Locus 1635

Sequence ID	3L_DroMel_CAF1
Location	4,760,079 – 4,760,176
Length	97
Max. P	0.985502

overview

Window 1

Location	4,760,079 – 4,760,176
Length	97
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	97.96
Mean single sequence MFE	-30.90
Consensus MFE	-28.60
Energy contribution	-28.60
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.65
Structure conservation index	0.93
SVM decision value	1.44
SVM RNA-class probability	0.954394
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4760079 97 + 23771897
U--GUGGGUGCGUUUGUUUGCUUACGAAACAACUUGAAGUUGUUG-GCCCUAAGUUGCUAGUAGCUGUUGUGGCUGUCGCUCGUAGGUUCUUGCUCCGUU
.--...((.(((...(...((((((((((((((.....))))))(-((((..(((((....)))))...).)))).....)))))))).).))).))... ( -29.90)
>DroSec_CAF1 22791 97 + 1
U--GUGGGUGCGUUUGUUUGCUUACGAAACAACUUGAAGUUGUUG-GCCCUAAGUUGCUAGUAGCUGUUGUGGCUGUCGCUCGUAGGUUCUUGCUCCGUU
.--...((.(((...(...((((((((((((((.....))))))(-((((..(((((....)))))...).)))).....)))))))).).))).))... ( -29.90)
>DroSim_CAF1 20094 97 + 1
U--GUGGGUGCGUUUGUUUGCUUACGAAACAACUUGAAGUUGUUG-GCCCUAAGUUGCUAGUAGCUGUUGUGGCUGUCGCUCGUAGGUUCUUGCUCCGUU
.--...((.(((...(...((((((((((((((.....))))))(-((((..(((((....)))))...).)))).....)))))))).).))).))... ( -29.90)
>DroEre_CAF1 12099 99 + 1
UGUGUGGGUGCGUUUGUUUGCUUACGAAACAACUUGAAGUUGUUG-GCCCUAAGUUGCUAGUAGCUGUUGUGGCUGUCGCUCGUAGGUUCUUGCUCCGUU
......((.(((...(...((((((((((((((.....))))))(-((((..(((((....)))))...).)))).....)))))))).).))).))... ( -29.90)
>DroYak_CAF1 18943 98 + 1
U--GCGGGUGCGUUUGUUUGCUUACGAAACAACUUGAAGUUGUUGGGCCCUAAGUUGCUAGUAGCUGUUGUGGCUGUCGCUCGUAGGUUCUUGCUCCGCU
.--(((((.(((...(...((((((((((((((.....)))))).(((((..(((((....)))))...).)))).....)))))))).).)))))))). ( -34.90)
>consensus
U__GUGGGUGCGUUUGUUUGCUUACGAAACAACUUGAAGUUGUUG_GCCCUAAGUUGCUAGUAGCUGUUGUGGCUGUCGCUCGUAGGUUCUUGCUCCGUU
......((.(((...(...((((((((((((((.....))))))..((((..(((((....)))))...).)))......)))))))).).))).))... (-28.60 = -28.60 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	4,760,079 – 4,760,176
Length	97
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	97.96
Mean single sequence MFE	-20.52
Consensus MFE	-19.80
Energy contribution	-19.80
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.71
Structure conservation index	0.96
SVM decision value	2.01
SVM RNA-class probability	0.985502
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4760079 97 - 23771897
AACGGAGCAAGAACCUACGAGCGACAGCCACAACAGCUACUAGCAACUUAGGGC-CAACAACUUCAAGUUGUUUCGUAAGCAAACAAACGCACCCAC--A
...((.((..........(.((....)))......(((((.((((((((..((.-......))..))))))))..)).)))........)).))...--. ( -19.50)
>DroSec_CAF1 22791 97 - 1
AACGGAGCAAGAACCUACGAGCGACAGCCACAACAGCUACUAGCAACUUAGGGC-CAACAACUUCAAGUUGUUUCGUAAGCAAACAAACGCACCCAC--A
...((.((..........(.((....)))......(((((.((((((((..((.-......))..))))))))..)).)))........)).))...--. ( -19.50)
>DroSim_CAF1 20094 97 - 1
AACGGAGCAAGAACCUACGAGCGACAGCCACAACAGCUACUAGCAACUUAGGGC-CAACAACUUCAAGUUGUUUCGUAAGCAAACAAACGCACCCAC--A
...((.((..........(.((....)))......(((((.((((((((..((.-......))..))))))))..)).)))........)).))...--. ( -19.50)
>DroEre_CAF1 12099 99 - 1
AACGGAGCAAGAACCUACGAGCGACAGCCACAACAGCUACUAGCAACUUAGGGC-CAACAACUUCAAGUUGUUUCGUAAGCAAACAAACGCACCCACACA
...((.((..........(.((....)))......(((((.((((((((..((.-......))..))))))))..)).)))........)).))...... ( -19.50)
>DroYak_CAF1 18943 98 - 1
AGCGGAGCAAGAACCUACGAGCGACAGCCACAACAGCUACUAGCAACUUAGGGCCCAACAACUUCAAGUUGUUUCGUAAGCAAACAAACGCACCCGC--A
.((((.((..........(.((....)))......(((((.((((((((..((........))..))))))))..)).)))........))..))))--. ( -24.60)
>consensus
AACGGAGCAAGAACCUACGAGCGACAGCCACAACAGCUACUAGCAACUUAGGGC_CAACAACUUCAAGUUGUUUCGUAAGCAAACAAACGCACCCAC__A
...((.((..........(.((....)))......(((((.((((((((..((........))..))))))))..)).)))........)).))...... (-19.80 = -19.80 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:31 2006