Locus 6750

Sequence ID	3R_DroMel_CAF1
Location	17,789,075 – 17,789,226
Length	151
Max. P	0.999174

overview

Window 4

Location	17,789,075 – 17,789,190
Length	115
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	94.79
Mean single sequence MFE	-28.62
Consensus MFE	-24.46
Energy contribution	-24.82
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-2.41
Structure conservation index	0.85
SVM decision value	2.75
SVM RNA-class probability	0.996812
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17789075 115 - 27905053
UUCUGCUGCUGGAUAACUUUUUCGCAAGGAAAUAUAAGCUUAGCAAAAUAUUUGCCUGAGCUCUUUAUUGCUAUAUUCAGGUAGAUUGCAUUAUCCCACGGAAAUCUUUUACGGA
(((((.((..((((((..(((((....)))))..........(((....((((((((((((........)).....))))))))))))).)))))))))))))............ ( -28.50)
>DroSec_CAF1 77499 112 - 1
UUCUG---CUGGAUAACUUUUUCGCAAGGAAAUAUAAGCUUAGCAAAAUAUUUGCCUGAGCUCUUUAUUGCUAUAUUCAGGUAGAUUGCAUUAUCCCACGGAAAUCUUUUACGGA
(((((---..((((((..(((((....)))))..........(((....((((((((((((........)).....))))))))))))).))))))..)))))............ ( -29.60)
>DroSim_CAF1 78239 112 - 1
UUCUG---CUGGAUAACUUUUUCGCAAGGAAAUAUAAGCUUAGCAAAAUAUUUGCCUGAGCUCUUUAUUGCUAUAUUCAGGUAGAUUGCAUUAUCCCACGGAAAUCUUUUACGGA
(((((---..((((((..(((((....)))))..........(((....((((((((((((........)).....))))))))))))).))))))..)))))............ ( -29.60)
>DroEre_CAF1 83252 112 - 1
UUCUG---CUGGAUAACUUUUUCGCAAGAAAAUAUAAGCUUAGCAAAAUAUUUGCCUGAGCUCUUUAUUGCUAUAUUCAGGUAGAGUCCAUUAUCCCACGGAAAUCUCUAGCGGC
..(((---(((((.....(((((....)))))..................(((((((((((........)).....))))))))).(((..........)))....)))))))). ( -27.60)
>DroYak_CAF1 83781 112 - 1
UUCUG---CUGGAUAACUUUUUCGCAAGAAAAUAUAAGCUUAGCAAAAUAUUUGCCUGAGCUCUUUAUUGCUGUAUUCAGAUAGAUUGCAUUAUCCCACGGAAAUCUUGCACGGC
.((((---(((((((...(((((....)))))....((((((((((.....))).)))))))...........))))))).)))).((((...(((...))).....)))).... ( -27.80)
>consensus
UUCUG___CUGGAUAACUUUUUCGCAAGGAAAUAUAAGCUUAGCAAAAUAUUUGCCUGAGCUCUUUAUUGCUAUAUUCAGGUAGAUUGCAUUAUCCCACGGAAAUCUUUUACGGA
(((((.....((((((..(((((....)))))..........(((....((((((((((((........)).....))))))))))))).))))))..)))))............ (-24.46 = -24.82 +   0.36)

alignment

secondary structure

dotplot

Window 5

Location	17,789,114 – 17,789,226
Length	112
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	97.64
Mean single sequence MFE	-23.81
Consensus MFE	-22.47
Energy contribution	-22.23
Covariance contribution	-0.24
Combinations/Pair	1.03
Mean z-score	-2.22
Structure conservation index	0.94
SVM decision value	3.22
SVM RNA-class probability	0.998776
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17789114 112 + 27905053
AUAUAGCAAUAAAGAGCUCAGGCAAAUAUUUUGCUAAGCUUAUAUUUCCUUGCGAAAAAGUUAUCCAGCAGCAGAAAACAAACCCCAACAGGGAUUUAACUUGUUGCACAGU
..(((((......(((((..(((((.....))))).)))))...((((.....))))..)))))...(((((((.....(((.(((....))).)))...)))))))..... ( -23.40)
>DroSec_CAF1 77538 109 + 1
AUAUAGCAAUAAAGAGCUCAGGCAAAUAUUUUGCUAAGCUUAUAUUUCCUUGCGAAAAAGUUAUCCAG---CAGAAAACAAACCCCAACAGGGAUUUAACUUGUUGCACAGU
.....(((((((.(((((..(((((.....))))).))))).((..((((((.......(((.((...---..)).))).........))))))..))..)))))))..... ( -23.39)
>DroSim_CAF1 78278 109 + 1
AUAUAGCAAUAAAGAGCUCAGGCAAAUAUUUUGCUAAGCUUAUAUUUCCUUGCGAAAAAGUUAUCCAG---CAGAAAACAAACCCCAACAGGGAUUUAACUUGUUGCACAGU
.....(((((((.(((((..(((((.....))))).))))).((..((((((.......(((.((...---..)).))).........))))))..))..)))))))..... ( -23.39)
>DroEre_CAF1 83291 109 + 1
AUAUAGCAAUAAAGAGCUCAGGCAAAUAUUUUGCUAAGCUUAUAUUUUCUUGCGAAAAAGUUAUCCAG---CAGAAAACAAACCCCAACAGGGAUUUAACUUGUUGCACAGC
.....(((((((.(((((..(((((.....))))).)))))...((((((.((..............)---))))))).....(((....))).......)))))))..... ( -24.44)
>DroYak_CAF1 83820 109 + 1
AUACAGCAAUAAAGAGCUCAGGCAAAUAUUUUGCUAAGCUUAUAUUUUCUUGCGAAAAAGUUAUCCAG---CAGAAAACAAACCCCAACAGGGAUUUAACUUGUUGCACAGU
.....(((((((.(((((..(((((.....))))).)))))...((((((.((..............)---))))))).....(((....))).......)))))))..... ( -24.44)
>consensus
AUAUAGCAAUAAAGAGCUCAGGCAAAUAUUUUGCUAAGCUUAUAUUUCCUUGCGAAAAAGUUAUCCAG___CAGAAAACAAACCCCAACAGGGAUUUAACUUGUUGCACAGU
.....(((((((.(((((..(((((.....))))).))))).((..((((((.......(((.((........)).))).........))))))..))..)))))))..... (-22.47 = -22.23 +  -0.24)

alignment

secondary structure

dotplot

Window 6

Location	17,789,114 – 17,789,226
Length	112
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	97.64
Mean single sequence MFE	-27.74
Consensus MFE	-27.34
Energy contribution	-27.10
Covariance contribution	-0.24
Combinations/Pair	1.03
Mean z-score	-2.11
Structure conservation index	0.99
SVM decision value	3.41
SVM RNA-class probability	0.999174
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17789114 112 - 27905053
ACUGUGCAACAAGUUAAAUCCCUGUUGGGGUUUGUUUUCUGCUGCUGGAUAACUUUUUCGCAAGGAAAUAUAAGCUUAGCAAAAUAUUUGCCUGAGCUCUUUAUUGCUAUAU
.....((((.....((((((((....)))))))).(((((..(((..((......))..))).)))))....((((((((((.....))).))))))).....))))..... ( -27.80)
>DroSec_CAF1 77538 109 - 1
ACUGUGCAACAAGUUAAAUCCCUGUUGGGGUUUGUUUUCUG---CUGGAUAACUUUUUCGCAAGGAAAUAUAAGCUUAGCAAAAUAUUUGCCUGAGCUCUUUAUUGCUAUAU
.....((((......(((((((....)))))))((((((((---(..((......))..)).)))))))...((((((((((.....))).))))))).....))))..... ( -27.10)
>DroSim_CAF1 78278 109 - 1
ACUGUGCAACAAGUUAAAUCCCUGUUGGGGUUUGUUUUCUG---CUGGAUAACUUUUUCGCAAGGAAAUAUAAGCUUAGCAAAAUAUUUGCCUGAGCUCUUUAUUGCUAUAU
.....((((......(((((((....)))))))((((((((---(..((......))..)).)))))))...((((((((((.....))).))))))).....))))..... ( -27.10)
>DroEre_CAF1 83291 109 - 1
GCUGUGCAACAAGUUAAAUCCCUGUUGGGGUUUGUUUUCUG---CUGGAUAACUUUUUCGCAAGAAAAUAUAAGCUUAGCAAAAUAUUUGCCUGAGCUCUUUAUUGCUAUAU
((...(((......((((((((....)))))))).....))---)..(((((..(((((....)))))....((((((((((.....))).)))))))..)))))))..... ( -27.80)
>DroYak_CAF1 83820 109 - 1
ACUGUGCAACAAGUUAAAUCCCUGUUGGGGUUUGUUUUCUG---CUGGAUAACUUUUUCGCAAGAAAAUAUAAGCUUAGCAAAAUAUUUGCCUGAGCUCUUUAUUGCUGUAU
...(((((.(((...(((((((....)))))))((((((((---(..((......))..)).)))))))...((((((((((.....))).))))))).....))).))))) ( -28.90)
>consensus
ACUGUGCAACAAGUUAAAUCCCUGUUGGGGUUUGUUUUCUG___CUGGAUAACUUUUUCGCAAGGAAAUAUAAGCUUAGCAAAAUAUUUGCCUGAGCUCUUUAUUGCUAUAU
.....((((......(((((((....)))))))(((.(((......))).))).(((((....)))))....((((((((((.....))).))))))).....))))..... (-27.34 = -27.10 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:29:05 2006