Locus 7212

Sequence ID	3L_DroMel_CAF1
Location	19,353,916 – 19,354,036
Length	120
Max. P	0.864635

overview

Window 3

Location	19,353,916 – 19,354,036
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.33
Mean single sequence MFE	-29.95
Consensus MFE	-22.39
Energy contribution	-22.70
Covariance contribution	0.31
Combinations/Pair	1.11
Mean z-score	-1.46
Structure conservation index	0.75
SVM decision value	0.03
SVM RNA-class probability	0.547463
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19353916 120 + 23771897
UAAAAAAGGAAGGGCUAAGCGAACCCCACAGUGAUAUAGAUGAGUACGAUAUGCUAUUUAGACUAGCCAGAGAUCCAGAAAAGAAUCGGGAUCUUCUGUUUGAUUUACUGAAACCCAAGG
.......((..(((..........))).((((((..(((((.((((.....))))))))).......(((((((((.((......)).))))).))))......))))))....)).... ( -25.10)
>DroSec_CAF1 4054 120 + 1
UAAAUAAGGAAGGGCUCAGCGAACACUACAGUGAUAUAGAUGAGUACGAUAUGCUAUUUAAACUAGCCAGAGAUCCUGAAAAGAACCGCGAUCUUCUGUUUGACUUACUGAAGCCCAAGG
...........((((((((....(((....))).......(((((.(((...((((.......))))((((((((.((........)).)))).)))).))))))))))).))))).... ( -28.90)
>DroSim_CAF1 4095 120 + 1
UAAAUAAGGAAGGGCUCAGCGAACACUACAGUGAUAUAGAUGAGUACGAUAUGCUAUUUAAACUAGCCAGAGAUCCUGAAAAGAACCGCGAUCUUCUGUUUGACUUACUGAAGCCCAAGG
...........((((((((....(((....))).......(((((.(((...((((.......))))((((((((.((........)).)))).)))).))))))))))).))))).... ( -28.90)
>DroYak_CAF1 7771 120 + 1
UAAAAUCGGAGGGGCUCAACGAACCCCAUAGUGAUAUAGAAGAGUUCGAUAUGUUAUUAAGCCUAGCCAGAGAUCAUGAGAAGAAUCGUGAUCUUCUGAUGGAGUUACUAAAGCCCAAGG
...........(((((.....(((.(((((((((((((...(....)..))))))))))........((((((((((((......)))))))).)))).))).))).....))))).... ( -36.90)
>consensus
UAAAAAAGGAAGGGCUCAGCGAACACCACAGUGAUAUAGAUGAGUACGAUAUGCUAUUUAAACUAGCCAGAGAUCCUGAAAAGAACCGCGAUCUUCUGUUUGACUUACUGAAGCCCAAGG
...........(((((....(....)..((((((..................((((.......))))(((((((((((........))))))).))))......)))))).))))).... (-22.39 = -22.70 +   0.31)

alignment

secondary structure

dotplot

Window 4

Location	19,353,916 – 19,354,036
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.33
Mean single sequence MFE	-29.50
Consensus MFE	-24.81
Energy contribution	-24.50
Covariance contribution	-0.31
Combinations/Pair	1.24
Mean z-score	-1.85
Structure conservation index	0.84
SVM decision value	0.84
SVM RNA-class probability	0.864635
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19353916 120 - 23771897
CCUUGGGUUUCAGUAAAUCAAACAGAAGAUCCCGAUUCUUUUCUGGAUCUCUGGCUAGUCUAAAUAGCAUAUCGUACUCAUCUAUAUCACUGUGGGGUUCGCUUAGCCCUUCCUUUUUUA
....(((((..((..((((..((((.((((((.((......)).))))))...((((.......)))).....................))))..))))..)).)))))........... ( -31.10)
>DroSec_CAF1 4054 120 - 1
CCUUGGGCUUCAGUAAGUCAAACAGAAGAUCGCGGUUCUUUUCAGGAUCUCUGGCUAGUUUAAAUAGCAUAUCGUACUCAUCUAUAUCACUGUAGUGUUCGCUGAGCCCUUCCUUAUUUA
....(((((.((((.((((...((((.((((..((......))..))))))))((((.......)))).....).)))((.(((((....)))))))...)))))))))........... ( -28.50)
>DroSim_CAF1 4095 120 - 1
CCUUGGGCUUCAGUAAGUCAAACAGAAGAUCGCGGUUCUUUUCAGGAUCUCUGGCUAGUUUAAAUAGCAUAUCGUACUCAUCUAUAUCACUGUAGUGUUCGCUGAGCCCUUCCUUAUUUA
....(((((.((((.((((...((((.((((..((......))..))))))))((((.......)))).....).)))((.(((((....)))))))...)))))))))........... ( -28.50)
>DroYak_CAF1 7771 120 - 1
CCUUGGGCUUUAGUAACUCCAUCAGAAGAUCACGAUUCUUCUCAUGAUCUCUGGCUAGGCUUAAUAACAUAUCGAACUCUUCUAUAUCACUAUGGGGUUCGUUGAGCCCCUCCGAUUUUA
....((((((..(.((((((((((((.(((((.((......)).)))))))))...............((((.((.....)).))))....)))))))))...))))))........... ( -29.90)
>consensus
CCUUGGGCUUCAGUAAGUCAAACAGAAGAUCGCGAUUCUUUUCAGGAUCUCUGGCUAGUCUAAAUAGCAUAUCGUACUCAUCUAUAUCACUGUAGGGUUCGCUGAGCCCUUCCUUAUUUA
....(((((.((((........((((.(((((.((......)).)))))))))((((.......)))).............(((((....))))).....)))))))))........... (-24.81 = -24.50 +  -0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:41:00 2006