Locus 1416

Sequence ID	3R_DroMel_CAF1
Location	4,098,983 – 4,099,316
Length	333
Max. P	0.981970

overview

Window 2

Location	4,098,983 – 4,099,094
Length	111
Sequences	3
Columns	114
Reading direction	forward
Mean pairwise identity	82.88
Mean single sequence MFE	-31.02
Consensus MFE	-28.87
Energy contribution	-29.20
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.99
Structure conservation index	0.93
SVM decision value	1.90
SVM RNA-class probability	0.981970
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4098983 111 + 27905053
CCAAAUCCAGAUCCUCAUUCUUCCUUCUACUCCUACUCC---UUCUCCCGGAGGUCAGUAGCGUCCCUUUCCGGGGGUUGAAUUCAAAGGAAUUCGCUGGGUCCUCCGGCACUC
.......................................---.....(((((((.(..((((.(((((....)))))..((((((....)))))))))).).)))))))..... ( -30.70)
>DroSim_CAF1 10918 102 + 1
CCA------GAU------UCCUCCAACUACUCCUACUCCUCCUCCUCCCGGAGGUCAGUAGCGUCCCUUUCCGGGGGUUGAAUUCAAAGGAAUUCGCUGGGUCCUCCGGCACUC
...------(((------((((.(((((....(((((...(((((....)))))..)))))...(((.....)))))))).......))))))).(((((.....))))).... ( -32.90)
>DroYak_CAF1 10894 99 + 1
---------GAUCCUCAUUUCUCCUCCUACUCC---UUC---UUCUCGCGGAGGUCAGUAGCGUCCCUUUCCGGGGGUUGAAUUCAAAGGAAUUCGCUGGGUCCUCCGGCACUC
---------(((((((.........((((((((---(((---.......)))))..))))).).........)))))))((((((....))))))(((((.....))))).... ( -29.47)
>consensus
CCA______GAUCCUCAUUCCUCCUACUACUCCUACUCC___UUCUCCCGGAGGUCAGUAGCGUCCCUUUCCGGGGGUUGAAUUCAAAGGAAUUCGCUGGGUCCUCCGGCACUC
...............................................(((((((.(..((((.(((((....)))))..((((((....)))))))))).).)))))))..... (-28.87 = -29.20 +   0.33)

alignment

secondary structure

dotplot

Window 3

Location	4,099,094 – 4,099,206
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.88
Mean single sequence MFE	-32.52
Consensus MFE	-29.11
Energy contribution	-29.07
Covariance contribution	-0.04
Combinations/Pair	1.02
Mean z-score	-1.18
Structure conservation index	0.90
SVM decision value	0.17
SVM RNA-class probability	0.618631
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4099094 112 + 27905053
UCACCUUUUCCGCGGCCAACAAAUC--------UUGAGUGCAACAAUAUGGCAAUUGUUGUGUAUUGCUACGAGAACUUGUUAAUUGUUUCGCGCUCGAGUGGCCAAGAGCUCUGAAUGG
...((..(((...(((((......(--------((((((((((((((.((((((((.(((((......))))).)).))))))))))))..)))))))))))))).((....))))).)) ( -33.60)
>DroSec_CAF1 11006 112 + 1
UCACCUUUUCCGCGGCCAACAAAUC--------UUGAGUGCAACAAUAUGGCAAUUGUUGUGUAUUGCUACGAGAACUUGUUAAUUGUUUCGCGCUCGAGUGGCCAAGAGCUCUGAAUGG
...((..(((...(((((......(--------((((((((((((((.((((((((.(((((......))))).)).))))))))))))..)))))))))))))).((....))))).)) ( -33.60)
>DroSim_CAF1 11020 112 + 1
UCACCUUUUCCGCGGCCAACAAAUC--------UUGAGUGCAACAAUAUGGCAAUUGUUGUGUAUUGCUACGAGAACUUGUUAAUUGUUUCGCGCUCGAGUGGCCAAGAGCUCUGAAUGG
...((..(((...(((((......(--------((((((((((((((.((((((((.(((((......))))).)).))))))))))))..)))))))))))))).((....))))).)) ( -33.60)
>DroEre_CAF1 11045 120 + 1
UCACCUUUUUCGCGGCUAACAAAUCUUCAAAUCUUGAGUGCAACAAUAUGGCAAUUGUUGUGUAUUGCUACGAGAACUUGUUAAUUGUUUCGCGCUCGAGUGGCCAAGAGCUCUGAAUGG
...((...((((.(((.......((((.....(((((((((((((((.((((((((.(((((......))))).)).))))))))))))..))))))))).....))))))).)))).)) ( -32.11)
>DroYak_CAF1 10993 120 + 1
UCACCUUUUUCGCGGCUAACAAAUCUUCAAAUCCUGAGUGCAACAAUAUGGCAAUUGUUGUGCGUUGCUACGAGAACUUGUUAAUUGUUUCGCGCUCGAGUGGCCAAGAGCUCUGAAUGG
......((((((..((.(((......(((.....)))(..(((((((......)))))))..))))))..))))))........(..(((.(.((((..........)))).).)))..) ( -29.70)
>consensus
UCACCUUUUCCGCGGCCAACAAAUC________UUGAGUGCAACAAUAUGGCAAUUGUUGUGUAUUGCUACGAGAACUUGUUAAUUGUUUCGCGCUCGAGUGGCCAAGAGCUCUGAAUGG
(((.(((((....(((((...............((((((((((((((.((((((((.(((((......))))).)).))))))))))))..)))))))).))))))))))...))).... (-29.11 = -29.07 +  -0.04)

alignment

secondary structure

dotplot

Window 4

Location	4,099,206 – 4,099,316
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.18
Mean single sequence MFE	-34.14
Consensus MFE	-26.53
Energy contribution	-26.53
Covariance contribution	-0.00
Combinations/Pair	1.09
Mean z-score	-1.72
Structure conservation index	0.78
SVM decision value	0.42
SVM RNA-class probability	0.730319
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4099206 110 - 27905053
ACUCCAUGAAUGAAUGGAGUUGGCCACAAUGGGCCGUC-UGGAAAGUGUUUUCCUGAAAAAAAAAACCCAAGGAGCACCUAGAAGC---------ACCGCGGAAUGAAGACUGCCGCAGC
(((((((......))))))).((((......)))).((-(((...((((..((((...............)))))))))))))...---------...((((...(....)..))))... ( -32.76)
>DroSec_CAF1 11118 106 - 1
ACUCCAUGAAUGAAUGGAGUUGGCCACAAUGGGCCGUC-UGGAAAGUGUUUUCCUGAA----AAAACCCAAGGAGCACCUAGAACC---------ACCGUGGAAUGGAGACUGCCGCAGC
(((((((......))))))).((((......)))).((-(((...((((..((((...----........)))))))))))))...---------...((((...(....)..))))... ( -35.50)
>DroSim_CAF1 11132 108 - 1
ACUCCAUGAAUGAAUGGAGUUGGCCACAAUGGGCCGUC-UGGAAAGUGUUUUCCUAAA--AAAAAACCCAAGGAGCACCUAGAAGC---------ACCGCGGAAUGGAGACCGCCGCAGC
(((((((......))))))).((((......)))).((-(((...((((..((((...--..........)))))))))))))...---------...((((...(....)..))))... ( -35.62)
>DroEre_CAF1 11165 105 - 1
ACUCCAUGAAUGAAUGGAGCUGGCCACAAUGGGCCGUCCUGGAAAGUGUUUCGCUGA------AAACCCAAGGAGCACCAAGAAGC---------ACCGCGGAAUGGAGACAGCCGCGGC
..(((((......)))))(((((((......))))..........(((((((..((.------.....)).))))))).....)))---------.((((((..((....)).)))))). ( -39.40)
>DroYak_CAF1 11113 114 - 1
ACUCCAUGAAUGAAUGGAGCUGGCCACAAUGAACCGUCCUGGAAAGUGUUUCGCAGA------AUACCCAAGGAGCACCAAGAAGCACCAAGAGCACCGCGGAAUGCAGACUGCCGCAGC
.((((((......))))))..(((.........((.....))...(((((((((.(.------.....)..((.((........)).)).........))))))))).....)))..... ( -27.40)
>consensus
ACUCCAUGAAUGAAUGGAGUUGGCCACAAUGGGCCGUC_UGGAAAGUGUUUUCCUGAA____AAAACCCAAGGAGCACCUAGAAGC_________ACCGCGGAAUGGAGACUGCCGCAGC
.((((((......))))))..((((......))))..........(((((((...................)))))))....................((((...(....)..))))... (-26.53 = -26.53 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:54 2006