Locus 5568

Sequence ID	2L_DroMel_CAF1
Location	15,834,077 – 15,834,221
Length	144
Max. P	0.841741

overview

Window 1

Location	15,834,077 – 15,834,183
Length	106
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	82.55
Mean single sequence MFE	-29.98
Consensus MFE	-18.02
Energy contribution	-18.90
Covariance contribution	0.88
Combinations/Pair	1.09
Mean z-score	-2.29
Structure conservation index	0.60
SVM decision value	0.67
SVM RNA-class probability	0.818244
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15834077 106 + 22407834
ACAAGCAUCUGGAUACACACAUUUAUAU--AGUACACAUCUGUGUGUAUAUGUA-----------UAUGGAGUGGCACAACACAUGCUUCGACUGC-UUCGCAGCUACGCUUUGCUGCCU
..((((((.((....(((.(((.(((((--(.((((((....))))))))))))-----------.)))..)))......)).)))))).......-...(((((........))))).. ( -30.60)
>DroSec_CAF1 7212 108 + 1
ACAAGCAUCUGGAUACACACUUUUAUAU--AGUACACAUCUGUAUGUAUAUGUA---------UAUAUGGAGUGGCACAACACAUGCUUCGACUGC-UUCGCAGCUACGCUUUGCUGCCU
..((((((.((......(((((((((((--((((.((((....)))).))).))---------)))).))))))......)).)))))).......-...(((((........))))).. ( -26.60)
>DroSim_CAF1 7401 106 + 1
ACAAGCAUUUGGAUACACACUUUUAUAU--AGUACACAUCUGUGUGUAUAUGUA-----------UAUGGAGUGGCACAACACAUGCUUCGACUGC-UUCGCAGCUACGCUUUGCUGCCU
..(((((.(((((....(((((((((((--((((((((....))))))).))))-----------)).))))))(((.......)))))))).)))-)).(((((........))))).. ( -33.20)
>DroPer_CAF1 15279 118 + 1
ACAUCUAUCUAGAUACAAACGCACAGAACAAGUA--CAUAUGUAUAUAUAAGUAUGGUGUCUCUAUAUGGAGUGGCACAACAUAUGCUUGAGCUGCCGUCGCAGCCACGCUUUGCUGCCU
..((((....))))....(((..(((..((((..--(((((((((((....)))).(((((.((......)).))))).)))))))))))..))).))).(((((........))))).. ( -29.50)
>consensus
ACAAGCAUCUGGAUACACACUUUUAUAU__AGUACACAUCUGUAUGUAUAUGUA___________UAUGGAGUGGCACAACACAUGCUUCGACUGC_UUCGCAGCUACGCUUUGCUGCCU
..((((((....((((((((.....................))))))))......................(((......)))))))))...........(((((........))))).. (-18.02 = -18.90 +   0.88)

alignment

secondary structure

dotplot

Window 2

Location	15,834,077 – 15,834,183
Length	106
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	82.55
Mean single sequence MFE	-31.07
Consensus MFE	-22.29
Energy contribution	-22.60
Covariance contribution	0.31
Combinations/Pair	1.15
Mean z-score	-1.94
Structure conservation index	0.72
SVM decision value	0.75
SVM RNA-class probability	0.841741
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15834077 106 - 22407834
AGGCAGCAAAGCGUAGCUGCGAA-GCAGUCGAAGCAUGUGUUGUGCCACUCCAUA-----------UACAUAUACACACAGAUGUGUACU--AUAUAAAUGUGUGUAUCCAGAUGCUUGU
..(((((........))))).((-(((.((.....((((((.(((......))))-----------)))))(((((((((..(((((...--)))))..)))))))))...))))))).. ( -31.20)
>DroSec_CAF1 7212 108 - 1
AGGCAGCAAAGCGUAGCUGCGAA-GCAGUCGAAGCAUGUGUUGUGCCACUCCAUAUA---------UACAUAUACAUACAGAUGUGUACU--AUAUAAAAGUGUGUAUCCAGAUGCUUGU
..(((((........)))))...-.......((((((.((..((((((((...((((---------((..(((((((....))))))).)--)))))..)))).)))).)).)))))).. ( -31.90)
>DroSim_CAF1 7401 106 - 1
AGGCAGCAAAGCGUAGCUGCGAA-GCAGUCGAAGCAUGUGUUGUGCCACUCCAUA-----------UACAUAUACACACAGAUGUGUACU--AUAUAAAAGUGUGUAUCCAAAUGCUUGU
..(((((........)))))...-.......((((((.((..((((((((..(((-----------((....((((((....)))))).)--))))...)))).)))).)).)))))).. ( -27.80)
>DroPer_CAF1 15279 118 - 1
AGGCAGCAAAGCGUGGCUGCGACGGCAGCUCAAGCAUAUGUUGUGCCACUCCAUAUAGAGACACCAUACUUAUAUAUACAUAUG--UACUUGUUCUGUGCGUUUGUAUCUAGAUAGAUGU
.(((((((..((.(((((((....))))).)).))...)))..)))).(((......)))....(((.((..((.(((((.(((--(((.......)))))).))))).))...))))). ( -33.40)
>consensus
AGGCAGCAAAGCGUAGCUGCGAA_GCAGUCGAAGCAUGUGUUGUGCCACUCCAUA___________UACAUAUACACACAGAUGUGUACU__AUAUAAAAGUGUGUAUCCAGAUGCUUGU
.(((((((..((...(((((....)))))....))...)))..))))........................((((((((...(((((.....)))))...))))))))............ (-22.29 = -22.60 +   0.31)

alignment

secondary structure

dotplot

Window 3

Location	15,834,115 – 15,834,221
Length	106
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	84.09
Mean single sequence MFE	-32.42
Consensus MFE	-24.16
Energy contribution	-25.73
Covariance contribution	1.56
Combinations/Pair	1.04
Mean z-score	-1.41
Structure conservation index	0.75
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15834115 106 - 22407834
GCAAACAUGGAGGGCAGGGGCUG--AAUGGCCUGAAAAGAAGGCAGCAAAGCGUAGCUGCGAA-GCAGUCGAAGCAUGUGUUGUGCCACUCCAUA-----------UACAUAUACACACA
......(((((((((..(((((.--...))))).........((((((..((...(((((...-)))))....))...))))))))).)))))).-----------.............. ( -35.40)
>DroSec_CAF1 7250 109 - 1
GCAAACAUGGUGGGCAGGGGCUG-GAAUGGCCUGAAAAGAAGGCAGCAAAGCGUAGCUGCGAA-GCAGUCGAAGCAUGUGUUGUGCCACUCCAUAUA---------UACAUAUACAUACA
......((((.((((..(((((.-....))))).........((((((..((...(((((...-)))))....))...))))))))).).))))...---------.............. ( -31.20)
>DroSim_CAF1 7439 107 - 1
GCAAACAUGGUGGGCAGGGGCUG-GAAUGGCCUGAAAAGAAGGCAGCAAAGCGUAGCUGCGAA-GCAGUCGAAGCAUGUGUUGUGCCACUCCAUA-----------UACAUAUACACACA
......((((.((((..(((((.-....))))).........((((((..((...(((((...-)))))....))...))))))))).).)))).-----------.............. ( -31.20)
>DroPer_CAF1 15317 119 - 1
GCAAACAAG-CGCUCGGAGGCGGCCAAGGGCGAGAAAAGAAGGCAGCAAAGCGUGGCUGCGACGGCAGCUCAAGCAUAUGUUGUGCCACUCCAUAUAGAGACACCAUACUUAUAUAUACA
((......)-)....((.(((.(((...)))...........((((((..((.(((((((....))))).)).))...))))))))).(((......)))...))............... ( -31.90)
>consensus
GCAAACAUGGUGGGCAGGGGCUG_GAAUGGCCUGAAAAGAAGGCAGCAAAGCGUAGCUGCGAA_GCAGUCGAAGCAUGUGUUGUGCCACUCCAUA___________UACAUAUACACACA
......((((.((((..(((((......))))).........((((((..((...(((((....)))))....))...))))))))).).)))).......................... (-24.16 = -25.73 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:21 2006