Locus 8579

Sequence ID	3R_DroMel_CAF1
Location	22,942,395 – 22,942,511
Length	116
Max. P	0.551624

overview

Window 0

Location	22,942,395 – 22,942,511
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.05
Mean single sequence MFE	-33.57
Consensus MFE	-22.36
Energy contribution	-23.05
Covariance contribution	0.69
Combinations/Pair	1.15
Mean z-score	-1.70
Structure conservation index	0.67
SVM decision value	-0.01
SVM RNA-class probability	0.529937
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22942395 116 + 27905053
UUGUCGCUAUUGGUGAGCAGACU-CGAUAGCCUACCCAAUCGAUAGUA---GCCGCUCAUCGAUAGGCAACAGCUGAUUGAGUGAUUUUAGCUGCAGAAGGUCACAUCAAAACGAACUUU
((((.(((((((((((((..(((-((((.(......).)))))..)).---...))))))))))).)).))))....((((((((((((........)))))))).)))).......... ( -31.70)
>DroSec_CAF1 4016 117 + 1
UUGUCGUUAUGGAUGAGCAGACUAUGAUAGCCUACCCAAUCGAUAGUC---ACCGCUCAUCGAUAGGCAACAGCUGAUUAAGUGAUUUUAGCUGCAGAAGGUGACACCAAAACGAACUUU
...(((((((.(((((((.(((((((((.(......).))).))))))---...))))))).)).((...(((((((..........))))))).....(....).))..)))))..... ( -33.40)
>DroSim_CAF1 4035 117 + 1
UUGUCGUUAUGGAUGAGCAGACUAUGAUAGCCUACCCAAUCGAUAGUC---GCCGCUCAUCGAUAGGCAACAGCUGAUUAAGUGAUUUUAGCUGUAGAAGGUCACACCAAAACGAACUUU
...(((((.(((((((((.(((((((((.(......).))).))))))---...)))))))(((...(.((((((((..........)))))))).)...)))....)).)))))..... ( -37.50)
>DroYak_CAF1 4057 120 + 1
UUGUGGUUAUUGGUGAACCGACUUCGAUACCCCACUUCAUCGAUAGUGUCGGCGGCUUAUCGAUAGGCAACAGCUGACUAAGAGAUUUUAGCUGCAGAAGGUCACACCAAAACGAACUUU
..((.(((.((((((.((((((.(((((..........)))))....))).((((((.(((....(((....)))........)))...))))))....)))..)))))))))..))... ( -31.70)
>consensus
UUGUCGUUAUGGAUGAGCAGACUACGAUAGCCUACCCAAUCGAUAGUC___GCCGCUCAUCGAUAGGCAACAGCUGAUUAAGUGAUUUUAGCUGCAGAAGGUCACACCAAAACGAACUUU
((((..((((((((((((.(((((((((..........)))).)))))......))))))))))))))))(((((((..........))))))).....((.....))............ (-22.36 = -23.05 +   0.69)

alignment

secondary structure

dotplot

Window 1

Location	22,942,395 – 22,942,511
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.05
Mean single sequence MFE	-33.15
Consensus MFE	-22.83
Energy contribution	-23.27
Covariance contribution	0.44
Combinations/Pair	1.18
Mean z-score	-1.61
Structure conservation index	0.69
SVM decision value	0.04
SVM RNA-class probability	0.551624
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22942395 116 - 27905053
AAAGUUCGUUUUGAUGUGACCUUCUGCAGCUAAAAUCACUCAAUCAGCUGUUGCCUAUCGAUGAGCGGC---UACUAUCGAUUGGGUAGGCUAUCG-AGUCUGCUCACCAAUAGCGACAA
.......(((((((.((((................))))))))...(((((((...((((((.((....---..))))))))((((((((((....-)))))))))).)))))))))).. ( -30.59)
>DroSec_CAF1 4016 117 - 1
AAAGUUCGUUUUGGUGUCACCUUCUGCAGCUAAAAUCACUUAAUCAGCUGUUGCCUAUCGAUGAGCGGU---GACUAUCGAUUGGGUAGGCUAUCAUAGUCUGCUCAUCCAUAACGACAA
...((.((((.(((.((((((....((((((..............)))))).(((.......).)))))---))).......(((((((((((...))))))))))).))).)))))).. ( -37.44)
>DroSim_CAF1 4035 117 - 1
AAAGUUCGUUUUGGUGUGACCUUCUACAGCUAAAAUCACUUAAUCAGCUGUUGCCUAUCGAUGAGCGGC---GACUAUCGAUUGGGUAGGCUAUCAUAGUCUGCUCAUCCAUAACGACAA
...((.((((.(((.((((......((((((..............))))))..((.(((((((...(..---..)))))))).))((((((((...))))))))))))))).)))))).. ( -32.64)
>DroYak_CAF1 4057 120 - 1
AAAGUUCGUUUUGGUGUGACCUUCUGCAGCUAAAAUCUCUUAGUCAGCUGUUGCCUAUCGAUAAGCCGCCGACACUAUCGAUGAAGUGGGGUAUCGAAGUCGGUUCACCAAUAACCACAA
...((..(((((((((.((((..((((((((..............))))))......((((((..(((((((.....))).....))))..))))))))..)))))))))).))).)).. ( -31.94)
>consensus
AAAGUUCGUUUUGGUGUGACCUUCUGCAGCUAAAAUCACUUAAUCAGCUGUUGCCUAUCGAUGAGCGGC___GACUAUCGAUUGGGUAGGCUAUCAUAGUCUGCUCACCAAUAACGACAA
...((.((((((((((.(((.....((((((..............))))))((((((((((((............))))))).)))))..........)))....)))))).)))))).. (-22.83 = -23.27 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:14:32 2006