Locus 5214

Sequence ID	3L_DroMel_CAF1
Location	14,374,715 – 14,374,846
Length	131
Max. P	0.806836

overview

Window 0

Location	14,374,715 – 14,374,806
Length	91
Sequences	3
Columns	91
Reading direction	forward
Mean pairwise identity	85.35
Mean single sequence MFE	-31.10
Consensus MFE	-28.59
Energy contribution	-29.60
Covariance contribution	1.01
Combinations/Pair	1.10
Mean z-score	-0.92
Structure conservation index	0.92
SVM decision value	-0.01
SVM RNA-class probability	0.529271
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14374715 91 + 23771897
UGCUUUGUGAUGGCAUACAUGGCGCUGCCAACUCGCACACAACUAUCGACGGCCGAUAAUUCGGGGACGACUGACUGUUGUGCGCGCGUUG
.((..(((.(((.....))).)))..))((((.(((.(((((((((((.....)))))..(((....)))......)))))).))).)))) ( -33.70)
>DroSim_CAF1 1385 90 + 1
UGCUAUGACAU-GCAGACAUGGCGCUGCCAACUCGCACACAACUAUCGACGGCCGAUAAUCCGGGGACGACUGACUGUUGUGCGCGCGUUG
.((((((.(..-...).)))))).....((((.(((.(((((((((((.....)))))...((....)).......)))))).))).)))) ( -31.40)
>DroYak_CAF1 3525 89 + 1
UGCUGUGU--UUGCCGACACUGCGCUGCCAACUCGCACACAACUAUCGAUGGUCGAUAAUACGGAGAGGGCCGAUUGUUGUGCGCGCGAUG
.((.((((--(....))))).))........(.(((.(((((((((((.....)))))...(((......)))...)))))).))).)... ( -28.20)
>consensus
UGCUAUGU_AU_GCAGACAUGGCGCUGCCAACUCGCACACAACUAUCGACGGCCGAUAAUACGGGGACGACUGACUGUUGUGCGCGCGUUG
.((((((((......)))))))).....((((.(((.(((((((((((.....)))))...(((......)))...)))))).))).)))) (-28.59 = -29.60 +   1.01)

alignment

secondary structure

dotplot

Window 1

Location	14,374,715 – 14,374,806
Length	91
Sequences	3
Columns	91
Reading direction	reverse
Mean pairwise identity	85.35
Mean single sequence MFE	-32.70
Consensus MFE	-27.07
Energy contribution	-28.63
Covariance contribution	1.56
Combinations/Pair	1.07
Mean z-score	-1.90
Structure conservation index	0.83
SVM decision value	0.44
SVM RNA-class probability	0.739054
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14374715 91 - 23771897
CAACGCGCGCACAACAGUCAGUCGUCCCCGAAUUAUCGGCCGUCGAUAGUUGUGUGCGAGUUGGCAGCGCCAUGUAUGCCAUCACAAAGCA
((((.((((((((((.(((.(.((...((((....)))).)).)))).)))))))))).)))).....((..(((........)))..)). ( -32.80)
>DroSim_CAF1 1385 90 - 1
CAACGCGCGCACAACAGUCAGUCGUCCCCGGAUUAUCGGCCGUCGAUAGUUGUGUGCGAGUUGGCAGCGCCAUGUCUGC-AUGUCAUAGCA
((((.((((((((((.(((.(.((...(((......))).)).)))).)))))))))).)))).....((.(((.(...-..).))).)). ( -33.60)
>DroYak_CAF1 3525 89 - 1
CAUCGCGCGCACAACAAUCGGCCCUCUCCGUAUUAUCGACCAUCGAUAGUUGUGUGCGAGUUGGCAGCGCAGUGUCGGCAA--ACACAGCA
....(((((((((((...(((......)))...(((((.....))))))))))))))..(((((((......)))))))..--.....)). ( -31.70)
>consensus
CAACGCGCGCACAACAGUCAGUCGUCCCCGAAUUAUCGGCCGUCGAUAGUUGUGUGCGAGUUGGCAGCGCCAUGUCUGC_AU_ACAAAGCA
((((.((((((((((.(((.(.((...(((......))).)).)))).)))))))))).)))).....((.((((........)))).)). (-27.07 = -28.63 +   1.56)

alignment

secondary structure

dotplot

Window 2

Location	14,374,736 – 14,374,846
Length	110
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	70.72
Mean single sequence MFE	-41.93
Consensus MFE	-23.34
Energy contribution	-26.40
Covariance contribution	3.06
Combinations/Pair	1.15
Mean z-score	-1.73
Structure conservation index	0.56
SVM decision value	0.63
SVM RNA-class probability	0.806836
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14374736 110 - 23771897
AAUCGACGUUGCGUAGUUUUCUGCCAGUGCUGCACAGCGUCAACGCGCGCACAACAGUCAGUCGUCC----CCGA---AUUAUCGGCCGUCGAUAGUUGUGUGCGAGUUGGCAGCGC---
.......((((.(((((...........))))).))))((((((.((((((((((.(((.(.((...----((((---....)))).)).)))).)))))))))).)))))).....--- ( -44.90)
>DroAna_CAF1 7080 104 - 1
---CGAUGUUGCACGGC-UGCGGACAGUGUUGCAAAGCGACUU------------AGGUUGUCGUGUUGCAUGGGAUAUUUAUCGGUAAUCGAUAACGCAAUGCGGGUUGGCAGCACCUC
---............((-(((.(((.(((((((....(.....------------.)(((((((.(((((.(((........))))))))))))))))))))))..))).)))))..... ( -34.50)
>DroSim_CAF1 1405 110 - 1
AAUCGGCGUUGCGUAGUUUUCGGCCAGUGCUGCACAGCGUCAACGCGCGCACAACAGUCAGUCGUCC----CCGG---AUUAUCGGCCGUCGAUAGUUGUGUGCGAGUUGGCAGCGC---
.....((((((.(((((...(.....).))))).))))((((((.((((((((((.(((.(.((...----(((.---.....))).)).)))).)))))))))).)))))).))..--- ( -46.40)
>DroYak_CAF1 3544 110 - 1
AAUCGCCGUUGCGUAGUUUUCGGCCAGUGUUGCACAGCGUCAUCGCGCGCACAACAAUCGGCCCUCU----CCGU---AUUAUCGACCAUCGAUAGUUGUGUGCGAGUUGGCAGCGC---
....((((..((...))...))))..(((((((.((((.......((((((((((...(((......----))).---..(((((.....))))))))))))))).)))))))))))--- ( -41.90)
>consensus
AAUCGACGUUGCGUAGUUUUCGGCCAGUGCUGCACAGCGUCAACGCGCGCACAACAGUCAGUCGUCC____CCGG___AUUAUCGGCCAUCGAUAGUUGUGUGCGAGUUGGCAGCGC___
......(((((((((((...(.....).))))).......((((.((((((((((.......((........))......(((((.....))))))))))))))).)))))))))).... (-23.34 = -26.40 +   3.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:43 2006