Locus 4365

Sequence ID	3R_DroMel_CAF1
Location	11,508,141 – 11,508,265
Length	124
Max. P	0.858059

overview

Window 5

Location	11,508,141 – 11,508,233
Length	92
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	77.75
Mean single sequence MFE	-30.05
Consensus MFE	-21.19
Energy contribution	-20.67
Covariance contribution	-0.52
Combinations/Pair	1.41
Mean z-score	-1.49
Structure conservation index	0.71
SVM decision value	0.82
SVM RNA-class probability	0.858059
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11508141 92 + 27905053
UGCCCUGCGGUUUUGUUUCUGCGGUCAAU---UUGUUUGUUGGCUGGCGGGCCGGCCGGCCAACUGCAGUGAAAUUAUGCAAUGGUCAUUCCGAU
(((.((((((........))))))(((..---.(((..((((((((((......)))))))))).))).)))......))).(((.....))).. ( -33.30)
>DroSec_CAF1 42188 92 + 1
UGCCCUGCGGUUUUGUCUCUGCGGUGAGU---UUGUUUGUUGGCUGGCUGGCCGGCCGGCCAACUGCAGUGAAAUUAUGCAAUGGUCAUUCCGAU
.(((.((((......((.(((((((....---........(((((((((....)))))))))))))))).)).....))))..)))......... ( -33.80)
>DroSim_CAF1 43305 92 + 1
UGCCCUGCGGUUUUGUUUCUGCGGUCAGU---UUGUUUGUCGGCUGGCUGGCCGGCCGGCCAACUGCAGUGAAAUUAUGCAAUGGUCAUUCCGAU
(((.((((((........))))))(((.(---..(((.(((((((((....))))))))).)))...).)))......))).(((.....))).. ( -32.20)
>DroEre_CAF1 45743 88 + 1
UGCCCUGCGGUUUUGUCUCUGCGGUCAGU---UUGUUUGUUGGCUG----GCUGGCCGGCCGACUGCAGUGAAAUUAUGCAAUGGUCAUUCCGAU
.(((.((((......((.((((((((((.---....))...(((((----(....)))))))))))))).)).....))))..)))......... ( -31.60)
>DroAna_CAF1 128145 87 + 1
CGGCUUGCGGCUUUGUCGUUGCGGUCAGU---CUGUUUGUUU-CUGGCCGACUGACCGGUCAACUGCAGUGAAAAUAUGCAAUGGUCAUAU----
..((..(((((...))))).))(((((((---(.(((.....-..))).))))))))(..((..((((((....)).)))).))..)....---- ( -30.10)
>DroPer_CAF1 13285 85 + 1
----UCGAAGUCUUUCAUUUGCGGUCAAUGUUUUGUUUGCCUGCUGGCUGGCU-GCUGGUCAACUGCAACG---UUGUGCAAUGGUCAAAACU--
----................(((((((...........(((....))))))))-))((..((..((((...---...)))).))..)).....-- ( -19.30)
>consensus
UGCCCUGCGGUUUUGUCUCUGCGGUCAGU___UUGUUUGUUGGCUGGCUGGCCGGCCGGCCAACUGCAGUGAAAUUAUGCAAUGGUCAUUCCGAU
....((((((........))))))..........(((.(((((((((....))))))))).)))((((.........)))).............. (-21.19 = -20.67 +  -0.52)

alignment

secondary structure

dotplot

Window 6

Location	11,508,141 – 11,508,233
Length	92
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	77.75
Mean single sequence MFE	-22.42
Consensus MFE	-14.11
Energy contribution	-14.94
Covariance contribution	0.84
Combinations/Pair	1.32
Mean z-score	-1.32
Structure conservation index	0.63
SVM decision value	0.05
SVM RNA-class probability	0.557173
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11508141 92 - 27905053
AUCGGAAUGACCAUUGCAUAAUUUCACUGCAGUUGGCCGGCCGGCCCGCCAGCCAACAAACAA---AUUGACCGCAGAAACAAAACCGCAGGGCA
.......((.((.((((.........((((.((((((.(((......))).))))))...(..---...)...))))..........)))))))) ( -23.91)
>DroSec_CAF1 42188 92 - 1
AUCGGAAUGACCAUUGCAUAAUUUCACUGCAGUUGGCCGGCCGGCCAGCCAGCCAACAAACAA---ACUCACCGCAGAGACAAAACCGCAGGGCA
...(((((............))))).((((.((((((.(((......))).))))))......---.(((......)))........)))).... ( -26.20)
>DroSim_CAF1 43305 92 - 1
AUCGGAAUGACCAUUGCAUAAUUUCACUGCAGUUGGCCGGCCGGCCAGCCAGCCGACAAACAA---ACUGACCGCAGAAACAAAACCGCAGGGCA
...(((((............))))).((((.((((((.(((......))).))))))......---.(((....)))..........)))).... ( -25.20)
>DroEre_CAF1 45743 88 - 1
AUCGGAAUGACCAUUGCAUAAUUUCACUGCAGUCGGCCGGCCAGC----CAGCCAACAAACAA---ACUGACCGCAGAGACAAAACCGCAGGGCA
.......((.((.((((......((.((((.((((((.((....)----).))).........---...))).)))).)).......)))))))) ( -20.32)
>DroAna_CAF1 128145 87 - 1
----AUAUGACCAUUGCAUAUUUUCACUGCAGUUGACCGGUCAGUCGGCCAG-AAACAAACAG---ACUGACCGCAACGACAAAGCCGCAAGCCG
----..........((((.........))))((((..(((((((((......-.........)---))))))))...))))...(.(....).). ( -21.96)
>DroPer_CAF1 13285 85 - 1
--AGUUUUGACCAUUGCACAA---CGUUGCAGUUGACCAGC-AGCCAGCCAGCAGGCAAACAAAACAUUGACCGCAAAUGAAAGACUUCGA----
--((((((...((((((....---.(((((.........))-)))..(((....)))................)).)))).))))))....---- ( -16.90)
>consensus
AUCGGAAUGACCAUUGCAUAAUUUCACUGCAGUUGGCCGGCCAGCCAGCCAGCCAACAAACAA___ACUGACCGCAGAGACAAAACCGCAGGGCA
.............((((.........((((.((((((.(((......))).))))))...((......))...))))..........)))).... (-14.11 = -14.94 +   0.84)

alignment

secondary structure

dotplot

Window 7

Location	11,508,170 – 11,508,265
Length	95
Sequences	4
Columns	102
Reading direction	forward
Mean pairwise identity	87.76
Mean single sequence MFE	-35.75
Consensus MFE	-23.73
Energy contribution	-24.60
Covariance contribution	0.87
Combinations/Pair	1.04
Mean z-score	-1.65
Structure conservation index	0.66
SVM decision value	-0.03
SVM RNA-class probability	0.520270
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11508170 95 + 27905053
UUGUUUGUUGGCUGGCGGGCCGGCCGGCCAACUGCAGUGAAAUUAUGCAAUGGUCAUUCCGAUGGGGCUUUCGAGUGUUGAU-------CGGGGGGGCAAUG
......((((((((((......))))))))))((((.........))))...(((.(((((((((.(((....))).)).))-------))))).))).... ( -35.60)
>DroSec_CAF1 42217 94 + 1
UUGUUUGUUGGCUGGCUGGCCGGCCGGCCAACUGCAGUGAAAUUAUGCAAUGGUCAUUCCGAUGGGGCUUUCGAGUGGUGAU-------CAGG-GGGCAAUG
((((..(((((((((((....))))))))))).))))........(((..((((((((((((........))).).))))))-------))..-..)))... ( -36.60)
>DroSim_CAF1 43334 94 + 1
UUGUUUGUCGGCUGGCUGGCCGGCCGGCCAACUGCAGUGAAAUUAUGCAAUGGUCAUUCCGAUGGGGCUUUCGAGUGGUGAU-------CGGG-GGGCAAUG
....(..((((((((....))))))(((((..((((.........)))).))))).....))..)(.((..(((.......)-------))..-)).).... ( -34.50)
>DroEre_CAF1 45772 97 + 1
UUGUUUGUUGGCUG----GCUGGCCGGCCGACUGCAGUGAAAUUAUGCAAUGGUCAUUCCGAUGGGCCUUUCGAGUGUGGGGAGGGGGGAGGG-GGGCCAUG
......((((((((----(....)))))))))((((.........))))((((((.((((......(((..(.......)..))).....)))-))))))). ( -36.30)
>consensus
UUGUUUGUUGGCUGGCUGGCCGGCCGGCCAACUGCAGUGAAAUUAUGCAAUGGUCAUUCCGAUGGGGCUUUCGAGUGGUGAU_______CGGG_GGGCAAUG
((((((((((((((((......))))))))))((((.........)))).....(((((.((........))))))).................)))))).. (-23.73 = -24.60 +   0.87)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:22 2006