGAA_______GGUGUUGGUUACCAUUCGGUAGC________CAAUAUCUCUCUGGACA
...(((((....((((..(((.(((((.........))))).))).)))).....)))))((((........(((((((((((((....))))))........)))))))))))...... (-23.11 = -22.93 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:40 2006