Locus 2303

Sequence ID	3L_DroMel_CAF1
Location	6,478,364 – 6,478,459
Length	95
Max. P	0.968336

overview

Window 7

Location	6,478,364 – 6,478,459
Length	95
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	80.09
Mean single sequence MFE	-26.15
Consensus MFE	-17.32
Energy contribution	-19.08
Covariance contribution	1.77
Combinations/Pair	1.16
Mean z-score	-2.94
Structure conservation index	0.66
SVM decision value	1.53
SVM RNA-class probability	0.961970
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6478364 95 + 23771897
UAGAGAGUAUGGACCAGUGCGGACCAUGGUCCAAAAGCGUUCGAACUUUGAAUCCUUGACAAGCUCAAAAAAAUUGGACGCUUCAUGAGUGCAAA
......((((((((((..........))))))..((((((((((..(((((.............)))))....)))))))))).....))))... ( -24.32)
>DroSec_CAF1 12909 84 + 1
UAGAGAGUAUGGA----------CCAUGGUCCAAAAGCGUUCGAACUUUGAAUCCUUGACAAGUUCAAA-AAUUCGGACGCUUCAUGAGUGCAAA
......(((((((----------(....))))..(((((((((((.(((((((.........)))))))-..))))))))))).....))))... ( -27.60)
>DroSim_CAF1 12999 83 + 1
UAGAGAGUAUGGA----------CCAUGGUCCAAAAGCGUUCGAACUUUGAAUCCUUGACAAGUUCAAA-AAUUCGGGCGCUUCAUGAGUGCAA-
......(((((((----------(....))))..(((((((((((.(((((((.........)))))))-..))))))))))).....))))..- ( -27.10)
>DroEre_CAF1 13520 91 + 1
UAGAGAGCG---ACCAAUAUGGACCAUGGUCCAAAAGCGUUCGAACUUUGAAUCCUUGACAAGUUCAAA-AAUUCGGACGCUUCAUGAGUGCAAA
......(((---..((...(((((....))))).(((((((((((.(((((((.........)))))))-..)))))))))))..))..)))... ( -30.10)
>DroYak_CAF1 13485 91 + 1
UAGAGAGCA---ACCUAUAUGGACCAUGGUCCAAAAGCGUUCGAACUUUGAAUCCUUGACAAGUUCAAA-UAUUCGGACGCUUCAUGAGUGCAAA
......(((---..(....(((((....))))).(((((((((((.(((((((.........)))))))-..)))))))))))...)..)))... ( -29.10)
>DroAna_CAF1 14147 74 + 1
UGGUG-------ACCAAUAUGGACCAUGGUCCG-AAGCGUUCGAACUUUGAAUCCUUGACAAGUUCAAA-AAUUCGGCCA------------GAA
((((.-------.((.....))))))(((.(((-((...((.((((((............)))))).))-..))))))))------------... ( -18.70)
>consensus
UAGAGAGUA___ACCAAUAUGGACCAUGGUCCAAAAGCGUUCGAACUUUGAAUCCUUGACAAGUUCAAA_AAUUCGGACGCUUCAUGAGUGCAAA
......(((...........((((....))))..(((((((((((.(((((((.........)))))))...)))))))))))......)))... (-17.32 = -19.08 +   1.77)

alignment

secondary structure

dotplot

Window 8

Location	6,478,364 – 6,478,459
Length	95
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	80.09
Mean single sequence MFE	-26.13
Consensus MFE	-16.64
Energy contribution	-18.57
Covariance contribution	1.93
Combinations/Pair	1.08
Mean z-score	-3.13
Structure conservation index	0.64
SVM decision value	1.62
SVM RNA-class probability	0.968336
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6478364 95 - 23771897
UUUGCACUCAUGAAGCGUCCAAUUUUUUUGAGCUUGUCAAGGAUUCAAAGUUCGAACGCUUUUGGACCAUGGUCCGCACUGGUCCAUACUCUCUA
...........(((((((.(.....((((((((((....))).)))))))...).)))))))(((((((((.....)).)))))))......... ( -23.30)
>DroSec_CAF1 12909 84 - 1
UUUGCACUCAUGAAGCGUCCGAAUU-UUUGAACUUGUCAAGGAUUCAAAGUUCGAACGCUUUUGGACCAUGG----------UCCAUACUCUCUA
...........(((((((.((((((-((.((((((....))).))))))))))).)))))))(((((....)----------))))......... ( -26.60)
>DroSim_CAF1 12999 83 - 1
-UUGCACUCAUGAAGCGCCCGAAUU-UUUGAACUUGUCAAGGAUUCAAAGUUCGAACGCUUUUGGACCAUGG----------UCCAUACUCUCUA
-..........((((((..((((((-((.((((((....))).)))))))))))..))))))(((((....)----------))))......... ( -24.60)
>DroEre_CAF1 13520 91 - 1
UUUGCACUCAUGAAGCGUCCGAAUU-UUUGAACUUGUCAAGGAUUCAAAGUUCGAACGCUUUUGGACCAUGGUCCAUAUUGGU---CGCUCUCUA
...(((((.(((((((((.((((((-((.((((((....))).))))))))))).)))))).(((((....)))))))).)))---.))...... ( -29.10)
>DroYak_CAF1 13485 91 - 1
UUUGCACUCAUGAAGCGUCCGAAUA-UUUGAACUUGUCAAGGAUUCAAAGUUCGAACGCUUUUGGACCAUGGUCCAUAUAGGU---UGCUCUCUA
...(((..(..(((((((.(((((.-(((((((((....))).))))))))))).)))))))(((((....)))))....)..---)))...... ( -30.50)
>DroAna_CAF1 14147 74 - 1
UUC------------UGGCCGAAUU-UUUGAACUUGUCAAGGAUUCAAAGUUCGAACGCUU-CGGACCAUGGUCCAUAUUGGU-------CACCA
...------------((((((((((-(((((.....))))))))))...............-.((((....)))).....)))-------))... ( -22.70)
>consensus
UUUGCACUCAUGAAGCGUCCGAAUU_UUUGAACUUGUCAAGGAUUCAAAGUUCGAACGCUUUUGGACCAUGGUCCAUAUUGGU___UACUCUCUA
...........(((((((.(((((..(((((((((....))).))))))))))).))))))).((((....)))).................... (-16.64 = -18.57 +   1.93)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:05 2006